Van de Peer Y

References (24)

Title : A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes - Felix_2019_Sci.Rep_9_13144
Author(s) : Felix C , Meneses R , Goncalves MFM , Tilleman L , Duarte AS , Jorrin-Novo JV , Van de Peer Y , Deforce D , Van Nieuwerburgh F , Esteves AC , Alves A
Ref : Sci Rep , 9 :13144 , 2019
Abstract : Lasiodiplodia theobromae (Botryosphaeriaceae, Ascomycota) is a plant pathogen and human opportunist whose pathogenicity is modulated by temperature. The molecular effects of temperature on L. theobromae are mostly unknown, so we used a multi-omics approach to understand how temperature affects the molecular mechanisms of pathogenicity. The genome of L. theobromae LA-SOL3 was sequenced (Illumina MiSeq) and annotated. Furthermore, the transcriptome (Illumina TruSeq) and proteome (Orbitrap LC-MS/MS) of LA-SOL3 grown at 25 degreesC and 37 degreesC were analysed. Proteins related to pathogenicity (plant cell wall degradation, toxin synthesis, mitogen-activated kinases pathway and proteins involved in the velvet complex) were more abundant when the fungus grew at 25 degreesC. At 37 degreesC, proteins related to pathogenicity were less abundant than at 25 degreesC, while proteins related to cell wall organisation were more abundant. On the other hand, virulence factors involved in human pathogenesis, such as the SSD1 virulence protein, were expressed only at 37 degreesC. Taken together, our results showed that this species presents a typical phytopathogenic molecular profile that is compatible with a hemibiotrophic lifestyle. We showed that L. theobromae is equipped with the pathogenesis toolbox that enables it to infect not only plants but also animals.
ESTHER : Felix_2019_Sci.Rep_9_13144
PubMedSearch : Felix_2019_Sci.Rep_9_13144
PubMedID: 31511626
Gene_locus related to this paper: 9pezi-a0a5n5dna6 , 9pezi-a0a5n5di12 , 9pezi-a0a5n5d4q0

Title : The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization - Nishiyama_2018_Cell_174_448
Author(s) : Nishiyama T , Sakayama H , de Vries J , Buschmann H , Saint-Marcoux D , Ullrich KK , Haas FB , Vanderstraeten L , Becker D , Lang D , Vosolsobe S , Rombauts S , Wilhelmsson PKI , Janitza P , Kern R , Heyl A , Rumpler F , Villalobos L , Clay JM , Skokan R , Toyoda A , Suzuki Y , Kagoshima H , Schijlen E , Tajeshwar N , Catarino B , Hetherington AJ , Saltykova A , Bonnot C , Breuninger H , Symeonidi A , Radhakrishnan GV , Van Nieuwerburgh F , Deforce D , Chang C , Karol KG , Hedrich R , Ulvskov P , Glockner G , Delwiche CF , Petrasek J , Van de Peer Y , Friml J , Beilby M , Dolan L , Kohara Y , Sugano S , Fujiyama A , Delaux PM , Quint M , Theissen G , Hagemann M , Harholt J , Dunand C , Zachgo S , Langdale J , Maumus F , Van Der Straeten D , Gould SB , Rensing SA
Ref : Cell , 174 :448 , 2018
Abstract : Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.
ESTHER : Nishiyama_2018_Cell_174_448
PubMedSearch : Nishiyama_2018_Cell_174_448
PubMedID: 30007417
Gene_locus related to this paper: chabu-a0a388kgf1 , chabu-a0a388jwy2

Title : Gene cluster conservation provides insight into cercosporin biosynthesis and extends production to the genus Colletotrichum - de Jonge_2018_Proc.Natl.Acad.Sci.U.S.A_115_E5459
Author(s) : de Jonge R , Ebert MK , Huitt-Roehl CR , Pal P , Suttle JC , Spanner RE , Neubauer JD , Jurick WM, 2nd , Stott KA , Secor GA , Thomma B , Van de Peer Y , Townsend CA , Bolton MD
Ref : Proc Natl Acad Sci U S A , 115 :E5459 , 2018
Abstract : Species in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean, and other major food crops. Here, we sequenced the genome of the sugar beet pathogen Cercospora beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide-host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae Although cercosporin biosynthesis has been thought to rely on an eight-gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein, previously shown to be involved with cercosporin autoresistance, and four additional genes required for cercosporin biosynthesis, including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Lastly, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.
ESTHER : de Jonge_2018_Proc.Natl.Acad.Sci.U.S.A_115_E5459
PubMedSearch : de Jonge_2018_Proc.Natl.Acad.Sci.U.S.A_115_E5459
PubMedID: 29844193
Gene_locus related to this paper: cernc-q6dqw3 , 9pezi-a0a2s6cl14

Title : The Apostasia genome and the evolution of orchids - Zhang_2017_Nature_549_379
Author(s) : Zhang GQ , Liu KW , Li Z , Lohaus R , Hsiao YY , Niu SC , Wang JY , Lin YC , Xu Q , Chen LJ , Yoshida K , Fujiwara S , Wang ZW , Zhang YQ , Mitsuda N , Wang M , Liu GH , Pecoraro L , Huang HX , Xiao XJ , Lin M , Wu XY , Wu WL , Chen YY , Chang SB , Sakamoto S , Ohme-Takagi M , Yagi M , Zeng SJ , Shen CY , Yeh CM , Luo YB , Tsai WC , Van de Peer Y , Liu ZJ
Ref : Nature , 549 :379 , 2017
Abstract : Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth. Here we report the draft genome sequence of Apostasia shenzhenica, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
ESTHER : Zhang_2017_Nature_549_379
PubMedSearch : Zhang_2017_Nature_549_379
PubMedID: 28902843
Gene_locus related to this paper: 9aspa-a0a2i0b2l6 , 9aspa-a0a2i0w093 , 9aspa-a0a2i0asr1 , 9aspa-a0a2i0vyy1 , 9aspa-a0a2i0a218 , 9aspa-a0a2i0x5j6 , 9aspa-a0a2i0aji0 , 9aspa-a0a2i0a3k8 , 9aspa-a0a2i0win6 , 9aspa-a0a2i0vg82 , 9aspa-a0a2h9zyy3

Title : The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution - Zhang_2016_Sci.Rep_6_19029
Author(s) : Zhang GQ , Xu Q , Bian C , Tsai WC , Yeh CM , Liu KW , Yoshida K , Zhang LS , Chang SB , Chen F , Shi Y , Su YY , Zhang YQ , Chen LJ , Yin Y , Lin M , Huang H , Deng H , Wang ZW , Zhu SL , Zhao X , Deng C , Niu SC , Huang J , Wang M , Liu GH , Yang HJ , Xiao XJ , Hsiao YY , Wu WL , Chen YY , Mitsuda N , Ohme-Takagi M , Luo YB , Van de Peer Y , Liu ZJ
Ref : Sci Rep , 6 :19029 , 2016
Abstract : Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.
ESTHER : Zhang_2016_Sci.Rep_6_19029
PubMedSearch : Zhang_2016_Sci.Rep_6_19029
PubMedID: 26754549
Gene_locus related to this paper: 9aspa-a0a2i0w093 , 9aspa-a0a2i0vyy1 , 9aspa-a0a2i0x5j6 , 9aspa-a0a2i0win6 , 9aspa-a0a2i0vg82

Title : The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea - Olsen_2016_Nature_530_331
Author(s) : Olsen JL , Rouze P , Verhelst B , Lin YC , Bayer T , Collen J , Dattolo E , De Paoli E , Dittami S , Maumus F , Michel G , Kersting A , Lauritano C , Lohaus R , Topel M , Tonon T , Vanneste K , Amirebrahimi M , Brakel J , Bostrom C , Chovatia M , Grimwood J , Jenkins JW , Jueterbock A , Mraz A , Stam WT , Tice H , Bornberg-Bauer E , Green PJ , Pearson GA , Procaccini G , Duarte CM , Schmutz J , Reusch TB , Van de Peer Y
Ref : Nature , 530 :331 , 2016
Abstract : Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.
ESTHER : Olsen_2016_Nature_530_331
PubMedSearch : Olsen_2016_Nature_530_331
PubMedID: 26814964
Gene_locus related to this paper: zosmr-a0a0k9p2z2 , zosmr-a0a0k9q3d3 , zosmr-a0a0k9nzq4 , zosmr-a0a0k9pcd8 , zosmr-a0a0k9p120 , zosmr-a0a0k9npe9

Title : The genome of Eucalyptus grandis - Myburg_2014_Nature_510_356
Author(s) : Myburg AA , Grattapaglia D , Tuskan GA , Hellsten U , Hayes RD , Grimwood J , Jenkins J , Lindquist E , Tice H , Bauer D , Goodstein DM , Dubchak I , Poliakov A , Mizrachi E , Kullan AR , Hussey SG , Pinard D , van der Merwe K , Singh P , van Jaarsveld I , Silva-Junior OB , Togawa RC , Pappas MR , Faria DA , Sansaloni CP , Petroli CD , Yang X , Ranjan P , Tschaplinski TJ , Ye CY , Li T , Sterck L , Vanneste K , Murat F , Soler M , Clemente HS , Saidi N , Cassan-Wang H , Dunand C , Hefer CA , Bornberg-Bauer E , Kersting AR , Vining K , Amarasinghe V , Ranik M , Naithani S , Elser J , Boyd AE , Liston A , Spatafora JW , Dharmwardhana P , Raja R , Sullivan C , Romanel E , Alves-Ferreira M , Kulheim C , Foley W , Carocha V , Paiva J , Kudrna D , Brommonschenkel SH , Pasquali G , Byrne M , Rigault P , Tibbits J , Spokevicius A , Jones RC , Steane DA , Vaillancourt RE , Potts BM , Joubert F , Barry K , Pappas GJ , Strauss SH , Jaiswal P , Grima-Pettenati J , Salse J , Van de Peer Y , Rokhsar DS , Schmutz J
Ref : Nature , 510 :356 , 2014
Abstract : Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.
ESTHER : Myburg_2014_Nature_510_356
PubMedSearch : Myburg_2014_Nature_510_356
PubMedID: 24919147
Gene_locus related to this paper: eucgr-a0a059d0n8 , eucgr-a0a059cm68 , eucgr-a0a059d783 , eucgr-a0a059af93 , eucgr-a0a059awi0 , eucgr-a0a059awt4 , eucgr-a0a059ar83 , eucgr-a0a059ayw5 , eucgr-a0a059az75 , eucgr-a0a059azj1 , eucgr-a0a059azq5 , eucgr-a0a059bkm2 , eucgr-a0a059bl38 , eucgr-a0a059a7m2 , eucgr-a0a059a6p6 , eucgr-a0a059a6p1 , eucgr-a0a059a5e9 , eucgr-a0a059cpq4 , eucgr-a0a059b8v5

Title : Exoproteome analysis of Starmerella bombicola results in the discovery of an esterase required for lactonization of sophorolipids - Ciesielska_2014_J.Proteomics_98_159
Author(s) : Ciesielska K , Van Bogaert IN , Chevineau S , Li B , Groeneboer S , Soetaert W , Van de Peer Y , Devreese B
Ref : J Proteomics , 98 :159 , 2014
Abstract : The yeast Starmerella bombicola secretes sophorolipids, a family of biosurfactants that find applications in green household products and cosmetics. Over the past years, a gene cluster was discovered that is responsible for the entire synthesis of the open (acidic) form of these molecules from glucose, fatty acids and acetyl-CoA building blocks. However, a significant fraction of the natural product is obtained as a ring closed form (lactonic). Both genetic and proteomic approaches hitherto failed to discover an enzyme responsible for the esterification reaction required for the ring closure step. We hypothesized that this enzyme is extracellularly secreted. Therefore, we characterized the composition of the S. bombicola exoproteome at different time points of the growth and compared it with known yeast exoproteomes. We identified 44 proteins, many of them commonly found in other fungi. Curiously, we discovered an enzyme with homology to Pseudozyma antarctica lipase A. A deletion mutation of its gene resulted in complete abolishment of the sophorolipid lactonization providing evidence that this might be the missing enzyme in the sophorolipid biosynthetic pathway. BIOLOGICAL SIGNIFICANCE: Growing concern about the impact of chemical processes on the environment increases consumers' demand for bio-based products. Lately, the household care and personal care sectors show increasing interest in naturally occurring biosurfactants, which constitute environment-friendly alternatives for chemical surfactants, typically derived from mineral oils. A particular group of biosurfactants, sophorolipids, already found their way to the market, being used in a range of household detergent products and in cosmetics. This work describes how proteomic approaches have led to the completion of our knowledge on the biosynthetic pathway of sophorolipids as performed by Starmerella bombicola, a fungus used in the industrial production of these biosurfactants. Moreover, we proved that by creating a deletion mutant in the lactone esterase discovered in this study, we can shape the biosynthesis towards custom-made sophorolipids with desired functions. Herewith, we demonstrate the potential of proteomics in industrial biotechnology.
ESTHER : Ciesielska_2014_J.Proteomics_98_159
PubMedSearch : Ciesielska_2014_J.Proteomics_98_159
PubMedID: 24418522
Gene_locus related to this paper: stabo-sble

Title : Pan genome of the phytoplankton Emiliania underpins its global distribution - Read_2013_Nature_499_209
Author(s) : Read BA , Kegel J , Klute MJ , Kuo A , Lefebvre SC , Maumus F , Mayer C , Miller J , Monier A , Salamov A , Young J , Aguilar M , Claverie JM , Frickenhaus S , Gonzalez K , Herman EK , Lin YC , Napier J , Ogata H , Sarno AF , Shmutz J , Schroeder D , de Vargas C , Verret F , von Dassow P , Valentin K , Van de Peer Y , Wheeler G , Dacks JB , Delwiche CF , Dyhrman ST , Glockner G , John U , Richards T , Worden AZ , Zhang X , Grigoriev IV
Ref : Nature , 499 :209 , 2013
Abstract : Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
ESTHER : Read_2013_Nature_499_209
PubMedSearch : Read_2013_Nature_499_209
PubMedID: 23760476

Title : The Medicago genome provides insight into the evolution of rhizobial symbioses - Young_2011_Nature_480_520
Author(s) : Young ND , Debelle F , Oldroyd GE , Geurts R , Cannon SB , Udvardi MK , Benedito VA , Mayer KF , Gouzy J , Schoof H , Van de Peer Y , Proost S , Cook DR , Meyers BC , Spannagl M , Cheung F , De Mita S , Krishnakumar V , Gundlach H , Zhou S , Mudge J , Bharti AK , Murray JD , Naoumkina MA , Rosen B , Silverstein KA , Tang H , Rombauts S , Zhao PX , Zhou P , Barbe V , Bardou P , Bechner M , Bellec A , Berger A , Berges H , Bidwell S , Bisseling T , Choisne N , Couloux A , Denny R , Deshpande S , Dai X , Doyle JJ , Dudez AM , Farmer AD , Fouteau S , Franken C , Gibelin C , Gish J , Goldstein S , Gonzalez AJ , Green PJ , Hallab A , Hartog M , Hua A , Humphray SJ , Jeong DH , Jing Y , Jocker A , Kenton SM , Kim DJ , Klee K , Lai H , Lang C , Lin S , Macmil SL , Magdelenat G , Matthews L , McCorrison J , Monaghan EL , Mun JH , Najar FZ , Nicholson C , Noirot C , O'Bleness M , Paule CR , Poulain J , Prion F , Qin B , Qu C , Retzel EF , Riddle C , Sallet E , Samain S , Samson N , Sanders I , Saurat O , Scarpelli C , Schiex T , Segurens B , Severin AJ , Sherrier DJ , Shi R , Sims S , Singer SR , Sinharoy S , Sterck L , Viollet A , Wang BB , Wang K , Wang M , Wang X , Warfsmann J , Weissenbach J , White DD , White JD , Wiley GB , Wincker P , Xing Y , Yang L , Yao Z , Ying F , Zhai J , Zhou L , Zuber A , Denarie J , Dixon RA , May GD , Schwartz DC , Rogers J , Quetier F , Town CD , Roe BA
Ref : Nature , 480 :520 , 2011
Abstract : Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing approximately 94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.
ESTHER : Young_2011_Nature_480_520
PubMedSearch : Young_2011_Nature_480_520
PubMedID: 22089132
Gene_locus related to this paper: medtr-b7fki4 , medtr-b7fmi1 , medtr-g7itl1 , medtr-g7iu67 , medtr-g7izm0 , medtr-g7j641 , medtr-g7jtf8 , medtr-g7jtg2 , medtr-g7jtg4 , medtr-g7kem3 , medtr-g7kml3 , medtr-g7ksx5 , medtr-g7leb3 , medtr-q1s5d8 , medtr-q1s9m3 , medtr-q1t171 , medtr-g7k9e1 , medtr-g7k9e3 , medtr-g7k9e5 , medtr-g7k9e8 , medtr-g7k9e9 , medtr-g7lbp2 , medtr-g7lch3 , medtr-g7ib94 , medtr-g7ljk8 , medtr-g7i6w5 , medtr-g7kvg4 , medtr-g7iam1 , medtr-g7iam3 , medtr-g7l754 , medtr-g7jr41 , medtr-g7l4f5 , medtr-g7l755 , medtr-a0a072vyl4 , medtr-g7jwk8 , medtr-a0a072vhg0 , medtr-a0a072vrv9 , medtr-g7kmk5 , medtr-a0a072uuf6 , medtr-a0a072urp3 , medtr-g7zzc3 , medtr-g7ie19 , medtr-g7kst7 , medtr-a0a072u5k5 , medtr-a0a072v056 , medtr-scp1 , medtr-g7kyn0 , medtr-g7inw6 , medtr-g7j3q3

Title : The Arabidopsis lyrata genome sequence and the basis of rapid genome size change - Hu_2011_Nat.Genet_43_476
Author(s) : Hu TT , Pattyn P , Bakker EG , Cao J , Cheng JF , Clark RM , Fahlgren N , Fawcett JA , Grimwood J , Gundlach H , Haberer G , Hollister JD , Ossowski S , Ottilar RP , Salamov AA , Schneeberger K , Spannagl M , Wang X , Yang L , Nasrallah ME , Bergelson J , Carrington JC , Gaut BS , Schmutz J , Mayer KF , Van de Peer Y , Grigoriev IV , Nordborg M , Weigel D , Guo YL
Ref : Nat Genet , 43 :476 , 2011
Abstract : We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3x dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago, likely constitutes the derived state for the family. We found evidence for DNA loss from large-scale rearrangements, but most of the difference in genome size can be attributed to hundreds of thousands of small deletions, mostly in noncoding DNA and transposons. Analysis of deletions and insertions still segregating in A. thaliana indicates that the process of DNA loss is ongoing, suggesting pervasive selection for a smaller genome. The high-quality reference genome sequence for A. lyrata will be an important resource for functional, evolutionary and ecological studies in the genus Arabidopsis.
ESTHER : Hu_2011_Nat.Genet_43_476
PubMedSearch : Hu_2011_Nat.Genet_43_476
PubMedID: 21478890
Gene_locus related to this paper: arall-d7kc59 , arall-d7kfz1 , arall-d7kjk9 , arall-d7kk58 , arall-d7kuj1 , arall-d7kwx5 , arall-d7kzq8 , arall-d7laf7 , arall-D7LAK6 , arall-d7ltj2 , arall-d7lu11 , arall-d7ly06 , arall-d7lyn6 , arall-d7m1k0 , arall-d7m1k1 , arall-d7m1k3 , arall-d7m1l4 , arall-d7m814 , arall-d7mbk0 , arall-d7mbn8 , arall-d7mgs1 , arall-d7mi04 , arall-d7mld7 , arall-d7mpg7 , arall-d7mul9 , arath-At2g45610 , arath-At1g05790 , arath-At1g09980 , arath-At1g18360 , arath-AT1G29120 , arath-AT1G73920 , arath-AT1G76140 , arath-AT2G05260 , arath-At2g15230 , arath-At2g24280 , arath-AT2G42690 , arath-At2g47630 , arath-AT3G12150 , arath-At3g61680 , arath-AT3g62590 , arath-AT4G00500 , arath-AT4G25770 , arath-AT4g30610 , arath-At5g11650 , arath-At5g13640 , arath-AT5G19050 , arath-AT5G20060 , arath-AT5G20520 , arath-AT5G27320 , arath-At5g42930 , arath-At5g47330 , arath-CGEP , arath-clh1 , arath-clh2 , arath-F1N13.220 , arath-F2G14.100 , arath-F12A4.4 , arath-F14O10.2 , arath-SCP27 , arath-HNL , arath-GID1B , arath-LIP2 , arath-At5g17670 , arath-pip , arath-PLA11 , arath-PLA12 , arath-PLA13 , arath-PLA15 , arath-PLA17 , arath-Q8LPF5 , arath-Q9FFZ1 , arath-Q9FJ29 , arath-Q9FKP9 , arath-Q9FNF6 , arath-q9lhe8 , arath-Q9SFF6 , arath-q84w08 , arath-SCP7 , arath-SCP8 , arath-SCP26 , arath-SCP28 , arath-SCP33 , arath-SCP40 , arath-SCPL34 , arath-At4g12230 , arath-MES14 , arath-T19F11.2 , arath-MES10 , arath-At5g11790 , arath-T26B15.8 , arath-ZW18 , arall-d7l971 , arall-d7lfd3 , arall-d7lg04 , arall-d7lg05 , arall-d7lg06 , arall-d7lg07 , arall-d7mb17 , arall-d7mb18 , arall-d7l7v2 , arall-d7l7v3 , arall-d7lst0 , arall-d7lfw9 , arall-d7mgs6 , arall-d7mur3 , arall-d7kjr5 , arall-d7l7v1 , arall-d7ls88 , arall-d7kzg6 , arall-d7kcm6 , arall-d7krm0 , arall-d7kwe4 , arall-d7lri7 , arall-d7kq26

Title : The genome of Tetranychus urticae reveals herbivorous pest adaptations - Grbic_2011_Nature_479_487
Author(s) : Grbic M , Van Leeuwen T , Clark RM , Rombauts S , Rouze P , Grbic V , Osborne EJ , Dermauw W , Ngoc PC , Ortego F , Hernandez-Crespo P , Diaz I , Martinez M , Navajas M , Sucena E , Magalhaes S , Nagy L , Pace RM , Djuranovic S , Smagghe G , Iga M , Christiaens O , Veenstra JA , Ewer J , Villalobos RM , Hutter JL , Hudson SD , Velez M , Yi SV , Zeng J , Pires-daSilva A , Roch F , Cazaux M , Navarro M , Zhurov V , Acevedo G , Bjelica A , Fawcett JA , Bonnet E , Martens C , Baele G , Wissler L , Sanchez-Rodriguez A , Tirry L , Blais C , Demeestere K , Henz SR , Gregory TR , Mathieu J , Verdon L , Farinelli L , Schmutz J , Lindquist E , Feyereisen R , Van de Peer Y
Ref : Nature , 479 :487 , 2011
Abstract : The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T. urticae has the smallest sequenced arthropod genome. Compared with other arthropods, the spider mite genome shows unique changes in the hormonal environment and organization of the Hox complex, and also reveals evolutionary innovation of silk production. We find strong signatures of polyphagy and detoxification in gene families associated with feeding on different hosts and in new gene families acquired by lateral gene transfer. Deep transcriptome analysis of mites feeding on different plants shows how this pest responds to a changing host environment. The T. urticae genome thus offers new insights into arthropod evolution and plant-herbivore interactions, and provides unique opportunities for developing novel plant protection strategies.
ESTHER : Grbic_2011_Nature_479_487
PubMedSearch : Grbic_2011_Nature_479_487
PubMedID: 22113690
Gene_locus related to this paper: tetur-ACHE

Title : Obligate biotrophy features unraveled by the genomic analysis of rust fungi - Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
Author(s) : Duplessis S , Cuomo CA , Lin YC , Aerts A , Tisserant E , Veneault-Fourrey C , Joly DL , Hacquard S , Amselem J , Cantarel BL , Chiu R , Coutinho PM , Feau N , Field M , Frey P , Gelhaye E , Goldberg J , Grabherr MG , Kodira CD , Kohler A , Kues U , Lindquist EA , Lucas SM , Mago R , Mauceli E , Morin E , Murat C , Pangilinan JL , Park R , Pearson M , Quesneville H , Rouhier N , Sakthikumar S , Salamov AA , Schmutz J , Selles B , Shapiro H , Tanguay P , Tuskan GA , Henrissat B , Van de Peer Y , Rouze P , Ellis JG , Dodds PN , Schein JE , Zhong S , Hamelin RC , Grigoriev IV , Szabo LJ , Martin F
Ref : Proc Natl Acad Sci U S A , 108 :9166 , 2011
Abstract : Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
ESTHER : Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedSearch : Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedID: 21536894
Gene_locus related to this paper: pucgt-e3k840 , pucgt-e3kaq6 , pucgt-e3kw59 , pucgt-e3kz16 , pucgt-e3l9v6 , pucgt-e3l279 , pucgt-h6qt25 , mellp-f4reh4 , mellp-f4rhc8 , mellp-f4reh2 , mellp-f4r3y0 , mellp-f4rz15 , mellp-f4rz64 , mellp-f4rl14 , mellp-f4rz66 , mellp-f4s751 , mellp-f4s2g6 , pucgt-e3l1z7 , pucgt-e3l803 , pucgt-e3kst2 , pucgt-e3kst5 , mellp-f4ru03 , pucgt-e3l1z8 , pucgt-e3ktz7 , pucgt-e3jun4 , mellp-f4rl65 , mellp-f4rz16 , mellp-f4ru02 , mellp-f4sav4 , mellp-f4sav3 , mellp-f4s1j0 , mellp-f4rkp0 , mellp-f4s483 , pucgt-e3kzu5 , pucgt-h6qtq8 , mellp-f4r5l5 , pucgt-e3krw7 , pucgt-e3l7w5 , pucgt-e3k2w6 , pucgt-e3kfg2 , pucgt-kex1

Title : The Ectocarpus genome and the independent evolution of multicellularity in brown algae - Cock_2010_Nature_465_617
Author(s) : Cock JM , Sterck L , Rouze P , Scornet D , Allen AE , Amoutzias G , Anthouard V , Artiguenave F , Aury JM , Badger JH , Beszteri B , Billiau K , Bonnet E , Bothwell JH , Bowler C , Boyen C , Brownlee C , Carrano CJ , Charrier B , Cho GY , Coelho SM , Collen J , Corre E , Da Silva C , Delage L , Delaroque N , Dittami SM , Doulbeau S , Elias M , Farnham G , Gachon CM , Gschloessl B , Heesch S , Jabbari K , Jubin C , Kawai H , Kimura K , Kloareg B , Kupper FC , Lang D , Le Bail A , LeBlanc C , Lerouge P , Lohr M , Lopez PJ , Martens C , Maumus F , Michel G , Miranda-Saavedra D , Morales J , Moreau H , Motomura T , Nagasato C , Napoli CA , Nelson DR , Nyvall-Collen P , Peters AF , Pommier C , Potin P , Poulain J , Quesneville H , Read B , Rensing SA , Ritter A , Rousvoal S , Samanta M , Samson G , Schroeder DC , Segurens B , Strittmatter M , Tonon T , Tregear JW , Valentin K , von Dassow P , Yamagishi T , Van de Peer Y , Wincker P
Ref : Nature , 465 :617 , 2010
Abstract : Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.
ESTHER : Cock_2010_Nature_465_617
PubMedSearch : Cock_2010_Nature_465_617
PubMedID: 20520714
Gene_locus related to this paper: ectsi-d7fm61 , ectsi-d7fs16 , ectsi-d7fsv3 , ectsi-d7fte8 , ectsi-d7fux6 , ectsi-d7fvr0 , ectsi-d7fvu4 , ectsi-d7fwk0 , ectsi-d7fyh7 , ectsi-d7g0w7 , ectsi-d7g6g5 , ectsi-d7g484 , ectsi-d7g686 , ectsi-d8lca9 , ectsi-d8lfv2 , ectsi-d8lqg6 , ectsi-d8ltj9 , ectsi-d7fjz2 , ectsi-d7g376

Title : Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas - Worden_2009_Science_324_268
Author(s) : Worden AZ , Lee JH , Mock T , Rouze P , Simmons MP , Aerts AL , Allen AE , Cuvelier ML , Derelle E , Everett MV , Foulon E , Grimwood J , Gundlach H , Henrissat B , Napoli C , McDonald SM , Parker MS , Rombauts S , Salamov A , von Dassow P , Badger JH , Coutinho PM , Demir E , Dubchak I , Gentemann C , Eikrem W , Gready JE , John U , Lanier W , Lindquist EA , Lucas S , Mayer KF , Moreau H , Not F , Otillar R , Panaud O , Pangilinan J , Paulsen I , Piegu B , Poliakov A , Robbens S , Schmutz J , Toulza E , Wyss T , Zelensky A , Zhou K , Armbrust EV , Bhattacharya D , Goodenough UW , Van de Peer Y , Grigoriev IV
Ref : Science , 324 :268 , 2009
Abstract : Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.
ESTHER : Worden_2009_Science_324_268
PubMedSearch : Worden_2009_Science_324_268
PubMedID: 19359590
Gene_locus related to this paper: 9chlo-c1e363 , 9chlo-c1ehp8 , 9chlo-c1fhv2 , 9chlo-c1mis3 , 9chlo-c1na62 , micpc-c1mh04 , micpc-c1mhj0 , micpc-c1mie7 , micpc-c1mj20 , micpc-c1mjh0 , micpc-c1mny7 , micpc-c1mpb2 , micpc-c1mrl2 , micpc-c1msr1 , micpc-c1mvk4 , micpc-c1mvx4 , micpc-c1n5d2 , micpc-c1n6i2 , micpc-c1n842 , micsr-c1dzu1 , micsr-c1e0v8 , micsr-c1e2u5 , micsr-c1e4q6 , micsr-c1e6z5 , micsr-c1e046 , micsr-c1e286 , micsr-c1eap0 , micsr-c1ec00 , micsr-c1edy4 , micsr-c1efl2 , micsr-c1eh15 , micsr-c1ei44 , micsr-c1eii9 , micsr-c1eiz1 , micsr-c1fft1 , micsr-c1fi89 , micsr-c1fj57 , micsr-c1e9f6 , micsr-c1e9u2 , micsr-c1fgg8 , micpc-c1mie3 , micpc-c1ms20 , micpc-c1n640 , miccc-c1e278 , micpc-c1mpa6

Title : Genome sequence of the recombinant protein production host Pichia pastoris - De Schutter_2009_Nat.Biotechnol_27_561
Author(s) : De Schutter K , Lin YC , Tiels P , Van Hecke A , Glinka S , Weber-Lehmann J , Rouze P , Van de Peer Y , Callewaert N
Ref : Nat Biotechnol , 27 :561 , 2009
Abstract : The methylotrophic yeast Pichia pastoris is widely used for the production of proteins and as a model organism for studying peroxisomal biogenesis and methanol assimilation. P. pastoris strains capable of human-type N-glycosylation are now available, which increases the utility of this organism for biopharmaceutical production. Despite its biotechnological importance, relatively few genetic tools or engineered strains have been generated for P. pastoris. To facilitate progress in these areas, we present the 9.43 Mbp genomic sequence of the GS115 strain of P. pastoris. We also provide manually curated annotation for its 5,313 protein-coding genes.
ESTHER : De Schutter_2009_Nat.Biotechnol_27_561
PubMedSearch : De Schutter_2009_Nat.Biotechnol_27_561
PubMedID: 19465926
Gene_locus related to this paper: picp7-f2qwe3 , picpa-c1phg5 , picpa-cbpy , picpa-KEX1 , picpg-c4qw07 , picpg-c4r0k6 , picpg-c4r1s0 , picpg-c4r4a5 , picpg-c4r5w7 , picpg-c4r6t8 , picpg-c4r7h5 , picpg-c4r029 , picpg-c4r272 , picpg-c4r403 , picpg-c4r663 , picpg-c4r788 , picpa-a0a1b2jh35

Title : The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis - Martin_2008_Nature_452_88
Author(s) : Martin F , Aerts A , Ahren D , Brun A , Danchin EG , Duchaussoy F , Gibon J , Kohler A , Lindquist E , Pereda V , Salamov A , Shapiro HJ , Wuyts J , Blaudez D , Buee M , Brokstein P , Canback B , Cohen D , Courty PE , Coutinho PM , Delaruelle C , Detter JC , Deveau A , Difazio S , Duplessis S , Fraissinet-Tachet L , Lucic E , Frey-Klett P , Fourrey C , Feussner I , Gay G , Grimwood J , Hoegger PJ , Jain P , Kilaru S , Labbe J , Lin YC , Legue V , Le Tacon F , Marmeisse R , Melayah D , Montanini B , Muratet M , Nehls U , Niculita-Hirzel H , Oudot-Le Secq MP , Peter M , Quesneville H , Rajashekar B , Reich M , Rouhier N , Schmutz J , Yin T , Chalot M , Henrissat B , Kues U , Lucas S , Van de Peer Y , Podila GK , Polle A , Pukkila PJ , Richardson PM , Rouze P , Sanders IR , Stajich JE , Tunlid A , Tuskan G , Grigoriev IV
Ref : Nature , 452 :88 , 2008
Abstract : Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
ESTHER : Martin_2008_Nature_452_88
PubMedSearch : Martin_2008_Nature_452_88
PubMedID: 18322534
Gene_locus related to this paper: lacbs-b0cns1 , lacbs-b0cpl4 , lacbs-b0cr62 , lacbs-b0cr66 , lacbs-b0csq9 , lacbs-b0ct56 , lacbs-b0ctt5 , lacbs-b0cuw1 , lacbs-b0cv23 , lacbs-b0cxm7 , lacbs-b0cz37 , lacbs-b0czx3 , lacbs-b0d0z5 , lacbs-b0d4i0 , lacbs-b0d4j3 , lacbs-b0d5n6 , lacbs-b0d8k0 , lacbs-b0d263 , lacbs-b0dhh1 , lacbs-b0dkp6 , lacbs-b0dmr2 , lacbs-b0dmt4 , lacbs-b0dsx5 , lacbs-b0dt05 , lacbs-b0dtw4 , lacbs-b0du88 , lacbs-b0dsl6

Title : The Phaeodactylum genome reveals the evolutionary history of diatom genomes - Bowler_2008_Nature_456_239
Author(s) : Bowler C , Allen AE , Badger JH , Grimwood J , Jabbari K , Kuo A , Maheswari U , Martens C , Maumus F , Otillar RP , Rayko E , Salamov A , Vandepoele K , Beszteri B , Gruber A , Heijde M , Katinka M , Mock T , Valentin K , Verret F , Berges JA , Brownlee C , Cadoret JP , Chiovitti A , Choi CJ , Coesel S , De Martino A , Detter JC , Durkin C , Falciatore A , Fournet J , Haruta M , Huysman MJ , Jenkins BD , Jiroutova K , Jorgensen RE , Joubert Y , Kaplan A , Kroger N , Kroth PG , La Roche J , Lindquist E , Lommer M , Martin-Jezequel V , Lopez PJ , Lucas S , Mangogna M , McGinnis K , Medlin LK , Montsant A , Oudot-Le Secq MP , Napoli C , Obornik M , Parker MS , Petit JL , Porcel BM , Poulsen N , Robison M , Rychlewski L , Rynearson TA , Schmutz J , Shapiro H , Siaut M , Stanley M , Sussman MR , Taylor AR , Vardi A , von Dassow P , Vyverman W , Willis A , Wyrwicz LS , Rokhsar DS , Weissenbach J , Armbrust EV , Green BR , Van de Peer Y , Grigoriev IV
Ref : Nature , 456 :239 , 2008
Abstract : Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes ( approximately 40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
ESTHER : Bowler_2008_Nature_456_239
PubMedSearch : Bowler_2008_Nature_456_239
PubMedID: 18923393
Gene_locus related to this paper: phatc-b7fp91 , phatc-b7fqd3 , phatc-b7frf9 , phatc-b7fry8 , phatc-b7ftw8 , phatc-b7fv70 , phatc-b7fw66 , phatc-b7g2b2 , phatc-b7g5z5 , phatc-b7g6f1 , phatc-b7g6r8 , phatc-b7g957 , phatc-b7ga73 , phatc-b7gb22 , phatc-b7gc60 , phatc-b7gdm3 , phatc-b7gdq6 , phatc-b7ge82 , phatc-b7gee0 , phatr-b7frs5 , phatr-b7g1k3 , phatr-b7s4a4 , thaps-b8bsy4 , thaps-b8cfn8 , phatc-b7g635 , phatc-b7gaj3 , thaps-b8c079

Title : The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants - Rensing_2008_Science_319_64
Author(s) : Rensing SA , Lang D , Zimmer AD , Terry A , Salamov A , Shapiro H , Nishiyama T , Perroud PF , Lindquist EA , Kamisugi Y , Tanahashi T , Sakakibara K , Fujita T , Oishi K , Shin IT , Kuroki Y , Toyoda A , Suzuki Y , Hashimoto S , Yamaguchi K , Sugano S , Kohara Y , Fujiyama A , Anterola A , Aoki S , Ashton N , Barbazuk WB , Barker E , Bennetzen JL , Blankenship R , Cho SH , Dutcher SK , Estelle M , Fawcett JA , Gundlach H , Hanada K , Heyl A , Hicks KA , Hughes J , Lohr M , Mayer K , Melkozernov A , Murata T , Nelson DR , Pils B , Prigge M , Reiss B , Renner T , Rombauts S , Rushton PJ , Sanderfoot A , Schween G , Shiu SH , Stueber K , Theodoulou FL , Tu H , Van de Peer Y , Verrier PJ , Waters E , Wood A , Yang L , Cove D , Cuming AC , Hasebe M , Lucas S , Mishler BD , Reski R , Grigoriev IV , Quatrano RS , Boore JL
Ref : Science , 319 :64 , 2008
Abstract : We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.
ESTHER : Rensing_2008_Science_319_64
PubMedSearch : Rensing_2008_Science_319_64
PubMedID: 18079367
Gene_locus related to this paper: phypa-a9rbi6 , phypa-a9rfh1 , phypa-a9rg19 , phypa-a9rgt9 , phypa-a9rhz9 , phypa-a9rkj1 , phypa-a9rns2 , phypa-a9rp52 , phypa-a9rq03 , phypa-a9ry17 , phypa-a9ry72 , phypa-a9s5n8 , phypa-a9s6w1 , phypa-a9s8c7 , phypa-a9s299 , phypa-a9san7 , phypa-a9sc75 , phypa-a9se75 , phypa-a9sg07 , phypa-a9skf7 , phypa-a9skr1 , phypa-a9skw1 , phypa-a9sl58 , phypa-a9slp7 , phypa-a9smq5 , phypa-a9sp13 , phypa-a9ssb0 , phypa-a9sse1 , phypa-a9ssf6 , phypa-a9st85 , phypa-a9sx74 , phypa-a9sy58 , phypa-a9syy4 , phypa-a9t0n4 , phypa-a9t0p4 , phypa-a9t1j2 , phypa-a9t5h1 , phypa-a9t7g6 , phypa-a9t8u8 , phypa-a9t9c9 , phypa-a9t9d9 , phypa-a0a7i4d2t7 , phypa-a9t498 , phypa-a9tbu4 , phypa-a9tc36 , phypa-a9tds0 , phypa-a9te64 , phypa-a9tfw2 , phypa-a9tin6 , phypa-a9tja4 , phypa-a9tmp3 , phypa-a9tmr4 , phypa-a9tql4 , phypa-a9tr83 , phypa-a9tsl1 , phypa-a9tsv6 , phypa-a9tu05 , phypa-a9tw81 , phypa-a9tyr8 , phypa-a9u0c9 , phypa-a9u0k3 , phypa-a9u0p4 , phypa-a9u2u7 , phypa-a9u3s0 , phypa-a9tfm7 , phypa-a9tfp6 , phypa-a9syg9 , phypa-a9tzk2 , phypa-a9tvg4 , phypa-a9t1y4 , phypa-a9tqt6 , phypa-a9st18 , phypa-a9tix9 , phypa-a0a2k1kfe3 , phypa-a9sqk3 , phypa-a0a2k1ie71 , phypa-a0a2k1kg29 , phypa-a0a2k1iji3

Title : Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis - Carlton_2007_Science_315_207
Author(s) : Carlton JM , Hirt RP , Silva JC , Delcher AL , Schatz M , Zhao Q , Wortman JR , Bidwell SL , Alsmark UC , Besteiro S , Sicheritz-Ponten T , Noel CJ , Dacks JB , Foster PG , Simillion C , Van de Peer Y , Miranda-Saavedra D , Barton GJ , Westrop GD , Muller S , Dessi D , Fiori PL , Ren Q , Paulsen I , Zhang H , Bastida-Corcuera FD , Simoes-Barbosa A , Brown MT , Hayes RD , Mukherjee M , Okumura CY , Schneider R , Smith AJ , Vanacova S , Villalvazo M , Haas BJ , Pertea M , Feldblyum TV , Utterback TR , Shu CL , Osoegawa K , de Jong PJ , Hrdy I , Horvathova L , Zubacova Z , Dolezal P , Malik SB , Logsdon JM, Jr. , Henze K , Gupta A , Wang CC , Dunne RL , Upcroft JA , Upcroft P , White O , Salzberg SL , Tang P , Chiu CH , Lee YS , Embley TM , Coombs GH , Mottram JC , Tachezy J , Fraser-Liggett CM , Johnson PJ
Ref : Science , 315 :207 , 2007
Abstract : We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.
ESTHER : Carlton_2007_Science_315_207
PubMedSearch : Carlton_2007_Science_315_207
PubMedID: 17218520
Gene_locus related to this paper: triva-a2d7i4 , triva-a2d9w5 , triva-a2d766 , triva-a2dah5 , triva-a2dlx9 , triva-a2dul1 , triva-a2dy49 , triva-a2e6h5 , triva-a2e7p9 , triva-a2e9l3 , triva-a2e414 , triva-a2e613 , triva-a2e983 , triva-a2eau8 , triva-a2ekb9 , triva-a2en58 , triva-a2erp5 , triva-a2et59 , triva-a2f7u4 , triva-a2f801 , triva-a2fa76 , triva-a2fbq3 , triva-a2fe47 , triva-a2fgl0 , triva-a2fhp7 , triva-a2fie6 , triva-a2fk22 , triva-a2fla2 , triva-a2fqm0 , triva-a2fqq2 , triva-a2frq0 , triva-a2frr3 , triva-a2fsq9 , triva-a2fsz5 , triva-a2fux4 , triva-a2fz57 , triva-a2g2h0 , triva-a2g9x0 , triva-a2fqi4

Title : The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation - Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
Author(s) : Palenik B , Grimwood J , Aerts A , Rouze P , Salamov A , Putnam N , Dupont C , Jorgensen R , Derelle E , Rombauts S , Zhou K , Otillar R , Merchant SS , Podell S , Gaasterland T , Napoli C , Gendler K , Manuell A , Tai V , Vallon O , Piganeau G , Jancek S , Heijde M , Jabbari K , Bowler C , Lohr M , Robbens S , Werner G , Dubchak I , Pazour GJ , Ren Q , Paulsen I , Delwiche C , Schmutz J , Rokhsar D , Van de Peer Y , Moreau H , Grigoriev IV
Ref : Proc Natl Acad Sci U S A , 104 :7705 , 2007
Abstract : The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.
ESTHER : Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
PubMedSearch : Palenik_2007_Proc.Natl.Acad.Sci.U.S.A_104_7705
PubMedID: 17460045
Gene_locus related to this paper: ostlu-a4rrl5 , ostlu-a4ruh2 , ostlu-a4rut7 , ostlu-a4ruy3 , ostlu-a4rxn1 , ostlu-a4ry37 , ostlu-a4s2e6 , ostlu-a4s2y4 , ostlu-a4s3d7 , ostlu-a4s4v4 , ostlu-a4s5e4 , ostlu-a4s5y6 , ostlu-a4s7a8 , ostlu-a4s7z5 , ostlu-a4s8g3 , ostlu-a4s8n8 , ostlu-a4s8s1 , ostlu-a4s958 , ostlu-a4sac2 , ostlu-a4saz3 , ostlu-a4sbb7 , ostlu-a4s6q5 , ostlu-a4s1q9 , ostlu-a4s8b2 , ostlu-a4s262

Title : A high quality draft consensus sequence of the genome of a heterozygous grapevine variety - Velasco_2007_PLoS.One_2_e1326
Author(s) : Velasco R , Zharkikh A , Troggio M , Cartwright DA , Cestaro A , Pruss D , Pindo M , FitzGerald LM , Vezzulli S , Reid J , Malacarne G , Iliev D , Coppola G , Wardell B , Micheletti D , Macalma T , Facci M , Mitchell JT , Perazzolli M , Eldredge G , Gatto P , Oyzerski R , Moretto M , Gutin N , Stefanini M , Chen Y , Segala C , Davenport C , Dematte L , Mraz A , Battilana J , Stormo K , Costa F , Tao Q , Si-Ammour A , Harkins T , Lackey A , Perbost C , Taillon B , Stella A , Solovyev V , Fawcett JA , Sterck L , Vandepoele K , Grando SM , Toppo S , Moser C , Lanchbury J , Bogden R , Skolnick M , Sgaramella V , Bhatnagar SK , Fontana P , Gutin A , Van de Peer Y , Salamini F , Viola R
Ref : PLoS ONE , 2 :e1326 , 2007
Abstract : BACKGROUND: Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. PRINCIPAL FINDINGS: We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). CONCLUSIONS: Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.
ESTHER : Velasco_2007_PLoS.One_2_e1326
PubMedSearch : Velasco_2007_PLoS.One_2_e1326
PubMedID: 18094749
Gene_locus related to this paper: vitvi-a5ajc4 , vitvi-a5ama3 , vitvi-a5ane2 , vitvi-a5ayn8 , vitvi-a5b3m9 , vitvi-a5b5p5 , vitvi-a5b6n6 , vitvi-a5b6r9 , vitvi-a5b7c0 , vitvi-a5b7e5 , vitvi-a5b8k1 , vitvi-a5b8l9 , vitvi-a5b8q6 , vitvi-a5bft8 , vitvi-a5bji4 , vitvi-a5bkl0 , vitvi-a5blq0 , vitvi-a5bm71 , vitvi-a5bub9 , vitvi-a5c1g2 , vitvi-a5c6e7 , vitvi-a5c8m8 , vitvi-a5c8p7 , vitvi-a5c9w6 , vitvi-a7pnb4 , vitvi-d7t940 , vitvi-d7tpk8 , vitvi-f6hhx5 , vitvi-f6hqf1 , vitvi-d7tum4 , vitvi-d7stm8 , vitvi-a5bej7 , vitvi-e0cv10 , vitvi-f6gtp7 , vitvi-a5bej5

Title : The genome of black cottonwood, Populus trichocarpa (Torr. &\; Gray) - Tuskan_2006_Science_313_1596
Author(s) : Tuskan GA , Difazio S , Jansson S , Bohlmann J , Grigoriev I , Hellsten U , Putnam N , Ralph S , Rombauts S , Salamov A , Schein J , Sterck L , Aerts A , Bhalerao RR , Bhalerao RP , Blaudez D , Boerjan W , Brun A , Brunner A , Busov V , Campbell M , Carlson J , Chalot M , Chapman J , Chen GL , Cooper D , Coutinho PM , Couturier J , Covert S , Cronk Q , Cunningham R , Davis J , Degroeve S , Dejardin A , dePamphilis C , Detter J , Dirks B , Dubchak I , Duplessis S , Ehlting J , Ellis B , Gendler K , Goodstein D , Gribskov M , Grimwood J , Groover A , Gunter L , Hamberger B , Heinze B , Helariutta Y , Henrissat B , Holligan D , Holt R , Huang W , Islam-Faridi N , Jones S , Jones-Rhoades M , Jorgensen R , Joshi C , Kangasjarvi J , Karlsson J , Kelleher C , Kirkpatrick R , Kirst M , Kohler A , Kalluri U , Larimer F , Leebens-Mack J , Leple JC , Locascio P , Lou Y , Lucas S , Martin F , Montanini B , Napoli C , Nelson DR , Nelson C , Nieminen K , Nilsson O , Pereda V , Peter G , Philippe R , Pilate G , Poliakov A , Razumovskaya J , Richardson P , Rinaldi C , Ritland K , Rouze P , Ryaboy D , Schmutz J , Schrader J , Segerman B , Shin H , Siddiqui A , Sterky F , Terry A , Tsai CJ , Uberbacher E , Unneberg P , Vahala J , Wall K , Wessler S , Yang G , Yin T , Douglas C , Marra M , Sandberg G , Van de Peer Y , Rokhsar D
Ref : Science , 313 :1596 , 2006
Abstract : We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.
ESTHER : Tuskan_2006_Science_313_1596
PubMedSearch : Tuskan_2006_Science_313_1596
PubMedID: 16973872
Gene_locus related to this paper: burvg-a4jw31 , delas-a9c1v9 , poptr-a9pfp5 , poptr-a9ph43 , poptr-a9ph71 , poptr-a9pha7 , poptr-b9giq0 , poptr-b9gjs0 , poptr-b9gl72 , poptr-b9gmx8 , poptr-b9gnp9 , poptr-b9gny4 , poptr-b9grg2 , poptr-b9gsc2 , poptr-b9gvp3 , poptr-b9gvs3 , poptr-b9gwn9 , poptr-b9gy32 , poptr-b9gyq1 , poptr-b9gys8 , poptr-b9h0h0 , poptr-b9h4j2 , poptr-b9h6c2 , poptr-b9h6c5 , poptr-b9h6l8 , poptr-b9h8c9 , poptr-b9h301 , poptr-b9h579 , poptr-b9hbl2 , poptr-b9hbw5 , poptr-b9hcn9 , poptr-b9hee0 , poptr-b9hee2 , poptr-b9hee5 , poptr-b9hee6 , poptr-b9hef3 , poptr-b9hfa7 , poptr-b9hfd3 , poptr-b9hfi6 , poptr-b9hft8 , poptr-b9hg83 , poptr-b9hif5 , poptr-b9hll5 , poptr-b9hmd0 , poptr-b9hnv3 , poptr-b9hqr6 , poptr-b9hqr7 , poptr-b9hrv7 , poptr-b9hs66 , poptr-b9huf0 , poptr-b9hur3 , poptr-b9hux1 , poptr-b9hwp2 , poptr-b9hxr7 , poptr-b9hyk8 , poptr-b9hyx2 , poptr-b9i2q8 , poptr-b9i5b8 , poptr-b9i5j8 , poptr-b9i5j9 , poptr-b9i5k0 , poptr-b9i6b6 , poptr-b9i7b7 , poptr-b9i9p8 , poptr-b9i484 , poptr-b9i994 , poptr-b9ial3 , poptr-b9ial4 , poptr-b9ib28 , poptr-b9ibr8 , poptr-b9id97 , poptr-b9idr4 , poptr-b9iid9 , poptr-b9iip0 , poptr-b9ik80 , poptr-b9ik90 , poptr-b9il63 , poptr-b9ink7 , poptr-b9iqa0 , poptr-b9iqd5 , poptr-b9mwf1 , poptr-b9mwi8 , poptr-b9n0c6 , poptr-b9n0n1 , poptr-b9n0n4 , poptr-b9n0z5 , poptr-b9n1t8 , poptr-b9n1z3 , poptr-b9n3m7 , poptr-b9n233 , poptr-b9n236 , poptr-b9n395 , poptr-b9nd33 , poptr-b9nd34 , poptr-b9ndi6 , poptr-b9ndj5 , poptr-b9p9i8 , poptr-a9pfa7 , poptr-b9hdp2 , poptr-b9inj0 , poptr-b9n5g7 , poptr-b9i8q4 , poptr-u5g0r4 , poptr-u5gf59 , poptr-u7e1l9 , poptr-b9hj61 , poptr-b9hwd0 , poptr-u5fz17 , poptr-a0a2k2brq1 , poptr-a0a2k2b9i6 , poptr-a0a2k1x9y8 , poptr-a9pch4 , poptr-a0a2k1wwt1 , poptr-a0a2k1wv10 , poptr-a0a2k2a850 , poptr-a0a2k2asj6 , poptr-a0a2k1x6k1 , poptr-u5fv96 , poptr-a0a2k2blg2 , poptr-a0a2k1xpi3 , poptr-a0a2k1xpj0 , poptr-a0a2k2b331 , poptr-a0a2k2byl7 , poptr-b9iek5 , poptr-a9pfg4 , poptr-a0a2k1xzs5 , poptr-b9gga9 , poptr-b9guw6 , poptr-b9hff2

Title : Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features - Derelle_2006_Proc.Natl.Acad.Sci.U.S.A_103_11647
Author(s) : Derelle E , Ferraz C , Rombauts S , Rouze P , Worden AZ , Robbens S , Partensky F , Degroeve S , Echeynie S , Cooke R , Saeys Y , Wuyts J , Jabbari K , Bowler C , Panaud O , Piegu B , Ball SG , Ral JP , Bouget FY , Piganeau G , De Baets B , Picard A , Delseny M , Demaille J , Van de Peer Y , Moreau H
Ref : Proc Natl Acad Sci U S A , 103 :11647 , 2006
Abstract : The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C(4) photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.
ESTHER : Derelle_2006_Proc.Natl.Acad.Sci.U.S.A_103_11647
PubMedSearch : Derelle_2006_Proc.Natl.Acad.Sci.U.S.A_103_11647
PubMedID: 16868079
Gene_locus related to this paper: ostta-q00t45 , ostta-q00te9 , ostta-q00tt1 , ostta-q00tx0 , ostta-q00v73 , ostta-q00vq9 , ostta-q00w59 , ostta-q00y09 , ostta-q00y84 , ostta-q00ys6 , ostta-q01ca2 , ostta-q01ca8 , ostta-q01ck9 , ostta-q01dg2 , ostta-q01e72 , ostta-q01fz0 , ostta-q01g03 , ostta-q01gl9 , ostta-q010m0 , ostta-q011b1 , ostta-q011b9 , ostta-q011x6 , ostta-q018f5 , ostta-q018x2 , ostta-q00wt8 , ostta-a0a090md33 , ostta-q00ua3 , ostta-a0a090m3x7