Jenkins J

References (15)

Title : The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization - McCormick_2018_Plant.J_93_338
Author(s) : McCormick RF , Truong SK , Sreedasyam A , Jenkins J , Shu S , Sims D , Kennedy M , Amirebrahimi M , Weers BD , McKinley B , Mattison A , Morishige DT , Grimwood J , Schmutz J , Mullet JE
Ref : Plant J , 93 :338 , 2018
Abstract : Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement.
ESTHER : McCormick_2018_Plant.J_93_338
PubMedSearch : McCormick_2018_Plant.J_93_338
PubMedID: 29161754
Gene_locus related to this paper: sorbi-a0a194ysf6 , sorbi-a0a1b6pnr2 , sorbi-a0a1b6qcb9 , sorbi-c5xx30 , sorbi-a0a1b6psg4 , sorbi-a0a1z5rj80 , sorbi-a0a1b6qfm2 , sorbi-a0a1b6qmu5 , sorbi-c6jru0

Title : The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution - Lang_2018_Plant.J_93_515
Author(s) : Lang D , Ullrich KK , Murat F , Fuchs J , Jenkins J , Haas FB , Piednoel M , Gundlach H , Van Bel M , Meyberg R , Vives C , Morata J , Symeonidi A , Hiss M , Muchero W , Kamisugi Y , Saleh O , Blanc G , Decker EL , van Gessel N , Grimwood J , Hayes RD , Graham SW , Gunter LE , McDaniel SF , Hoernstein SNW , Larsson A , Li FW , Perroud PF , Phillips J , Ranjan P , Rokshar DS , Rothfels CJ , Schneider L , Shu S , Stevenson DW , Thummler F , Tillich M , Villarreal Aguilar JC , Widiez T , Wong GK , Wymore A , Zhang Y , Zimmer AD , Quatrano RS , Mayer KFX , Goodstein D , Casacuberta JM , Vandepoele K , Reski R , Cuming AC , Tuskan GA , Maumus F , Salse J , Schmutz J , Rensing SA
Ref : Plant J , 93 :515 , 2018
Abstract : The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
ESTHER : Lang_2018_Plant.J_93_515
PubMedSearch : Lang_2018_Plant.J_93_515
PubMedID: 29237241
Gene_locus related to this paper: phypa-a9tc36 , phypa-a0a2k1kfe3 , phypa-a9sqk3 , phypa-a0a2k1ie71 , phypa-a0a2k1kg29 , phypa-a0a2k1iji3

Title : Genome evolution in the allotetraploid frog Xenopus laevis - Session_2016_Nature_538_336
Author(s) : Session AM , Uno Y , Kwon T , Chapman JA , Toyoda A , Takahashi S , Fukui A , Hikosaka A , Suzuki A , Kondo M , van Heeringen SJ , Quigley I , Heinz S , Ogino H , Ochi H , Hellsten U , Lyons JB , Simakov O , Putnam N , Stites J , Kuroki Y , Tanaka T , Michiue T , Watanabe M , Bogdanovic O , Lister R , Georgiou G , Paranjpe SS , van Kruijsbergen I , Shu S , Carlson J , Kinoshita T , Ohta Y , Mawaribuchi S , Jenkins J , Grimwood J , Schmutz J , Mitros T , Mozaffari SV , Suzuki Y , Haramoto Y , Yamamoto TS , Takagi C , Heald R , Miller K , Haudenschild C , Kitzman J , Nakayama T , Izutsu Y , Robert J , Fortriede J , Burns K , Lotay V , Karimi K , Yasuoka Y , Dichmann DS , Flajnik MF , Houston DW , Shendure J , DuPasquier L , Vize PD , Zorn AM , Ito M , Marcotte EM , Wallingford JB , Ito Y , Asashima M , Ueno N , Matsuda Y , Veenstra GJ , Fujiyama A , Harland RM , Taira M , Rokhsar DS
Ref : Nature , 538 :336 , 2016
Abstract : To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.
ESTHER : Session_2016_Nature_538_336
PubMedSearch : Session_2016_Nature_538_336
PubMedID: 27762356
Gene_locus related to this paper: xenla-a0a1l8f4t7 , xenla-a0a1l8fbc6 , xenla-a0a1l8fct2 , xenla-q2tap9 , xenla-q4klb6 , xenla-q5xh09 , xenla-q6ax59 , xenla-q6dcw6 , xenla-q6irp4 , xenla-q6pad5 , xenla-q7sz70 , xenla-Q7ZXQ6 , xenla-q66kx1 , xenla-q640y7 , xenla-q642r3 , xenla-Q860X9 , xenla-BCHE2 , xenla-a0a1l8g7v4 , xenla-a0a1l8g1u7 , xenla-a0a1l8fmc5 , xenla-a0a1l8g467 , xenla-a0a1l8g4e4 , xenla-a0a1l8ga66 , xenla-a0a1l8gaw4 , xenla-a0a1l8gt68 , xenla-a0a1l8h0b2 , xenla-a0a1l8fdr1 , xenla-a0a1l8fdt7 , xenla-a0a1l8fi72 , xenla-a0a1l8fi73 , xenla-a0a1l8fi77 , xenla-a0a1l8fi96 , xenla-a0a1l8hc38 , xenla-a0a1l8hn27 , xenla-a0a1l8hry6 , xenla-a0a1l8hw96 , xenla-a0a1l8i2x6 , xenla-a0a1l8hei7 , xenla-a0a1l8gnd1 , xenla-a0a1l8i2g3 , xenla-a0a1l8hdn0 , xenla-a0a1l8h622

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 : A reference genome for common bean and genome-wide analysis of dual domestications - Schmutz_2014_Nat.Genet_46_707
Author(s) : Schmutz J , McClean PE , Mamidi S , Wu GA , Cannon SB , Grimwood J , Jenkins J , Shu S , Song Q , Chavarro C , Torres-Torres M , Geffroy V , Moghaddam SM , Gao D , Abernathy B , Barry K , Blair M , Brick MA , Chovatia M , Gepts P , Goodstein DM , Gonzales M , Hellsten U , Hyten DL , Jia G , Kelly JD , Kudrna D , Lee R , Richard MM , Miklas PN , Osorno JM , Rodrigues J , Thareau V , Urrea CA , Wang M , Yu Y , Zhang M , Wing RA , Cregan PB , Rokhsar DS , Jackson SA
Ref : Nat Genet , 46 :707 , 2014
Abstract : Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
ESTHER : Schmutz_2014_Nat.Genet_46_707
PubMedSearch : Schmutz_2014_Nat.Genet_46_707
PubMedID: 24908249
Gene_locus related to this paper: phavu-v7azs2 , phavu-v7awu7 , phavu-v7bpt6 , phavu-v7b6k3 , phavu-v7cry4

Title : Fine-scale variation in meiotic recombination in Mimulus inferred from population shotgun sequencing - Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
Author(s) : Hellsten U , Wright KM , Jenkins J , Shu S , Yuan Y , Wessler SR , Schmutz J , Willis JH , Rokhsar DS
Ref : Proc Natl Acad Sci U S A , 110 :19478 , 2013
Abstract : Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.
ESTHER : Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
PubMedSearch : Hellsten_2013_Proc.Natl.Acad.Sci.U.S.A_110_19478
PubMedID: 24225854
Gene_locus related to this paper: erygu-a0a022qsc9 , erygu-a0a022qjb4 , erygu-a0a022px28 , erygu-a0a022rcn8 , erygu-a0a022r7z4 , erygu-a0a022rcp2 , erygu-a0a022r9s7 , erygu-a0a022put8 , erygu-a0a022r922 , erygu-a0a022qmg0 , erygu-a0a022rf01 , erygu-a0a022qnf5 , erygu-a0a022qs63 , erygu-a0a022rvn4 , erygu-a0a022rnw2 , erygu-a0a022s0h3 , erygu-a0a022qr26 , erygu-a0a022qi72 , erygu-a0a022qi30 , erygu-a0a022q165 , erygu-a0a022r728 , erygu-a0a022r7n8 , erygu-a0a022rm64 , erygu-a0a022s4c6 , erygu-a0a022rbl0 , erygu-a0a022rwi3 , erygu-a0a022rzg9

Title : The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color - Motamayor_2013_Genome.Biol_14_r53
Author(s) : Motamayor JC , Mockaitis K , Schmutz J , Haiminen N , Livingstone D, 3rd , Cornejo O , Findley SD , Zheng P , Utro F , Royaert S , Saski C , Jenkins J , Podicheti R , Zhao M , Scheffler BE , Stack JC , Feltus FA , Mustiga GM , Amores F , Phillips W , Marelli JP , May GD , Shapiro H , Ma J , Bustamante CD , Schnell RJ , Main D , Gilbert D , Parida L , Kuhn DN
Ref : Genome Biol , 14 :r53 , 2013
Abstract : BACKGROUND: Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.
RESULTS: We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation.
CONCLUSIONS: We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
ESTHER : Motamayor_2013_Genome.Biol_14_r53
PubMedSearch : Motamayor_2013_Genome.Biol_14_r53
PubMedID: 23731509
Gene_locus related to this paper: thecc-a0a061drp5 , thecc-a0a061f547 , thecc-a0a061et00 , thecc-a0a061g081 , thecc-a0a061g216 , thecc-a0a061g7l1 , thecc-a0a061g739 , thecc-a0a061emb5 , thecc-a0a061e5y9 , thecc-a0a061g267 , thecc-a0a061fqk7 , thecc-a0a061fxr9 , thecc-a0a061glp9 , thecc-a0a061gj91 , thecc-a0a061eb00 , thecc-a0a061faz2 , thecc-a0a061eik0 , thecc-a0a061dz39 , thecc-a0a061dgb4 , thecc-a0a061dgb9 , thecc-a0a061dgg3 , thecc-a0a061dn78 , thecc-a0a061fbl1 , thecc-a0a061gjz3 , thecc-a0a061fu06 , thecc-a0a061f9z5

Title : The Reference Genome of the Halophytic Plant Eutrema salsugineum - Yang_2013_Front.Plant.Sci_4_46
Author(s) : Yang R , Jarvis DE , Chen H , Beilstein MA , Grimwood J , Jenkins J , Shu S , Prochnik S , Xin M , Ma C , Schmutz J , Wing RA , Mitchell-Olds T , Schumaker KS , Wang X
Ref : Front Plant Sci , 4 :46 , 2013
Abstract : Halophytes are plants that can naturally tolerate high concentrations of salt in the soil, and their tolerance to salt stress may occur through various evolutionary and molecular mechanisms. Eutrema salsugineum is a halophytic species in the Brassicaceae that can naturally tolerate multiple types of abiotic stresses that typically limit crop productivity, including extreme salinity and cold. It has been widely used as a laboratorial model for stress biology research in plants. Here, we present the reference genome sequence (241 Mb) of E. salsugineum at 8x coverage sequenced using the traditional Sanger sequencing-based approach with comparison to its close relative Arabidopsis thaliana. The E. salsugineum genome contains 26,531 protein-coding genes and 51.4% of its genome is composed of repetitive sequences that mostly reside in pericentromeric regions. Comparative analyses of the genome structures, protein-coding genes, microRNAs, stress-related pathways, and estimated translation efficiency of proteins between E. salsugineum and A. thaliana suggest that halophyte adaptation to environmental stresses may occur via a global network adjustment of multiple regulatory mechanisms. The E. salsugineum genome provides a resource to identify naturally occurring genetic alterations contributing to the adaptation of halophytic plants to salinity and that might be bioengineered in related crop species.
ESTHER : Yang_2013_Front.Plant.Sci_4_46
PubMedSearch : Yang_2013_Front.Plant.Sci_4_46
PubMedID: 23518688
Gene_locus related to this paper: theha-e4mxu0 , thesl-v4nk72 , eutsa-v4l4z1 , eutsa-v4kk46 , eutsa-v4mej3 , eutsa-v4ns11 , eutsa-v4mg02 , eutsa-v4mqm9 , eutsa-v4k1y6 , eutsa-v4lad0 , eutsa-v4nr92 , eutsa-v4kqc3 , eutsa-v4l0s2 , eutsa-v4lip3 , eutsa-v4kkg2 , eutsa-v4kvd3 , eutsa-v4m9g4 , eutsa-v4lqg2 , eutsa-v4lp36 , eutsa-v4km66 , eutsa-v4nhr8 , eutsa-v4kqx9 , eutsa-v4lv73

Title : The Capsella rubella genome and the genomic consequences of rapid mating system evolution - Slotte_2013_Nat.Genet_45_831
Author(s) : Slotte T , Hazzouri KM , Agren JA , Koenig D , Maumus F , Guo YL , Steige K , Platts AE , Escobar JS , Newman LK , Wang W , Mandakova T , Vello E , Smith LM , Henz SR , Steffen J , Takuno S , Brandvain Y , Coop G , Andolfatto P , Hu TT , Blanchette M , Clark RM , Quesneville H , Nordborg M , Gaut BS , Lysak MA , Jenkins J , Grimwood J , Chapman J , Prochnik S , Shu S , Rokhsar D , Schmutz J , Weigel D , Wright SI
Ref : Nat Genet , 45 :831 , 2013
Abstract : The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
ESTHER : Slotte_2013_Nat.Genet_45_831
PubMedSearch : Slotte_2013_Nat.Genet_45_831
PubMedID: 23749190
Gene_locus related to this paper: arath-CGEP , 9bras-r0h1k6 , 9bras-r0gvg3 , 9bras-r0gv62 , 9bras-r0g5k5 , 9bras-r0f1u1 , 9bras-r0guy4 , 9bras-r0ien7 , 9bras-r0i2r7 , 9bras-r0fbh7 , 9bras-r0fnq1 , 9bras-r0hae6 , 9bras-r0gwt8 , 9bras-r0ewe4 , 9bras-r0gsz7 , 9bras-r0ij26 , 9bras-r0h783 , 9bras-r0i5w1 , 9bras-r0fgs3 , 9bras-r0h1e1 , 9bras-r0fme4 , 9bras-r0ieh8 , 9bras-r0f5l9 , 9bras-r0ffy6

Title : The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution - Verde_2013_Nat.Genet_45_487
Author(s) : Verde I , Abbott AG , Scalabrin S , Jung S , Shu S , Marroni F , Zhebentyayeva T , Dettori MT , Grimwood J , Cattonaro F , Zuccolo A , Rossini L , Jenkins J , Vendramin E , Meisel LA , Decroocq V , Sosinski B , Prochnik S , Mitros T , Policriti A , Cipriani G , Dondini L , Ficklin S , Goodstein DM , Xuan P , Del Fabbro C , Aramini V , Copetti D , Gonzalez S , Horner DS , Falchi R , Lucas S , Mica E , Maldonado J , Lazzari B , Bielenberg D , Pirona R , Miculan M , Barakat A , Testolin R , Stella A , Tartarini S , Tonutti P , Arus P , Orellana A , Wells C , Main D , Vizzotto G , Silva H , Salamini F , Schmutz J , Morgante M , Rokhsar DS
Ref : Nat Genet , 45 :487 , 2013
Abstract : Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
ESTHER : Verde_2013_Nat.Genet_45_487
PubMedSearch : Verde_2013_Nat.Genet_45_487
PubMedID: 23525075
Gene_locus related to this paper: prupe-a0a251pfr7 , prupe-a0a251r634 , prupe-m5x0p5 , prupe-m5xkg4 , prupe-m5x0q4 , prupe-m5vqa7 , prupe-m5wiw5 , prupe-a0a0u2wu32 , prupe-a0a251mtk1 , prupe-m5vl29 , prupe-m5vn82 , prupe-m5vq88 , prupe-m5y2s7 , prupe-m5wye7 , prupe-m5wxm4 , prupe-m5xqp6 , prupe-m5x4q4 , prupe-m5x4m1 , prupe-m5x6b3 , prupe-m5vlb6 , prupe-m5w4h3 , prupe-m5vlu4 , prupe-m5vln3 , prupe-a0a251myy7 , prupe-a0a251mws4 , prupe-m5vi18 , prupe-m5vh66 , prupe-m5xd54 , prupe-m5xqn2 , prupe-m5xr64 , prupe-m5vrm7 , prupe-m5vrk6 , prupe-m5vqp6 , prupe-a0a251nbb1 , prupe-a0a251nbd3 , prupe-a0a251nbb3 , prupe-a0a251nba0 , prupe-a0a251ndd4 , prupe-a0a251nbb6 , prupe-m5w315 , prupe-a0a251mwh1 , prupe-a0a251qn57 , prupe-m5vzh8 , prupe-m5xpz7 , prupe-m5xrp5 , prupe-m5wsr5 , prupe-m5xs20 , prupe-m5vl10 , prupe-a0a251nay9 , prupe-a0a251ndz1 , prupe-a0a251puf0 , prupe-m5wr61 , prupe-a0a251nyu6 , prupe-m5vl63

Title : Reference genome sequence of the model plant Setaria - Bennetzen_2012_Nat.Biotechnol_30_555
Author(s) : Bennetzen JL , Schmutz J , Wang H , Percifield R , Hawkins J , Pontaroli AC , Estep M , Feng L , Vaughn JN , Grimwood J , Jenkins J , Barry K , Lindquist E , Hellsten U , Deshpande S , Wang X , Wu X , Mitros T , Triplett J , Yang X , Ye CY , Mauro-Herrera M , Wang L , Li P , Sharma M , Sharma R , Ronald PC , Panaud O , Kellogg EA , Brutnell TP , Doust AN , Tuskan GA , Rokhsar D , Devos KM
Ref : Nat Biotechnol , 30 :555 , 2012
Abstract : We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The approximately 400-Mb assembly covers approximately 80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).
ESTHER : Bennetzen_2012_Nat.Biotechnol_30_555
PubMedSearch : Bennetzen_2012_Nat.Biotechnol_30_555
PubMedID: 22580951
Gene_locus related to this paper: setit-k3xwe0 , setit-k3xfs7 , setit-k3yh36 , setit-k3zes3 , setit-k3zlj8 , setvi-a0a4u6wd58 , setit-a0a368qif6 , setit-a0a368sru6 , setit-a0a368q9x4 , setit-k3zri0 , setit-k3ysv0 , setit-k3xj49 , setit-k4ac30

Title : Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres - Paterson_2012_Nature_492_423
Author(s) : Paterson AH , Wendel JF , Gundlach H , Guo H , Jenkins J , Jin D , Llewellyn D , Showmaker KC , Shu S , Udall J , Yoo MJ , Byers R , Chen W , Doron-Faigenboim A , Duke MV , Gong L , Grimwood J , Grover C , Grupp K , Hu G , Lee TH , Li J , Lin L , Liu T , Marler BS , Page JT , Roberts AW , Romanel E , Sanders WS , Szadkowski E , Tan X , Tang H , Xu C , Wang J , Wang Z , Zhang D , Zhang L , Ashrafi H , Bedon F , Bowers JE , Brubaker CL , Chee PW , Das S , Gingle AR , Haigler CH , Harker D , Hoffmann LV , Hovav R , Jones DC , Lemke C , Mansoor S , ur Rahman M , Rainville LN , Rambani A , Reddy UK , Rong JK , Saranga Y , Scheffler BE , Scheffler JA , Stelly DM , Triplett BA , Van Deynze A , Vaslin MF , Waghmare VN , Walford SA , Wright RJ , Zaki EA , Zhang T , Dennis ES , Mayer KF , Peterson DG , Rokhsar DS , Wang X , Schmutz J
Ref : Nature , 492 :423 , 2012
Abstract : Polyploidy often confers emergent properties, such as the higher fibre productivity and quality of tetraploid cottons than diploid cottons bred for the same environments. Here we show that an abrupt five- to sixfold ploidy increase approximately 60 million years (Myr) ago, and allopolyploidy reuniting divergent Gossypium genomes approximately 1-2 Myr ago, conferred about 30-36-fold duplication of ancestral angiosperm (flowering plant) genes in elite cottons (Gossypium hirsutum and Gossypium barbadense), genetic complexity equalled only by Brassica among sequenced angiosperms. Nascent fibre evolution, before allopolyploidy, is elucidated by comparison of spinnable-fibred Gossypium herbaceum A and non-spinnable Gossypium longicalyx F genomes to one another and the outgroup D genome of non-spinnable Gossypium raimondii. The sequence of a G. hirsutum A(t)D(t) (in which 't' indicates tetraploid) cultivar reveals many non-reciprocal DNA exchanges between subgenomes that may have contributed to phenotypic innovation and/or other emergent properties such as ecological adaptation by polyploids. Most DNA-level novelty in G. hirsutum recombines alleles from the D-genome progenitor native to its New World habitat and the Old World A-genome progenitor in which spinnable fibre evolved. Coordinated expression changes in proximal groups of functionally distinct genes, including a nuclear mitochondrial DNA block, may account for clusters of cotton-fibre quantitative trait loci affecting diverse traits. Opportunities abound for dissecting emergent properties of other polyploids, particularly angiosperms, by comparison to diploid progenitors and outgroups.
ESTHER : Paterson_2012_Nature_492_423
PubMedSearch : Paterson_2012_Nature_492_423
PubMedID: 23257886
Gene_locus related to this paper: gosra-a0a0d2qg22 , gosra-a0a0d2w3z1 , gosra-a0a0d2uuz7 , gosra-a0a0d2rxs2 , gosra-a0a0d2sdk0 , gosra-a0a0d2tng2 , gosra-a0a0d2twz7 , gosra-a0a0d2vdc5 , gosra-a0a0d2vj24 , gosra-a0a0d2sr31 , goshi-a0a1u8knd1 , goshi-a0a1u8nhw9 , goshi-a0a1u8kis4 , gosra-a0a0d2pul0 , gosra-a0a0d2p3f2 , gosra-a0a0d2ril5 , gosra-a0a0d2s7d5 , gosra-a0a0d2t9b3 , gosra-a0a0d2tw88 , gosra-a0a0d2umz5 , gosra-a0a0d2pzd7 , gosra-a0a0d2scu7 , gosra-a0a0d2vcx6

Title : Alteration of lipase chain length specificity in the hydrolysis of esters by random mutagenesis - Gaskin_2001_Biotechnol.Bioeng_73_433
Author(s) : Gaskin DJ , Romojaro A , Turner NA , Jenkins J , Vulfson EN
Ref : Biotechnol Bioeng , 73 :433 , 2001
Abstract : The feasibility of altering the chain length specificity of industrially important Rhizomucor miehei lipase was investigated by randomly mutating Phe94 in the protein groove which is responsible for accommodating the acyl chain of the substrate. The recombinant lipase was initially expressed in E. coli. Individual colonies were selected, grown, and the DNA sequence of the lipase gene determined. Fourteen of the 19 possible mutants were identified and each of these was transformed into Pichia pastoris which expresses the enzyme extracellularly. The yeast was grown and the supernatants assessed in several assays with long and short chain substrates. Based on this preliminary screen, one mutant, Phe94Gly, was selected and purified to homogeneity for further analysis. It was found that the substitution of phenylalanine 94 with glycine led to an enzyme which was about six times less active against resorufin ester but displayed 3-4 times higher activity with short chain substrates such as butyric acid esters. The observed alteration to the enzyme specificity was rationalised using the available 3D structure of the lipase.
ESTHER : Gaskin_2001_Biotechnol.Bioeng_73_433
PubMedSearch : Gaskin_2001_Biotechnol.Bioeng_73_433
PubMedID: 11344447

Title : Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana - Salanoubat_2000_Nature_408_820
Author(s) : Salanoubat M , Lemcke K , Rieger M , Ansorge W , Unseld M , Fartmann B , Valle G , Blocker H , Perez-Alonso M , Obermaier B , Delseny M , Boutry M , Grivell LA , Mache R , Puigdomenech P , de Simone V , Choisne N , Artiguenave F , Robert C , Brottier P , Wincker P , Cattolico L , Weissenbach J , Saurin W , Quetier F , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Benes V , Wurmbach E , Drzonek H , Erfle H , Jordan N , Bangert S , Wiedelmann R , Kranz H , Voss H , Holland R , Brandt P , Nyakatura G , Vezzi A , D'Angelo M , Pallavicini A , Toppo S , Simionati B , Conrad A , Hornischer K , Kauer G , Lohnert TH , Nordsiek G , Reichelt J , Scharfe M , Schon O , Bargues M , Terol J , Climent J , Navarro P , Collado C , Perez-Perez A , Ottenwalder B , Duchemin D , Cooke R , Laudie M , Berger-Llauro C , Purnelle B , Masuy D , de Haan M , Maarse AC , Alcaraz JP , Cottet A , Casacuberta E , Monfort A , Argiriou A , Flores M , Liguori R , Vitale D , Mannhaupt G , Haase D , Schoof H , Rudd S , Zaccaria P , Mewes HW , Mayer KF , Kaul S , Town CD , Koo HL , Tallon LJ , Jenkins J , Rooney T , Rizzo M , Walts A , Utterback T , Fujii CY , Shea TP , Creasy TH , Haas B , Maiti R , Wu D , Peterson J , Van Aken S , Pai G , Militscher J , Sellers P , Gill JE , Feldblyum TV , Preuss D , Lin X , Nierman WC , Salzberg SL , White O , Venter JC , Fraser CM , Kaneko T , Nakamura Y , Sato S , Kato T , Asamizu E , Sasamoto S , Kimura T , Idesawa K , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : Nature , 408 :820 , 2000
Abstract : Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
ESTHER : Salanoubat_2000_Nature_408_820
PubMedSearch : Salanoubat_2000_Nature_408_820
PubMedID: 11130713
Gene_locus related to this paper: arath-MES17 , arath-AT3G12150 , arath-At3g61680 , arath-AT3g62590 , arath-CXE12 , arath-eds1 , arath-SCP25 , arath-F1P2.110 , arath-F1P2.140 , arath-F11F8.28 , arath-F14D17.80 , arath-F16B3.4 , arath-SCP27 , arath-At3g50790 , arath-At3g05600 , arath-PAD4 , arath-At3g51000 , arath-SCP16 , arath-gid1 , arath-GID1B , arath-Q9LUG8 , arath-Q84JS1 , arath-Q9SFF6 , arath-q9m236 , arath-q9sr22 , arath-q9sr23 , arath-SCP7 , arath-SCP14 , arath-SCP15 , arath-SCP17 , arath-SCP36 , arath-SCP37 , arath-SCP39 , arath-SCP40 , arath-SCP49 , arath-T19F11.2

Title : Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana - Theologis_2000_Nature_408_816
Author(s) : Theologis A , Ecker JR , Palm CJ , Federspiel NA , Kaul S , White O , Alonso J , Altafi H , Araujo R , Bowman CL , Brooks SY , Buehler E , Chan A , Chao Q , Chen H , Cheuk RF , Chin CW , Chung MK , Conn L , Conway AB , Conway AR , Creasy TH , Dewar K , Dunn P , Etgu P , Feldblyum TV , Feng J , Fong B , Fujii CY , Gill JE , Goldsmith AD , Haas B , Hansen NF , Hughes B , Huizar L , Hunter JL , Jenkins J , Johnson-Hopson C , Khan S , Khaykin E , Kim CJ , Koo HL , Kremenetskaia I , Kurtz DB , Kwan A , Lam B , Langin-Hooper S , Lee A , Lee JM , Lenz CA , Li JH , Li Y , Lin X , Liu SX , Liu ZA , Luros JS , Maiti R , Marziali A , Militscher J , Miranda M , Nguyen M , Nierman WC , Osborne BI , Pai G , Peterson J , Pham PK , Rizzo M , Rooney T , Rowley D , Sakano H , Salzberg SL , Schwartz JR , Shinn P , Southwick AM , Sun H , Tallon LJ , Tambunga G , Toriumi MJ , Town CD , Utterback T , Van Aken S , Vaysberg M , Vysotskaia VS , Walker M , Wu D , Yu G , Fraser CM , Venter JC , Davis RW
Ref : Nature , 408 :816 , 2000
Abstract : The genome of the flowering plant Arabidopsis thaliana has five chromosomes. Here we report the sequence of the largest, chromosome 1, in two contigs of around 14.2 and 14.6 megabases. The contigs extend from the telomeres to the centromeric borders, regions rich in transposons, retrotransposons and repetitive elements such as the 180-base-pair repeat. The chromosome represents 25% of the genome and contains about 6,850 open reading frames, 236 transfer RNAs (tRNAs) and 12 small nuclear RNAs. There are two clusters of tRNA genes at different places on the chromosome. One consists of 27 tRNA(Pro) genes and the other contains 27 tandem repeats of tRNA(Tyr)-tRNA(Tyr)-tRNA(Ser) genes. Chromosome 1 contains about 300 gene families with clustered duplications. There are also many repeat elements, representing 8% of the sequence.
ESTHER : Theologis_2000_Nature_408_816
PubMedSearch : Theologis_2000_Nature_408_816
PubMedID: 11130712
Gene_locus related to this paper: arath-At1g05790 , arath-At1g09280 , arath-At1g09980 , arath-AT1G29120 , arath-AT1G52695 , arath-AT1G66900 , arath-At1g73750 , arath-AT1G73920 , arath-AT1G74640 , arath-AT1G76140 , arath-AT1G78210 , arath-clh1 , arath-F1O17.3 , arath-F1O17.4 , arath-F1O17.5 , arath-F5I6.3 , arath-At1g52700 , arath-F6D8.27 , arath-F6D8.32 , arath-F9L1.44 , arath-F9P14.11 , arath-F12A4.4 , arath-MES11 , arath-F14G24.2 , arath-F14G24.3 , arath-F14I3.4 , arath-F14O10.2 , arath-F16N3.25 , arath-LCAT2 , arath-At1g34340 , arath-MES15 , arath-CXE6 , arath-ICML1 , arath-At1g72620 , arath-LCAT1 , arath-PLA12 , arath-PLA15 , arath-PLA17 , arath-Q8L7S1 , arath-At1g15070 , arath-SCP2 , arath-SCP4 , arath-SCP5 , arath-SCP18 , arath-SCP32 , arath-SCP44 , arath-SCP45 , arath-SCPL6 , arath-F4IE65 , arath-At1g30370 , arath-T6L1.8 , arath-T6L1.20 , arath-T14P4.6 , arath-MES14 , arath-SCP3 , arath-AXR4 , arath-At1g10040 , arath-ZW18 , arath-pae2 , arath-pae1 , arath-a0a1p8awg3