Rokhsar D

References (11)

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 : 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 : The Selaginella genome identifies genetic changes associated with the evolution of vascular plants - Banks_2011_Science_332_960
Author(s) : Banks JA , Nishiyama T , Hasebe M , Bowman JL , Gribskov M , dePamphilis C , Albert VA , Aono N , Aoyama T , Ambrose BA , Ashton NW , Axtell MJ , Barker E , Barker MS , Bennetzen JL , Bonawitz ND , Chapple C , Cheng C , Correa LG , Dacre M , DeBarry J , Dreyer I , Elias M , Engstrom EM , Estelle M , Feng L , Finet C , Floyd SK , Frommer WB , Fujita T , Gramzow L , Gutensohn M , Harholt J , Hattori M , Heyl A , Hirai T , Hiwatashi Y , Ishikawa M , Iwata M , Karol KG , Koehler B , Kolukisaoglu U , Kubo M , Kurata T , Lalonde S , Li K , Li Y , Litt A , Lyons E , Manning G , Maruyama T , Michael TP , Mikami K , Miyazaki S , Morinaga S , Murata T , Mueller-Roeber B , Nelson DR , Obara M , Oguri Y , Olmstead RG , Onodera N , Petersen BL , Pils B , Prigge M , Rensing SA , Riano-Pachon DM , Roberts AW , Sato Y , Scheller HV , Schulz B , Schulz C , Shakirov EV , Shibagaki N , Shinohara N , Shippen DE , Sorensen I , Sotooka R , Sugimoto N , Sugita M , Sumikawa N , Tanurdzic M , Theissen G , Ulvskov P , Wakazuki S , Weng JK , Willats WW , Wipf D , Wolf PG , Yang L , Zimmer AD , Zhu Q , Mitros T , Hellsten U , Loque D , Otillar R , Salamov A , Schmutz J , Shapiro H , Lindquist E , Lucas S , Rokhsar D , Grigoriev IV
Ref : Science , 332 :960 , 2011
Abstract : Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
ESTHER : Banks_2011_Science_332_960
PubMedSearch : Banks_2011_Science_332_960
PubMedID: 21551031
Gene_locus related to this paper: selml-d8qua5 , selml-d8qva1 , selml-d8qyh7 , selml-d8qza0 , selml-d8r5d4 , selml-d8r6d4 , selml-d8r504 , selml-d8r506 , selml-d8rbi1 , selml-d8rbs1 , selml-d8rck8 , selml-d8rf38 , selml-d8rkl6 , selml-d8rpr1 , selml-d8rpy0 , selml-d8ru47 , selml-d8ry54 , selml-d8rzp6 , selml-d8rzy7 , selml-d8s0c9 , selml-d8s0u3 , selml-d8s2t1 , selml-d8s3z8 , selml-d8s401 , selml-d8sba6 , selml-d8sch9 , selml-d8spq2 , selml-d8sq37 , selml-d8ssx7 , selml-d8swp2 , selml-d8t7a3 , selml-d8t8v4 , selml-d8taz4 , selml-d8tdq6 , selml-d8rai8 , selml-d8qt54 , selml-d8r2d8 , selml-d8rmd3 , selml-d8rra9 , selml-d8slg4 , selml-d8swp0 , selml-d8s7i0 , selml-d8qz37 , selml-d8sz00 , selml-d8s776 , selml-d8qw15 , selml-d8ska7 , selml-d8t0c4 , selml-d8r194 , selml-d8s5m8 , selml-d8s7r2 , selml-d8ta80 , selml-d8ru55

Title : Genome sequence of the palaeopolyploid soybean - Schmutz_2010_Nature_463_178
Author(s) : Schmutz J , Cannon SB , Schlueter J , Ma J , Mitros T , Nelson W , Hyten DL , Song Q , Thelen JJ , Cheng J , Xu D , Hellsten U , May GD , Yu Y , Sakurai T , Umezawa T , Bhattacharyya MK , Sandhu D , Valliyodan B , Lindquist E , Peto M , Grant D , Shu S , Goodstein D , Barry K , Futrell-Griggs M , Abernathy B , Du J , Tian Z , Zhu L , Gill N , Joshi T , Libault M , Sethuraman A , Zhang XC , Shinozaki K , Nguyen HT , Wing RA , Cregan P , Specht J , Grimwood J , Rokhsar D , Stacey G , Shoemaker RC , Jackson SA
Ref : Nature , 463 :178 , 2010
Abstract : Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.
ESTHER : Schmutz_2010_Nature_463_178
PubMedSearch : Schmutz_2010_Nature_463_178
PubMedID: 20075913
Gene_locus related to this paper: soybn-c6t4m5 , soybn-c6t4p4 , soybn-c6tav4 , soybn-c6tdf9 , soybn-c6tiz7 , soybn-c6tmg3 , soybn-i1jgq5 , soybn-i1kpj2 , soybn-i1kwe7 , soybn-i1l7e3 , soybn-i1l497 , soybn-i1ll09 , soybn-i1lpi4 , soybn-i1jcw2 , soybn-i1jcw3 , soybn-i1jcw4 , soybn-i1jcw7 , soybn-i1k217 , soybn-i1kfz3 , soybn-i1lhi0 , soybn-k7k6s4 , soybn-i1jtw1 , soybn-c6tas4 , soybn-i1m910 , soybn-c6t7k8 , soybn-i1k636 , soybn-i1kju7 , soybn-i1j4c6 , soybn-i1lbk2 , soybn-i1jqy5 , soybn-i1nbj8 , soybn-i1j855 , soybn-i1l5a3 , soybn-k7mt28 , soybn-i1lau7 , soybn-i1lay0 , soybn-i1net3 , soybn-i1jr09 , soybn-i1ms08 , soybn-i1mmh5 , soybn-i1mly5 , soybn-i1mmh3 , soybn-i1mmh4 , soybn-i1ngu7 , soybn-k7ll20 , soybn-i1mly4 , soybn-a0a0r0i9y7 , soybn-a0a0r0j241 , soybn-i1les8 , soybn-k7n313 , soybn-i1kfj1 , soybn-a0a0r0k7x4 , soybn-i1ly30 , soybn-i1mwr8 , soybn-i1kfg5 , soybn-i1kly2 , soybn-a0a0r0ixi2 , soybn-i1jew0 , glyso-a0a445l5n1 , soybn-i1kfz9 , soybn-i1jqs1 , soybn-i1nbc7 , soybn-k7mm57 , soybn-a0a0r0fec7 , soybn-a0a0r0hcn9 , soybn-i1jx17 , soybn-k7kvv2 , soybn-i1kcl6 , soybn-i1kcl7 , soybn-i1jrc3 , soybn-i1nbz1 , soybn-a0a0r0euk2 , soybn-a0a0r0fx16 , soybn-a0a0r0k3t3 , soybn-i1kuc7 , soybn-i1lvy4

Title : Genome sequencing and analysis of the model grass Brachypodium distachyon. -
Author(s) : Vogel JP , Garvin DF , Mockler TC , Schmutz J , Rokhsar D , Bevan MW , Barry K , Lucas S , Harmon-Smith M , Lail K , Tice H , Grimwood J , McKenzie N , Huo N , Gu YQ , Lazo GR , Anderson OD , You FM , Luo MC , Dvorak J , Wright J , Febrer M , Idziak D , Hasterok R , Lindquist E , Wang M , Fox SE , Priest HD , Filichkin SA , Givan SA , Bryant DW , Chang JH , Wu H , Wu W , Hsia AP , Schnable PS , Kalyanaraman A , Barbazuk B , Michael TP , Hazen SP , Bragg JN , Laudencia-Chingcuanco D , Weng Y , Haberer G , Spannagl M , Mayer K , Rattei T , Mitros T , Lee SJ , Rose JK , Mueller LA , York TL , Wicker T , Buchmann JP , Tanskanen J , Schulman AH , Gundlach H , Bevan M , de Oliveira AC , Maia Lda C , Belknap W , Jiang N , Lai J , Zhu L , Ma J , Sun C , Pritham E , Salse J , Murat F , Abrouk M , Bruggmann R , Messing J , Fahlgren N , Sullivan CM , Carrington JC , Chapman EJ , May GD , Zhai J , Ganssmann M , Gurazada SG , German M , Meyers BC , Green PJ , Tyler L , Wu J , Thomson J , Chen S , Scheller HV , Harholt J , Ulvskov P , Kimbrel JA , Bartley LE , Cao P , Jung KH , Sharma MK , Vega-Sanchez M , Ronald P , Dardick CD , De Bodt S , Verelst W , Inz D , Heese M , Schnittger A , Yang X , Kalluri UC , Tuskan GA , Hua Z , Vierstra RD , Cui Y , Ouyang S , Sun Q , Liu Z , Yilmaz A , Grotewold E , Sibout R , Hematy K , Mouille G , Hofte H , Michael T , Pelloux J , O'Connor D , Schnable J , Rowe S , Harmon F , Cass CL , Sedbrook JC , Byrne ME , Walsh S , Higgins J , Li P , Brutnell T , Unver T , Budak H , Belcram H , Charles M , Chalhoub B , Baxter I
Ref : Nature , 463 :763 , 2010
PubMedID: 20148030
Gene_locus related to this paper: bradi-i1grm0 , bradi-i1gx82 , bradi-i1hb80 , bradi-i1hkv6 , bradi-i1hpu6 , bradi-i1i3e4 , bradi-i1i9i0 , bradi-i1i435 , bradi-i1ix93 , bradi-i1gsk6 , bradi-i1hk44 , bradi-i1hk45 , bradi-i1hnk7 , bradi-i1hsd5 , bradi-i1huy4 , bradi-i1huy9 , bradi-i1huz0 , bradi-i1gxx9 , bradi-i1hl25 , bradi-i1hcw7 , bradi-i1hyv6 , bradi-i1hyb5 , bradi-i1hvr8 , bradi-i1hmu2 , bradi-i1hf05 , bradi-i1gry7 , bradi-i1hf06 , bradi-i1i5z8 , bradi-i1icy3 , bradi-i1j1h3 , bradi-i1h1e3 , bradi-i1hvr9 , bradi-a0a0q3r7i7 , bradi-i1i377 , bradi-i1hjg5 , bradi-i1h3i9 , bradi-i1gsg5 , bradi-a0a0q3mph9 , bradi-i1h682 , bradi-a0a0q3lc91 , bradi-i1gx49 , bradi-i1i839 , bradi-a0a2k2dsp5 , bradi-i1gsb5

Title : Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion - Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954
Author(s) : Martinez D , Challacombe J , Morgenstern I , Hibbett D , Schmoll M , Kubicek CP , Ferreira P , Ruiz-Duenas FJ , Martinez AT , Kersten P , Hammel KE , Vanden Wymelenberg A , Gaskell J , Lindquist E , Sabat G , Bondurant SS , Larrondo LF , Canessa P , Vicuna R , Yadav J , Doddapaneni H , Subramanian V , Pisabarro AG , Lavin JL , Oguiza JA , Master E , Henrissat B , Coutinho PM , Harris P , Magnuson JK , Baker SE , Bruno K , Kenealy W , Hoegger PJ , Kues U , Ramaiya P , Lucas S , Salamov A , Shapiro H , Tu H , Chee CL , Misra M , Xie G , Teter S , Yaver D , James T , Mokrejs M , Pospisek M , Grigoriev IV , Brettin T , Rokhsar D , Berka R , Cullen D
Ref : Proc Natl Acad Sci U S A , 106 :1954 , 2009
Abstract : Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.
ESTHER : Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954
PubMedSearch : Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954
PubMedID: 19193860
Gene_locus related to this paper: pospm-b8p1f3 , pospm-b8p2q7 , pospm-b8p4n0 , pospm-b8p4n9 , pospm-b8p5g9 , pospm-b8p5r9 , pospm-b8p6h2 , pospm-b8p7b1 , pospm-b8p7c4 , pospm-b8p8w7 , pospm-b8p9j1 , pospm-b8p164 , pospm-b8p280 , pospm-b8p423.1 , pospm-b8p423.2 , pospm-b8p858 , pospm-b8pam2 , pospm-b8pam5 , pospm-b8pb68 , pospm-b8pbm3 , pospm-b8pc54 , pospm-b8pc56 , pospm-b8pce4 , pospm-b8pd91 , pospm-b8pdk6 , pospm-b8ph32 , pospm-b8ph43 , pospm-b8phc9 , pospm-b8php7 , pospm-b8phy5 , pospm-b8pjg8 , pospm-b8pji9 , pospm-b8plr5 , pospm-b8pmk3 , pospm-b8pfg0 , pospm-b8pg35 , pospm-b8pa20.1 , pospm-b8pa20.2 , pospm-b8p4g8 , pospm-b8phn6

Title : The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans - King_2008_Nature_451_783
Author(s) : King N , Westbrook MJ , Young SL , Kuo A , Abedin M , Chapman J , Fairclough S , Hellsten U , Isogai Y , Letunic I , Marr M , Pincus D , Putnam N , Rokas A , Wright KJ , Zuzow R , Dirks W , Good M , Goodstein D , Lemons D , Li W , Lyons JB , Morris A , Nichols S , Richter DJ , Salamov A , Sequencing JG , Bork P , Lim WA , Manning G , Miller WT , McGinnis W , Shapiro H , Tjian R , Grigoriev IV , Rokhsar D
Ref : Nature , 451 :783 , 2008
Abstract : Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.
ESTHER : King_2008_Nature_451_783
PubMedSearch : King_2008_Nature_451_783
PubMedID: 18273011
Gene_locus related to this paper: monbe-a9up87 , monbe-a9uq69 , monbe-a9uq70 , monbe-a9uqa7 , monbe-a9urz6 , monbe-a9usu1 , monbe-a9usy8 , monbe-a9uta2 , monbe-a9uu09 , monbe-a9uxl2 , monbe-a9uy23 , monbe-a9uy95 , monbe-a9uym3 , monbe-a9uyw1 , monbe-a9uzc1 , monbe-a9v0e1 , monbe-a9v2b0 , monbe-a9v3a5 , monbe-a9v3t2 , monbe-a9v4h5 , monbe-a9v6i1 , monbe-a9v7b2 , monbe-a9v7c1 , monbe-a9v8k9 , monbe-a9v8u8 , monbe-a9v9i9 , monbe-a9v9k6 , monbe-a9v028 , monbe-a9v108 , monbe-a9v315 , monbe-a9v345 , monbe-a9v368 , monbe-a9v719 , monbe-a9v871 , monbe-a9vac5 , monbe-a9vah5 , monbe-a9van7 , monbe-a9vbp2 , monbe-a9vcn6 , monbe-a9vd99 , monbe-a9vdj5 , monbe-a9vag0

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 : 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 : Reverse methanogenesis: testing the hypothesis with environmental genomics - Hallam_2004_Science_305_1457
Author(s) : Hallam SJ , Putnam N , Preston CM , Detter JC , Rokhsar D , Richardson PM , DeLong EF
Ref : Science , 305 :1457 , 2004
Abstract : Microbial methane consumption in anoxic sediments significantly impacts the global environment by reducing the flux of greenhouse gases from ocean to atmosphere. Despite its significance, the biological mechanisms controlling anaerobic methane oxidation are not well characterized. One current model suggests that relatives of methane-producing Archaea developed the capacity to reverse methanogenesis and thereby to consume methane to produce cellular carbon and energy. We report here a test of the "reverse-methanogenesis" hypothesis by genomic analyses of methane-oxidizing Archaea from deep-sea sediments. Our results show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs. These genome-based observations support previous hypotheses and provide an informed foundation for metabolic modeling of anaerobic methane oxidation.
ESTHER : Hallam_2004_Science_305_1457
PubMedSearch : Hallam_2004_Science_305_1457
PubMedID: 15353801
Gene_locus related to this paper: 9arch-q64ad0 , 9arch-q64bc9 , 9arch-q648n1

Title : Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes - Aparicio_2002_Science_297_1301
Author(s) : Aparicio S , Chapman J , Stupka E , Putnam N , Chia JM , Dehal P , Christoffels A , Rash S , Hoon S , Smit A , Gelpke MD , Roach J , Oh T , Ho IY , Wong M , Detter C , Verhoef F , Predki P , Tay A , Lucas S , Richardson P , Smith SF , Clark MS , Edwards YJ , Doggett N , Zharkikh A , Tavtigian SV , Pruss D , Barnstead M , Evans C , Baden H , Powell J , Glusman G , Rowen L , Hood L , Tan YH , Elgar G , Hawkins T , Venkatesh B , Rokhsar D , Brenner S
Ref : Science , 297 :1301 , 2002
Abstract : The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.
ESTHER : Aparicio_2002_Science_297_1301
PubMedSearch : Aparicio_2002_Science_297_1301
PubMedID: 12142439
Gene_locus related to this paper: fugru-2balip , fugru-2cxest , fugru-3cxest , fugru-3neur , fugru-4cxest , fugru-4neur , fugru-ACHE , fugru-ACHEE , fugru-balip , fugru-BCHE , fugru-BCHEB , fugru-BCHEC , fugru-cxest , takru-1neur , takru-2bneur , takru-3bneur , takru-h2rsj9 , takru-nlgn2a , takru-nlgn4a