Author Report for: Marra MANo contact information in database for Marra MA
DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U and Breuil C <13 more author(s)> DiGuistini S, Wang Y, Liao NY, Taylor G, Tanguay P, Feau N, Henrissat B, Chan SK, Hesse-Orce U, Alamouti SM, Tsui CK, Docking RT, Levasseur A, Haridas S, Robertson G, Birol I, Holt RA, Marra MA, Hamelin RC, Hirst M, Jones SJ, Bohlmann J, Breuil C (- 13) Ref: Proc Natl Acad Sci U S A, 108:2504, 2011 : PubMed ESTHER: Diguistini_2011_Proc.Natl.Acad.Sci.U.S.A_108_2504 PubMedSearch: Diguistini 2011 Proc.Natl.Acad.Sci.U.S.A 108 2504 PubMedID: 21262841 Gene_locus related to this paper: grocl-dapb, grocl-f0x6y5, grocl-f0x7n2, grocl-f0x8u4, grocl-f0x9c7, grocl-f0x9d5, grocl-f0x966, grocl-f0xbs9, grocl-f0xc51, grocl-f0xcj4, grocl-f0xee9, grocl-f0xh50, grocl-f0xip5, grocl-f0xjv7, grocl-f0xk48, grocl-f0xke2, grocl-f0xkp2, grocl-f0xl11, grocl-f0xl25, grocl-f0xlh9, grocl-f0xm76, grocl-f0xnw8, grocl-f0xsu8, grocl-f0xtk0, grocl-f0xtm0, grocl-f0xv04, grocl-f0x8s2, grocl-f0xa18, grocl-f0xm17, grocl-f0x801, grocl-f0xfy2 Abstract In western North America, the current outbreak of the mountain pine beetle (MPB) and its microbial associates has destroyed wide areas of lodgepole pine forest, including more than 16 million hectares in British Columbia. Grosmannia clavigera (Gc), a critical component of the outbreak, is a symbiont of the MPB and a pathogen of pine trees. To better understand the interactions between Gc, MPB, and lodgepole pine hosts, we sequenced the approximately 30-Mb Gc genome and assembled it into 18 supercontigs. We predict 8,314 protein-coding genes, and support the gene models with proteome, expressed sequence tag, and RNA-seq data. We establish that Gc is heterothallic, and report evidence for repeat-induced point mutation. We report insights, from genome and transcriptome analyses, into how Gc tolerates conifer-defense chemicals, including oleoresin terpenoids, as they colonize a host tree. RNA-seq data indicate that terpenoids induce a substantial antimicrobial stress in Gc, and suggest that the fungus may detoxify these chemicals by using them as a carbon source. Terpenoid treatment strongly activated a approximately 100-kb region of the Gc genome that contains a set of genes that may be important for detoxification of these host-defense chemicals. This work is a major step toward understanding the biological interactions between the tripartite MPB/fungus/forest system. Title: Retinoblastoma-binding proteins 4 and 9 are important for human pluripotent stem cell maintenance O'Connor MD, Wederell E, Robertson G, Delaney A, Morozova O, Poon SS, Yap D, Fee J, Zhao Y and Eaves CJ <5 more author(s)> O'Connor MD, Wederell E, Robertson G, Delaney A, Morozova O, Poon SS, Yap D, Fee J, Zhao Y, McDonald H, Zeng T, Hirst M, Marra MA, Aparicio SA, Eaves CJ (- 5) Ref: Experimental Hematology, 39:866, 2011 : PubMed ESTHER: O'Connor_2011_Exp.Hematol_39_866 PubMedSearch: O'Connor 2011 Exp.Hematol 39 866 PubMedID: 21689726 Gene_locus related to this paper: human-RBBP9 Abstract OBJECTIVE: The molecular mechanisms that maintain human pluripotent stem (PS) cells are not completely understood. Here we sought to identify new candidate PS cell regulators to facilitate future improvements in their generation, expansion, and differentiation. MATERIALS AND METHODS: We used bioinformatic analyses of multiple serial-analysis-of-gene-expression libraries (generated from human PS cells and their differentiated derivatives), together with small interfering RNA (siRNA) screening to identify candidate pluripotency regulators. Validation of candidate regulators involved promoter analyses, Affymetrix profiling, real-time PCR, and immunoprecipitation. RESULTS: Promoter analysis of genes differentially expressed across multiple serial-analysis-of-gene-expression libraries identified E2F motifs in the promoters of many PS cell-specific genes (e.g., POU5F1, NANOG, SOX2, FOXD3). siRNA analyses identified two retinoblastoma binding proteins (RBBP4, RBBP9) as required for maintenance of multiple human PS cell types. Both RBBPs were bound to RB in human PS cells, and E2F motifs were present in the promoters of genes whose expression was altered by decreasing RBBP4 and RBBP9 expression. Affymetrix and real-time PCR studies of siRNA-treated human PS cells showed that reduced RBBP4 or RBBP9 expression concomitantly decreased expression of POU5F1, NANOG, SOX2, and/or FOXD3 plus certain cell cycle genes (e.g., CCNA2, CCNB1), while increasing expression of genes involved in organogenesis (particularly neurogenesis). CONCLUSIONS: These results reveal new candidate positive regulators of human PS cells, providing evidence of their ability to regulate expression of pluripotency, cell cycle, and differentiation genes in human PS cells. These data provide valuable new leads for further elucidating mechanisms of human pluripotency. Title: The genome sequence of taurine cattle: a window to ruminant biology and evolution Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L and Zhao FQ <297 more author(s)> Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Camara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Jr., Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, More DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, Jr., White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ (- 297) Ref: Science, 324:522, 2009 : PubMed ESTHER: Elsik_2009_Science_324_522 PubMedSearch: Elsik 2009 Science 324 522 PubMedID: 19390049 Gene_locus related to this paper: bovin-2neur, bovin-a0jnh8, bovin-a5d7b7, bovin-ACHE, bovin-balip, bovin-dpp4, bovin-dpp6, bovin-e1bi31, bovin-e1bn79, bovin-est8, bovin-f1mbd6, bovin-f1mi11, bovin-f1mr65, bovin-f1n1l4, bovin-g3mxp5, bovin-q0vcc8, bovin-q2kj30, bovin-q3t0r6, bovin-thyro Abstract To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production. Title: A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis) Ralph SG, Chun HJ, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S and Bohlmann J <5 more author(s)> Ralph SG, Chun HJ, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJ, Marra MA, Douglas CJ, Ritland K, Bohlmann J (- 5) Ref: BMC Genomics, 9:484, 2008 : PubMed ESTHER: Ralph_2008_BMC.Genomics_9_484 PubMedSearch: Ralph 2008 BMC.Genomics 9 484 PubMedID: 18854048 Gene_locus related to this paper: picgl-emb8, picsi-a9nkq4, picsi-a9nkw1, picsi-a9nln3, picsi-a9nlt8, picsi-a9nng6, picsi-a9np75, picsi-a9np95, picsi-a9nqw9, picsi-a9nsc2, picsi-a9nsf2, picsi-a9nux2, picsi-a9nvj5, picsi-a9nvl0, picsi-a9nwa5, picsi-a9nws5, picsi-a9nwz2, picsi-a9nyx6, picsi-a9nzz3, picsi-a9p0a1, picsi-a9p0c3, picsi-a9p1m0, picsi-a9p066, picsi-a9p157, picsi-a9nu19 Abstract BACKGROUND: Members of the pine family (Pinaceae), especially species of spruce (Picea spp.) and pine (Pinus spp.), dominate many of the world's temperate and boreal forests. These conifer forests are of critical importance for global ecosystem stability and biodiversity. They also provide the majority of the world's wood and fiber supply and serve as a renewable resource for other industrial biomaterials. In contrast to angiosperms, functional and comparative genomics research on conifers, or other gymnosperms, is limited by the lack of a relevant reference genome sequence. Sequence-finished full-length (FL)cDNAs and large collections of expressed sequence tags (ESTs) are essential for gene discovery, functional genomics, and for future efforts of conifer genome annotation. RESULTS: As part of a conifer genomics program to characterize defense against insects and adaptation to local environments, and to discover genes for the production of biomaterials, we developed 20 standard, normalized or full-length enriched cDNA libraries from Sitka spruce (P. sitchensis), white spruce (P. glauca), and interior spruce (P. glauca-engelmannii complex). We sequenced and analyzed 206,875 3'- or 5'-end ESTs from these libraries, and developed a resource of 6,464 high-quality sequence-finished FLcDNAs from Sitka spruce. Clustering and assembly of 147,146 3'-end ESTs resulted in 19,941 contigs and 26,804 singletons, representing 46,745 putative unique transcripts (PUTs). The 6,464 FLcDNAs were all obtained from a single Sitka spruce genotype and represent 5,718 PUTs. CONCLUSION: This paper provides detailed annotation and quality assessment of a large EST and FLcDNA resource for spruce. The 6,464 Sitka spruce FLcDNAs represent the third largest sequence-verified FLcDNA resource for any plant species, behind only rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), and the only substantial FLcDNA resource for a gymnosperm. Our emphasis on capturing FLcDNAs and ESTs from cDNA libraries representing herbivore-, wound- or elicitor-treated induced spruce tissues, along with incorporating normalization to capture rare transcripts, resulted in a rich resource for functional genomics and proteomics studies. Sequence comparisons against five plant genomes and the non-redundant GenBank protein database revealed that a substantial number of spruce transcripts have no obvious similarity to known angiosperm gene sequences. Opportunities for future applications of the sequence and clone resources for comparative and functional genomics are discussed. Title: Analysis of 4,664 high-quality sequence-finished poplar full-length cDNA clones and their utility for the discovery of genes responding to insect feeding Ralph SG, Chun HJ, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA and Bohlmann J <2 more author(s)> Ralph SG, Chun HJ, Cooper D, Kirkpatrick R, Kolosova N, Gunter L, Tuskan GA, Douglas CJ, Holt RA, Jones SJ, Marra MA, Bohlmann J (- 2) Ref: BMC Genomics, 9:57, 2008 : PubMed ESTHER: Ralph_2008_BMC.Genomics_9_57 PubMedSearch: Ralph 2008 BMC.Genomics 9 57 PubMedID: 18230180 Gene_locus related to this paper: poptr-a9pbm5, poptr-a9pfp5, poptr-a9pgl0, poptr-a9ph43, poptr-a9ph71, poptr-a9pha7, poptr-b9gnp9, poptr-b9gyq1, poptr-b9hxr7, poptr-b9i9p8, poptr-a9pfa7, poptr-a9pch4, poptr-a9pfg4 Abstract BACKGROUND: The genus Populus includes poplars, aspens and cottonwoods, which will be collectively referred to as poplars hereafter unless otherwise specified. Poplars are the dominant tree species in many forest ecosystems in the Northern Hemisphere and are of substantial economic value in plantation forestry. Poplar has been established as a model system for genomics studies of growth, development, and adaptation of woody perennial plants including secondary xylem formation, dormancy, adaptation to local environments, and biotic interactions. RESULTS: As part of the poplar genome sequencing project and the development of genomic resources for poplar, we have generated a full-length (FL)-cDNA collection using the biotinylated CAP trapper method. We constructed four FLcDNA libraries using RNA from xylem, phloem and cambium, and green shoot tips and leaves from the P. trichocarpa Nisqually-1 genotype, as well as insect-attacked leaves of the P. trichocarpa x P. deltoides hybrid. Following careful selection of candidate cDNA clones, we used a combined strategy of paired end reads and primer walking to generate a set of 4,664 high-accuracy, sequence-verified FLcDNAs, which clustered into 3,990 putative unique genes. Mapping FLcDNAs to the poplar genome sequence combined with BLAST comparisons to previously predicted protein coding sequences in the poplar genome identified 39 FLcDNAs that likely localize to gaps in the current genome sequence assembly. Another 173 FLcDNAs mapped to the genome sequence but were not included among the previously predicted genes in the poplar genome. Comparative sequence analysis against Arabidopsis thaliana and other species in the non-redundant database of GenBank revealed that 11.5% of the poplar FLcDNAs display no significant sequence similarity to other plant proteins. By mapping the poplar FLcDNAs against transcriptome data previously obtained with a 15.5 K cDNA microarray, we identified 153 FLcDNA clones for genes that were differentially expressed in poplar leaves attacked by forest tent caterpillars. CONCLUSION: This study has generated a high-quality FLcDNA resource for poplar and the third largest FLcDNA collection published to date for any plant species. We successfully used the FLcDNA sequences to reassess gene prediction in the poplar genome sequence, perform comparative sequence annotation, and identify differentially expressed transcripts associated with defense against insects. The FLcDNA sequences will be essential to the ongoing curation and annotation of the poplar genome, in particular for targeting gaps in the current genome assembly and further improvement of gene predictions. The physical FLcDNA clones will serve as useful reagents for functional genomics research in areas such as analysis of gene functions in defense against insects and perennial growth. Sequences from this study have been deposited in NCBI GenBank under the accession numbers EF144175 to EF148838. Title: Evolutionary and biomedical insights from the rhesus macaque genome Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC and Zwieg AS <166 more author(s)> Gibbs RA, Rogers J, Katze MG, Bumgarner R, Weinstock GM, Mardis ER, Remington KA, Strausberg RL, Venter JC, Wilson RK, Batzer MA, Bustamante CD, Eichler EE, Hahn MW, Hardison RC, Makova KD, Miller W, Milosavljevic A, Palermo RE, Siepel A, Sikela JM, Attaway T, Bell S, Bernard KE, Buhay CJ, Chandrabose MN, Dao M, Davis C, Delehaunty KD, Ding Y, Dinh HH, Dugan-Rocha S, Fulton LA, Gabisi RA, Garner TT, Godfrey J, Hawes AC, Hernandez J, Hines S, Holder M, Hume J, Jhangiani SN, Joshi V, Khan ZM, Kirkness EF, Cree A, Fowler RG, Lee S, Lewis LR, Li Z, Liu YS, Moore SM, Muzny D, Nazareth LV, Ngo DN, Okwuonu GO, Pai G, Parker D, Paul HA, Pfannkoch C, Pohl CS, Rogers YH, Ruiz SJ, Sabo A, Santibanez J, Schneider BW, Smith SM, Sodergren E, Svatek AF, Utterback TR, Vattathil S, Warren W, White CS, Chinwalla AT, Feng Y, Halpern AL, Hillier LW, Huang X, Minx P, Nelson JO, Pepin KH, Qin X, Sutton GG, Venter E, Walenz BP, Wallis JW, Worley KC, Yang SP, Jones SM, Marra MA, Rocchi M, Schein JE, Baertsch R, Clarke L, Csuros M, Glasscock J, Harris RA, Havlak P, Jackson AR, Jiang H, Liu Y, Messina DN, Shen Y, Song HX, Wylie T, Zhang L, Birney E, Han K, Konkel MK, Lee J, Smit AF, Ullmer B, Wang H, Xing J, Burhans R, Cheng Z, Karro JE, Ma J, Raney B, She X, Cox MJ, Demuth JP, Dumas LJ, Han SG, Hopkins J, Karimpour-Fard A, Kim YH, Pollack JR, Vinar T, Addo-Quaye C, Degenhardt J, Denby A, Hubisz MJ, Indap A, Kosiol C, Lahn BT, Lawson HA, Marklein A, Nielsen R, Vallender EJ, Clark AG, Ferguson B, Hernandez RD, Hirani K, Kehrer-Sawatzki H, Kolb J, Patil S, Pu LL, Ren Y, Smith DG, Wheeler DA, Schenck I, Ball EV, Chen R, Cooper DN, Giardine B, Hsu F, Kent WJ, Lesk A, Nelson DL, O'Brien W E, Prufer K, Stenson PD, Wallace JC, Ke H, Liu XM, Wang P, Xiang AP, Yang F, Barber GP, Haussler D, Karolchik D, Kern AD, Kuhn RM, Smith KE, Zwieg AS (- 166) Ref: Science, 316:222, 2007 : PubMed ESTHER: Gibbs_2007_Science_316_222 PubMedSearch: Gibbs 2007 Science 316 222 PubMedID: 17431167 Gene_locus related to this paper: macmu-3neur, macmu-ACHE, macmu-BCHE, macmu-f6rul6, macmu-f6sz31, macmu-f6the6, macmu-f6unj2, macmu-f6wtx1, macmu-f6zkq5, macmu-f7aa58, macmu-f7ai42, macmu-f7aim4, macmu-f7buk8, macmu-f7cfi8, macmu-f7cnr2, macmu-f7cu68, macmu-f7flv1, macmu-f7ggk1, macmu-f7hir7, macmu-g7n054, macmu-KANSL3, macmu-TEX30, macmu-Y4neur, macmu-g7n4x3, macmu-i2cy02, macmu-f7ba84, macmu-CES2, macmu-h9er02, macmu-a0a1d5rbr3, macmu-a0a1d5q4k5, macmu-g7mxj6, macmu-f7dn71, macmu-f7hkw9, macmu-f7hm08, macmu-g7mke4, macmu-a0a1d5rh04, macmu-h9fud6, macmu-f6qwx1, macmu-f7h4t2, macmu-h9zaw9, macmu-f7h550, macmu-a0a1d5q9w1, macmu-f7gkb9, macmu-f7hp78, macmu-a0a1d5qvu5 Abstract The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species. Title: Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L and Lindblad-Toh K <52 more author(s)> Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, Vandeberg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K (- 52) Ref: Nature, 447:167, 2007 : PubMed ESTHER: Mikkelsen_2007_Nature_447_167 PubMedSearch: Mikkelsen 2007 Nature 447 167 PubMedID: 17495919 Gene_locus related to this paper: mondo-ACHE, mondo-b2bsf5, mondo-b2bsz5, mondo-BCHE, mondo-d2x2i6, mondo-d2x2i8, mondo-f6slk2, mondo-f6wu00, mondo-f6wuf2, mondo-f6xfj4, mondo-f6yt13, mondo-f7c7p0, mondo-f7ckd0, mondo-f7cvq8, mondo-f7cvr5, mondo-f7eil6, mondo-f7ez13, mondo-f7f0i7, mondo-f7fg16, mondo-f7gcv7, mondo-f7gep4, mondo-f7gly2, mondo-f6u7q2, mondo-f7fw54, mondo-f7dpf6, mondo-f6pgj5, mondo-f6yg68, mondo-f7g8u4, mondo-f7eyv1, mondo-f6pq73, mondo-f7cre0, mondo-f7fdj0, mondo-f7fdj5, mondo-f7ft63, mondo-f7ge99, mondo-f7gea2, mondo-f6pxq2, mondo-f7awc1, mondo-f7c412, mondo-f7ev24, mondo-f7b6s6, mondo-f6vcx0, mondo-f7g148, mondo-f6tlv9, mondo-f6tdm5, mondo-f7f3w0, mondo-f7fg39, mondo-f7d6c2, mondo-f6sdn0, mondo-f7gi08, mondo-f6xss6, mondo-f6sa37, mondo-f7gd97, mondo-f6z6x9 Abstract We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation. Title: The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL and Eltis LD <19 more author(s)> McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD (- 19) Ref: Proc Natl Acad Sci U S A, 103:15582, 2006 : PubMed ESTHER: McLeod_2006_Proc.Natl.Acad.Sci.U.S.A_103_15582 PubMedSearch: McLeod 2006 Proc.Natl.Acad.Sci.U.S.A 103 15582 PubMedID: 17030794 Gene_locus related to this paper: rhoob-c1ar27, rhoob-c1arb5, rhoob-c1asz4, rhoob-c1at13, rhoob-c1ata3, rhoob-c1atk8, rhoob-c1atq0, rhoob-c1ats8, rhoob-c1att5, rhoob-c1au11, rhoob-c1auh5, rhoob-c1aux1, rhoob-c1av24, rhoob-c1awr1, rhoob-c1axf2, rhoob-c1ayb0, rhoob-c1b0a8, rhoob-c1b0g7, rhoob-c1b0w8, rhoob-c1b1i6, rhoob-c1b7t4, rhoob-c1b8z9, rhoob-c1b9l2, rhoob-c1b9v1, rhoob-c1b9y1, rhoob-c1b930, rhoob-c1b931, rhoob-c1b932, rhoob-c1b996, rhoob-c1bbl3, rhoob-c1bbq4, rhoop-pcaL, rhosp-bphD2, rhosp-EtbD1, rhosr-q0rwt2, rhosr-q0rwv3, rhosr-q0rxc8, rhosr-q0ryc0, rhosr-q0ryn3, rhosr-q0rz46, rhosr-q0rz78, rhosr-q0s0s0, rhosr-q0s1l0, rhosr-q0s1m1, rhosr-q0s1n4, rhosr-q0s1x5, rhosr-q0s1x6, rhosr-q0s2i6, rhosr-q0s2n9, rhosr-q0s2t5, rhosr-q0s3c8, rhosr-q0s3s6, rhosr-q0s4f1, rhosr-q0s5h5, rhosr-q0s5m7, rhosr-q0s6a9, rhosr-q0s6b3, rhosr-q0s6b5, rhosr-q0s7i7, rhosr-q0s7r1, rhosr-q0s008, rhosr-q0s8b3, rhosr-q0s8f4, rhosr-q0s8p7, rhosr-q0s8z9, rhosr-q0s9l3, rhosr-q0s9m1, rhosr-q0s101, rhosr-q0s125, rhosr-q0s230, rhosr-q0s252, rhosr-q0s393, rhosr-q0s477, rhosr-q0s545, rhojr-q0s546, rhosr-q0s837, rhosr-q0s849, rhosr-q0sa25, rhosr-q0sa26, rhosr-q0sa61, rhosr-q0saa5, rhosr-q0san0, rhosr-q0saw3, rhosr-q0sbd3, rhosr-q0sc04, rhosr-q0scq2, rhosr-q0sd10, rhosr-q0sdb8, rhosr-q0sdh6, rhosr-q0sdr2, rhosr-q0sdr5, rhosr-q0sdt1, rhosr-q0sdu5, rhosr-q0sej4, rhosr-q0ses6, rhosr-q0set7, rhosr-q0sex8, rhosr-q0sf05, rhosr-q0sfh8, rhosr-q0sfl2, rhosr-q0sfz6, rhosr-q0sgc8, rhosr-q0sgj4, rhosr-q0sgv4, rhosr-q0sgw4, rhosr-q0sh74, rhosr-q0shd6, rhosr-q0shi2, rhosr-q0sjy0, rhosr-q0skn1, rhoob-c1b934, rhosr-q0sab7, rhosr-q0rwx4, rhoob-c1asm3, rhosr-q0ruu2, rhosr-q0s747, rhosr-q0ry47, rhosr-q0rwa1, rhosr-q0sj22, 9noca-j2j8s8, rhojr-q0sd80, rhojr-q0sf05 Abstract Rhodococcus sp. RHA1 (RHA1) is a potent polychlorinated biphenyl-degrading soil actinomycete that catabolizes a wide range of compounds and represents a genus of considerable industrial interest. RHA1 has one of the largest bacterial genomes sequenced to date, comprising 9,702,737 bp (67% G+C) arranged in a linear chromosome and three linear plasmids. A targeted insertion methodology was developed to determine the telomeric sequences. RHA1's 9,145 predicted protein-encoding genes are exceptionally rich in oxygenases (203) and ligases (192). Many of the oxygenases occur in the numerous pathways predicted to degrade aromatic compounds (30) or steroids (4). RHA1 also contains 24 nonribosomal peptide synthase genes, six of which exceed 25 kbp, and seven polyketide synthase genes, providing evidence that rhodococci harbor an extensive secondary metabolism. Among sequenced genomes, RHA1 is most similar to those of nocardial and mycobacterial strains. The genome contains few recent gene duplications. Moreover, three different analyses indicate that RHA1 has acquired fewer genes by recent horizontal transfer than most bacteria characterized to date and far fewer than Burkholderia xenovorans LB400, whose genome size and catabolic versatility rival those of RHA1. RHA1 and LB400 thus appear to demonstrate that ecologically similar bacteria can evolve large genomes by different means. Overall, RHA1 appears to have evolved to simultaneously catabolize a diverse range of plant-derived compounds in an O(2)-rich environment. In addition to establishing RHA1 as an important model for studying actinomycete physiology, this study provides critical insights that facilitate the exploitation of these industrially important microorganisms. Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K and Wilson RK <111 more author(s)> Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, Van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK (- 111) Ref: Nature, 434:724, 2005 : PubMed ESTHER: Hillier_2005_Nature_434_724 PubMedSearch: Hillier 2005 Nature 434 724 PubMedID: 15815621 Gene_locus related to this paper: human-ABHD1, human-LDAH, human-ABHD18, human-KANSL3, human-PGAP1, human-PREPL Abstract Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions. Title: The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ and Hyman RW <44 more author(s)> Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW (- 44) Ref: Science, 307:1321, 2005 : PubMed ESTHER: Loftus_2005_Science_307_1321 PubMedSearch: Loftus 2005 Science 307 1321 PubMedID: 15653466 Gene_locus related to this paper: cryne-apth1, cryne-ppme1, cryne-q5k7g1, cryne-q5k7h2, cryne-q5k7p6, cryne-q5k8p2, cryne-q5k8s0, cryne-q5k9e7, cryne-q5k9p3, cryne-q5k9y9, cryne-q5k721, cryne-q5k987, cryne-q5ka03, cryne-q5ka24, cryne-q5ka58, cryne-q5kat4, cryne-q5kav3, cryne-q5kbu4, cryne-q5kbw4, cryne-q5kc00, cryne-q5kec5, cryne-q5kei3, cryne-q5kei7, cryne-q5ker2, cryne-q5key5, cryne-q5kf48, cryne-q5kfk6, cryne-q5kfz0, cryne-q5kgq3, cryne-q5kh37, cryne-q5khb0, cryne-q5khb9, cryne-q5kip7, cryne-q5kiu5, cryne-q5kj56, cryne-q5kjf8, cryne-q5kjh3, cryne-q5kjp9, cryne-q5kjw7, cryne-q5kky1, cryne-q5kkz7, cryne-q5kl13, cryne-q5klu9, cryne-q5km63, cryne-q5kme9, cryne-q5kni1, cryne-q5knq0, cryne-q5knr2, cryne-q5knw0, cryne-q5kq08, cryne-Q5KCH9, cryne-q55ta1, cryne-q5kjh4, crynj-q5knp8, crynj-q5kpe0 Abstract Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes. Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC) Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R and Malek J <104 more author(s)> Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J (- 104) Ref: Genome Res, 14:2121, 2004 : PubMed ESTHER: Gerhard_2004_Genome.Res_14_2121 PubMedSearch: Gerhard 2004 Genome.Res 14 2121 PubMedID: 15489334 Gene_locus related to this paper: human-AFMID, human-CES4A, human-CES5A, human-NOTUM, human-SERAC1, human-SERHL2, human-TMEM53, mouse-acot1, mouse-adcl4, mouse-Ces2f, mouse-Ces4a, mouse-notum, mouse-q6wqj1, mouse-Q9DAI6, mouse-rbbp9, mouse-SERHL, mouse-srac1, mouse-tmm53, rat-abhd6, rat-abhda, rat-abhea, rat-abheb, rat-Ldah, rat-cd029, rat-estd, rat-Kansl3, rat-nceh1, ratno-acph, ratno-CMBL, mouse-b2rwd2, rat-b5den3, rat-ab17c Abstract The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline. Title: The DNA sequence of human chromosome 7 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S and Wilson RK <97 more author(s)> Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK (- 97) Ref: Nature, 424:157, 2003 : PubMed ESTHER: Hillier_2003_Nature_424_157 PubMedSearch: Hillier 2003 Nature 424 157 PubMedID: 12853948 Gene_locus related to this paper: human-ABHD11, human-ACHE, human-CPVL, human-DPP6, human-MEST Abstract Human chromosome 7 has historically received prominent attention in the human genetics community, primarily related to the search for the cystic fibrosis gene and the frequent cytogenetic changes associated with various forms of cancer. Here we present more than 153 million base pairs representing 99.4% of the euchromatic sequence of chromosome 7, the first metacentric chromosome completed so far. The sequence has excellent concordance with previously established physical and genetic maps, and it exhibits an unusual amount of segmentally duplicated sequence (8.2%), with marked differences between the two arms. Our initial analyses have identified 1,150 protein-coding genes, 605 of which have been confirmed by complementary DNA sequences, and an additional 941 pseudogenes. Of genes confirmed by transcript sequences, some are polymorphic for mutations that disrupt the reading frame. Title: The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C and Waterston RH <26 more author(s)> Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH (- 26) Ref: PLoS Biol, 1:E45, 2003 : PubMed ESTHER: Stein_2003_PLoS.Biol_1_E45 PubMedSearch: Stein 2003 PLoS.Biol 1 E45 PubMedID: 14624247 Gene_locus related to this paper: caebr-a8wl70, caebr-a8wm66, caebr-a8wny7, caebr-a8wpj6, caebr-a8wpy7.1, caebr-a8wq91, caebr-a8wr10, caebr-A8WSQ5, caebr-a8wta1, caebr-A8WTU9, caebr-a8wux6, caebr-A8WX49, caebr-a8wxx0, caebr-a8wyd4, caebr-a8wye8, caebr-a8wz10, caebr-a8wz31.1, caebr-a8wz31.2, caebr-a8wz31.4, caebr-a8wzp9, caebr-a8wzr9.1, caebr-a8wzr9.2, caebr-a8wzs0, caebr-a8wzs1, caebr-a8x0r9, caebr-a8x0z5, caebr-a8x1l6, caebr-a8x1r6, caebr-a8x3t6, caebr-a8x4h0, caebr-a8x4u8, caebr-a8x4w8, caebr-a8x5l4, caebr-a8x5l5, caebr-a8x5r5, caebr-a8x5s6, caebr-a8x5t4, caebr-a8x6s0, caebr-a8x6s1, caebr-a8x7d1, caebr-a8x7h0, caebr-a8x7v6, caebr-A8X8P2, caebr-a8x8q5, caebr-a8x8y6, caebr-a8x9s4, caebr-a8x324.1, caebr-a8x324.2, caebr-a8x622, caebr-a8xac7, caebr-a8xag5, caebr-a8xb07, caebr-a8xb88, caebr-a8xby0, caebr-a8xdz0, caebr-a8xf42, caebr-a8xfd1, caebr-a8xfe6, caebr-a8xgi0, caebr-a8xgz4, caebr-a8xgz5, caebr-a8xh38, caebr-a8xhp8, caebr-a8xhx9, caebr-a8xjw4, caebr-a8xk02, caebr-a8xk46, caebr-a8xk76, caebr-a8xke1, caebr-A8XLQ2, caebr-a8xns2.1, caebr-a8xns2.2, caebr-a8xq21, caebr-a8xub3, caebr-a8xuc2, caebr-a8xuc8, caebr-a8xug3, caebr-a8xuh6, caebr-a8xui4, caebr-a8xui5, caebr-a8xui6, caebr-a8xui7, caebr-a8xum8, caebr-a8y0h0.1, caebr-a8y0h0.2, caebr-a8y0h1.1, caebr-a8y0h1.2, caebr-a8y1b5, caebr-a8y1r7, caebr-a8y2v4, caebr-a8y3e3, caebr-a8y3i5, caebr-a8y3j9, caebr-a8y4p9, caebr-a8y100, caebr-a8y101, caebr-ACHE1, caebr-ACHE2, caebr-ACHE3, caebr-ACHE4, caebr-b6ii84, caebr-G01D9.5, caebr-ges1e, caebr-a8y4l4, caebr-A8Y1T9, caebr-A8Y168, caebr-A8Y0Z5, caebr-A8XYQ5, caebr-A8XXK4, caebr-A8XWZ8, caebr-A8XUF0, caebr-A8XUB6, caebr-A8XSV2, caebr-A8XJ37, caebr-A8XG15, caebr-A8XFE8, caebr-A8XEY7, caebr-A8XEU8, caebr-A8XDT6, caebr-A8XDV3, caebr-A8XDQ3, caebr-A8XDK8, caebr-A8XBW4, caebr-A8XAG3, caebr-A8X8H5, caebr-A8X6Z9, caebr-A8X6H9, caebr-A8X629, caebr-A8X438, caebr-A8X4G2, caebr-A8X4H8, caebr-A8X4W2, caebr-A8X3P4, caebr-A8X3R1, caebr-A8X2Z4, caebr-A8X0N2, caebr-A8X0B3, caebr-A8WW80, caebr-U483, caebr-A8XPH6, caebr-A8XNJ0, caebr-A8XNA2, caebr-A8XLP0, caebr-A8XK33, caebr-A8WTK6, caebr-A8WU44, caebr-A8WPJ2, caebr-A8WNE5, caebr-A8WMB3, caebr-a8x1r2 Abstract The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes. Title: Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD and Marra MA <72 more author(s)> Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF, Zeeberg B, Buetow KH, Schaefer CF, Bhat NK, Hopkins RF, Jordan H, Moore T, Max SI, Wang J, Hsieh F, Diatchenko L, Marusina K, Farmer AA, Rubin GM, Hong L, Stapleton M, Soares MB, Bonaldo MF, Casavant TL, Scheetz TE, Brownstein MJ, Usdin TB, Toshiyuki S, Carninci P, Prange C, Raha SS, Loquellano NA, Peters GJ, Abramson RD, Mullahy SJ, Bosak SA, McEwan PJ, McKernan KJ, Malek JA, Gunaratne PH, Richards S, Worley KC, Hale S, Garcia AM, Gay LJ, Hulyk SW, Villalon DK, Muzny DM, Sodergren EJ, Lu X, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Young AC, Shevchenko Y, Bouffard GG, Blakesley RW, Touchman JW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Krzywinski MI, Skalska U, Smailus DE, Schnerch A, Schein JE, Jones SJ, Marra MA (- 72) Ref: Proc Natl Acad Sci U S A, 99:16899, 2002 : PubMed ESTHER: Strausberg_2002_Proc.Natl.Acad.Sci.U.S.A_99_16899 PubMedSearch: Strausberg 2002 Proc.Natl.Acad.Sci.U.S.A 99 16899 PubMedID: 12477932 Gene_locus related to this paper: bovin-q3zcj6, danre-OVCA2, danre-q4qrh4, danre-q4v960, danre-q32ls6, danre-q503e2, ratno-CPVL, ratno-q3mhs0, ratno-q4qr68, ratno-q5fvr5, ratno-q32q55, xenla-a2bd54, xenla-q2tap9, xenla-q3kq37, xenla-q3kq76, xenla-q4klb6, xenla-q32n48, xenla-q32ns5, xenla-q52l41, xentr-q4va73, danre-a7mbu9 Abstract The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov). | |||||||
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