Author Report for: Paterson AHNo contact information in database for Paterson AH
Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C and Wincker P <70 more author(s)> Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Correa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Canaguier A, Chauveau A, Berard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P (- 70) Ref: Science, 345:950, 2014 : PubMed ESTHER: Chalhoub_2014_Science_345_950 PubMedSearch: Chalhoub 2014 Science 345 950 PubMedID: 25146293 Gene_locus related to this paper: braol-Q8GTM3, braol-Q8GTM4, brana-a0a078j4a9, brana-a0a078e1m0, brana-a0a078cd75, brana-a0a078evd3, brana-a0a078j4f0, brana-a0a078cta5, brana-a0a078cus4, brana-a0a078f8c2, brana-a0a078jql1, brana-a0a078dgj3, brana-a0a078hw50, brana-a0a078cuu0, brana-a0a078iyl8, brana-a0a078dfa9, brana-a0a078ic91, brana-a0a078cnf7, brana-a0a078fh41, brana-a0a078ca65, brana-a0a078ctc8, brana-a0a078h021, brana-a0a078h0h8, brana-a0a078jx23, brana-a0a078ci96, brana-a0a078cqd7, brana-a0a078dh94, brana-a0a078h612, brana-a0a078ild2, brana-a0a078j2t3, braol-a0a0d3dpb2, braol-a0a0d3dx76, brana-a0a078jxa8, brana-a0a078i2k3, braol-a0a0d3ef55, brarp-m4dcj8, brana-a0a078fw53, brana-a0a078itf3, brana-a0a078jsn1, brana-a0a078jrt9, brana-a0a078i6d2, brana-a0a078jku0 Abstract Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72x genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement. Title: Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V and Sharpe AG <22 more author(s)> Parkin IA, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Pires JC, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chalhoub B, Sharpe AG (- 22) Ref: Genome Biol, 15:R77, 2014 : PubMed ESTHER: Parkin_2014_Genome.Biol_15_R77 PubMedSearch: Parkin 2014 Genome.Biol 15 R77 PubMedID: 24916971 Gene_locus related to this paper: braol-a0a0d3dpb2, braol-a0a0d3dx76, brana-a0a078jxa8, brana-a0a078i2k3, braol-a0a0d3ef55, braol-a0a0d3bur9, braol-a0a0d3ck99, braol-a0a0d3cns1, braol-a0a0d3e654, brana-a0a078i6d2, braol-a0a0d3a922 Abstract BACKGROUND: Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus. Title: Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.) Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC and Shen-Miller J <60 more author(s)> Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J (- 60) Ref: Genome Biol, 14:R41, 2013 : PubMed ESTHER: Ming_2013_Genome.Biol_14_R41 PubMedSearch: Ming 2013 Genome.Biol 14 R41 PubMedID: 23663246 Gene_locus related to this paper: nelnu-a0a1u8aj84, nelnu-a0a1u8bpe4, nelnu-a0a1u7z9m9, nelnu-a0a1u7ywy5, nelnu-a0a1u8aik2, nelnu-a0a1u7zmb5, nelnu-a0a1u8a7m7, nelnu-a0a1u8b0n9, nelnu-a0a1u8b461, nelnu-a0a1u7zzj3, nelnu-a0a1u8ave7, nelnu-a0a1u7yn26 Abstract BACKGROUND: Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan. RESULTS: The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101x and 5.2x. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. CONCLUSIONS: The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots. Title: Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S and Schmutz J <64 more 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 (- 64) Ref: Nature, 492:423, 2012 : PubMed 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 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. Title: The genome of the mesopolyploid crop species Brassica rapa Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I and Zhang Z <88 more author(s)> Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Jin H, Parkin IA, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Yu J, Meng J, Min J, Poulain J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Z, Li Z, Xiong Z, Zhang Z (- 88) Ref: Nat Genet, 43:1035, 2011 : PubMed ESTHER: Wang_2011_Nat.Genet_43_1035 PubMedSearch: Wang 2011 Nat.Genet 43 1035 PubMedID: 21873998 Gene_locus related to this paper: braol-Q8GTM3, braol-Q8GTM4, brarp-m4ei94, brarp-m4c988, brana-a0a078j4a9, brana-a0a078e1m0, brana-a0a078cd75, brarp-m4dwa6, brana-a0a078j4f0, brana-a0a078cus4, brana-a0a078f8c2, brana-a0a078jql1, brana-a0a078dgj3, brana-a0a078hw50, brana-a0a078cuu0, brana-a0a078dfa9, brana-a0a078ic91, brarp-m4ctw3, brana-a0a078ca65, brana-a0a078ctc8, brana-a0a078h021, brana-a0a078jx23, brarp-m4da84, brarp-m4dwr7, brana-a0a078dh94, brana-a0a078h612, brana-a0a078j2t3, braol-a0a0d3dpb2, braol-a0a0d3dx76, brana-a0a078jxa8, brana-a0a078i2k3, brarp-m4cwq4, brarp-m4dcj8, brarp-m4eh17, brarp-m4eey4, brarp-m4dnj8, brarp-m4ey83, brarp-m4ey84 Abstract We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops. Title: Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments Wisniewski-Dye F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS and Zhulin IB <16 more author(s)> Wisniewski-Dye F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, McDonald WH, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, Gonzalez V, Mavingui P, Zhulin IB (- 16) Ref: PLoS Genet, 7:e1002430, 2011 : PubMed ESTHER: Wisniewski-Dye_2011_PLoS.Genet_7_E1002430 PubMedSearch: Wisniewski-Dye 2011 PLoS.Genet 7 E1002430 PubMedID: 22216014 Gene_locus related to this paper: azobr-g8al65, azol4-g7zc95, azol4-g7zc98, azol4-g7zfp9, azol4-g7zcr5, azobr-g8b0i6 Abstract Fossil records indicate that life appeared in marine environments approximately 3.5 billion years ago (Gyr) and transitioned to terrestrial ecosystems nearly 2.5 Gyr. Sequence analysis suggests that "hydrobacteria" and "terrabacteria" might have diverged as early as 3 Gyr. Bacteria of the genus Azospirillum are associated with roots of terrestrial plants; however, virtually all their close relatives are aquatic. We obtained genome sequences of two Azospirillum species and analyzed their gene origins. While most Azospirillum house-keeping genes have orthologs in its close aquatic relatives, this lineage has obtained nearly half of its genome from terrestrial organisms. The majority of genes encoding functions critical for association with plants are among horizontally transferred genes. Our results show that transition of some aquatic bacteria to terrestrial habitats occurred much later than the suggested initial divergence of hydro- and terrabacterial clades. The birth of the genus Azospirillum approximately coincided with the emergence of vascular plants on land. Title: The Sorghum bicolor genome and the diversification of grasses Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T and Rokhsar DS <35 more author(s)> Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob ur R, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (- 35) Ref: Nature, 457:551, 2009 : PubMed ESTHER: Paterson_2009_Nature_457_551 PubMedSearch: Paterson 2009 Nature 457 551 PubMedID: 19189423 Gene_locus related to this paper: sorbi-b3vtb2, sorbi-c5wp75, sorbi-c5wts6, sorbi-c5wu07, sorbi-c5wvl7, sorbi-c5ww85, sorbi-c5ww86, sorbi-c5wxa4, sorbi-c5x1f6, sorbi-c5x2x9, sorbi-c5x5z9, sorbi-c5x6q0, sorbi-c5x230, sorbi-c5x290, sorbi-c5x345, sorbi-c5x399, sorbi-c5x610, sorbi-c5xbm4, sorbi-c5xct0, sorbi-c5xdv0, sorbi-c5xe87, sorbi-c5xf40, sorbi-c5xfu9, sorbi-c5xh40, sorbi-c5xh41, sorbi-c5xh42, sorbi-c5xh43, sorbi-c5xh44, sorbi-c5xh46, sorbi-c5xhr2, sorbi-c5xiw7, sorbi-c5xjf0, sorbi-c5xky2, sorbi-c5xm54, sorbi-c5xmb9, sorbi-c5xmz5, sorbi-c5xp10, sorbi-c5xpm6, sorbi-c5xr91, sorbi-c5xr92, sorbi-c5xs33, sorbi-c5xtz0, sorbi-c5xwd3, sorbi-c5y0d2, sorbi-c5y0h4, sorbi-c5y3i5, sorbi-c5y7x0, sorbi-c5y517, sorbi-c5y545, sorbi-c5ydr3, sorbi-c5yec0, sorbi-c5yf71, sorbi-c5yi32, sorbi-c5yih2, sorbi-c5ylw6, sorbi-c5yn66, sorbi-c5ynp8, sorbi-c5yt11, sorbi-c5yur5, sorbi-c5ywz3, sorbi-c5ywz4, sorbi-c5yx73, sorbi-c5yyn0, sorbi-c5z2m6, sorbi-c5z6a9, sorbi-c5z6j1, sorbi-c5z6s5, sorbi-c5z177, sorbi-Q9XE80, sorbi-c5xyg4, sorbi-c5z4q0, sorbi-c5xly4, sorbi-c5z4u8, sorbi-c5xxg5, sorbi-c5z9b9, sorbi-a0a1z5r970, sorbi-c5xhf9, sorbi-c5yxt7, sorbi-c5yxt6, sorbi-c5y1m2, sorbi-c5xdy6, sorbi-a0a194ysf6, sorbi-a0a1b6pnr2, sorbi-a0a1b6qcb9 Abstract Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance. Title: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA and Wilson RK <164 more author(s)> Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RP, Aerts J, van der Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MD, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WR, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Ka-Shu Wong G, Wang J, Liu B, Yu J, Yang H, Nefedov M, Koriabine M, deJong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SM, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betran E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK (- 164) Ref: Nature, 432:695, 2004 : PubMed ESTHER: Hillier_2004_Nature_432_695 PubMedSearch: Hillier 2004 Nature 432 695 PubMedID: 15592404 Gene_locus related to this paper: chick-a0a1d5pmd9, chick-b3tzb3, chick-BCHE, chick-cb043, chick-d3wgl5, chick-e1bsm0, chick-e1bvq6, chick-e1bwz0, chick-e1bwz1, chick-e1byn1, chick-e1bz81, chick-e1c0z8, chick-e1c7p7, chick-f1nby4, chick-f1ncz8, chick-f1ndp3, chick-f1nep4, chick-f1nj68, chick-f1njg6, chick-f1njk4, chick-f1njs4, chick-f1njs5, chick-f1nk87, chick-f1nmx9, chick-f1ntp8, chick-f1nvg7, chick-f1nwf2, chick-f1p1l1, chick-f1p3j5, chick-f1p4c6, chick-f1p508, chick-fas, chick-h9l0k6, chick-nlgn1, chick-NLGN3, chick-q5f3h8, chick-q5zhm0, chick-q5zi81, chick-q5zij5, chick-q5zin0, chick-thyro, chick-f1nrq2, chick-e1byd4, chick-e1c2h6, chick-a0a1d5pk92, chick-a0a1d5pzg7, chick-f1nbc2, chick-f1nf25, chick-f1nly5, chick-f1p4h5, chick-f1nzi7, chick-f1p5k3, chick-f1nm35, chick-a0a1d5pl11, chick-a0a1d5pj73, chick-f1nxu6, chick-a0a1d5nwc0, chick-e1bxs8, chick-f1p2g7, chick-f1nd96 Abstract We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture. | |||||||
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