Searle SM

References (11)

Title : The cavefish genome reveals candidate genes for eye loss - McGaugh_2014_Nat.Commun_5_5307
Author(s) : McGaugh SE , Gross JB , Aken B , Blin M , Borowsky R , Chalopin D , Hinaux H , Jeffery WR , Keene A , Ma L , Minx P , Murphy D , O'Quin KE , Retaux S , Rohner N , Searle SM , Stahl BA , Tabin C , Volff JN , Yoshizawa M , Warren WC
Ref : Nat Commun , 5 :5307 , 2014
Abstract : Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.
ESTHER : McGaugh_2014_Nat.Commun_5_5307
PubMedSearch : McGaugh_2014_Nat.Commun_5_5307
PubMedID: 25329095
Gene_locus related to this paper: astmx-w5kyj0 , astmx-w5l5v5 , astmx-w5k377 , astmx-w5kdz8 , astmx-w5k5k8 , astmx-w5kf08 , astmx-w5lfx9 , astmx-a0a3b1il55 , astmx-w5k188 , astmx-w5lig8 , astmx-a0a3b1it79 , astmx-a0a3b1kh87 , astmx-w5kk92 , astmx-w5kf44 , astmx-a0a3b1ihb9 , astmx-a0a3b1jet6 , astmx-w5lug4 , astmx-w5ln33 , astmx-a0a3b1k1i9 , astmx-w5l3f7

Title : The zebrafish reference genome sequence and its relationship to the human genome - Howe_2013_Nature_496_498
Author(s) : Howe K , Clark MD , Torroja CF , Torrance J , Berthelot C , Muffato M , Collins JE , Humphray S , McLaren K , Matthews L , Mclaren S , Sealy I , Caccamo M , Churcher C , Scott C , Barrett JC , Koch R , Rauch GJ , White S , Chow W , Kilian B , Quintais LT , Guerra-Assuncao JA , Zhou Y , Gu Y , Yen J , Vogel JH , Eyre T , Redmond S , Banerjee R , Chi J , Fu B , Langley E , Maguire SF , Laird GK , Lloyd D , Kenyon E , Donaldson S , Sehra H , Almeida-King J , Loveland J , Trevanion S , Jones M , Quail M , Willey D , Hunt A , Burton J , Sims S , McLay K , Plumb B , Davis J , Clee C , Oliver K , Clark R , Riddle C , Elliot D , Threadgold G , Harden G , Ware D , Begum S , Mortimore B , Kerry G , Heath P , Phillimore B , Tracey A , Corby N , Dunn M , Johnson C , Wood J , Clark S , Pelan S , Griffiths G , Smith M , Glithero R , Howden P , Barker N , Lloyd C , Stevens C , Harley J , Holt K , Panagiotidis G , Lovell J , Beasley H , Henderson C , Gordon D , Auger K , Wright D , Collins J , Raisen C , Dyer L , Leung K , Robertson L , Ambridge K , Leongamornlert D , McGuire S , Gilderthorp R , Griffiths C , Manthravadi D , Nichol S , Barker G , Whitehead S , Kay M , Brown J , Murnane C , Gray E , Humphries M , Sycamore N , Barker D , Saunders D , Wallis J , Babbage A , Hammond S , Mashreghi-Mohammadi M , Barr L , Martin S , Wray P , Ellington A , Matthews N , Ellwood M , Woodmansey R , Clark G , Cooper J , Tromans A , Grafham D , Skuce C , Pandian R , Andrews R , Harrison E , Kimberley A , Garnett J , Fosker N , Hall R , Garner P , Kelly D , Bird C , Palmer S , Gehring I , Berger A , Dooley CM , Ersan-Urun Z , Eser C , Geiger H , Geisler M , Karotki L , Kirn A , Konantz J , Konantz M , Oberlander M , Rudolph-Geiger S , Teucke M , Lanz C , Raddatz G , Osoegawa K , Zhu B , Rapp A , Widaa S , Langford C , Yang F , Schuster SC , Carter NP , Harrow J , Ning Z , Herrero J , Searle SM , Enright A , Geisler R , Plasterk RH , Lee C , Westerfield M , de Jong PJ , Zon LI , Postlethwait JH , Nusslein-Volhard C , Hubbard TJ , Roest Crollius H , Rogers J , Stemple DL
Ref : Nature , 496 :498 , 2013
Abstract : Zebrafish have become a popular organism for the study of vertebrate gene function. The virtually transparent embryos of this species, and the ability to accelerate genetic studies by gene knockdown or overexpression, have led to the widespread use of zebrafish in the detailed investigation of vertebrate gene function and increasingly, the study of human genetic disease. However, for effective modelling of human genetic disease it is important to understand the extent to which zebrafish genes and gene structures are related to orthologous human genes. To examine this, we generated a high-quality sequence assembly of the zebrafish genome, made up of an overlapping set of completely sequenced large-insert clones that were ordered and oriented using a high-resolution high-density meiotic map. Detailed automatic and manual annotation provides evidence of more than 26,000 protein-coding genes, the largest gene set of any vertebrate so far sequenced. Comparison to the human reference genome shows that approximately 70% of human genes have at least one obvious zebrafish orthologue. In addition, the high quality of this genome assembly provides a clearer understanding of key genomic features such as a unique repeat content, a scarcity of pseudogenes, an enrichment of zebrafish-specific genes on chromosome 4 and chromosomal regions that influence sex determination.
ESTHER : Howe_2013_Nature_496_498
PubMedSearch : Howe_2013_Nature_496_498
PubMedID: 23594743
Gene_locus related to this paper: danre-1neur , danre-ABHD10b , danre-a9jrf7 , danre-d2x2g3 , danre-e7ezq9 , danre-e7ff77 , danre-ndr3 , danre-nlgn4a , danre-q1mti5 , danre-q6nyz4 , danre-q6p2u2 , danre-q7t359 , danre-q08c93 , danre-A2BGU9 , danre-f1q676 , danre-e7f0z8 , danre-e7ez27 , danre-e7f2w1 , danre-f1qid7 , danre-a0a0g2kru2 , danre-f1qla7 , danre-a9jr90 , danre-e7f070 , danre-f172a , danre-e7fb35 , danre-a7mbu9 , danre-f1qtr2

Title : Insights into hominid evolution from the gorilla genome sequence - Scally_2012_Nature_483_169
Author(s) : Scally A , Dutheil JY , Hillier LW , Jordan GE , Goodhead I , Herrero J , Hobolth A , Lappalainen T , Mailund T , Marques-Bonet T , McCarthy S , Montgomery SH , Schwalie PC , Tang YA , Ward MC , Xue Y , Yngvadottir B , Alkan C , Andersen LN , Ayub Q , Ball EV , Beal K , Bradley BJ , Chen Y , Clee CM , Fitzgerald S , Graves TA , Gu Y , Heath P , Heger A , Karakoc E , Kolb-Kokocinski A , Laird GK , Lunter G , Meader S , Mort M , Mullikin JC , Munch K , O'Connor TD , Phillips AD , Prado-Martinez J , Rogers AS , Sajjadian S , Schmidt D , Shaw K , Simpson JT , Stenson PD , Turner DJ , Vigilant L , Vilella AJ , Whitener W , Zhu B , Cooper DN , de Jong P , Dermitzakis ET , Eichler EE , Flicek P , Goldman N , Mundy NI , Ning Z , Odom DT , Ponting CP , Quail MA , Ryder OA , Searle SM , Warren WC , Wilson RK , Schierup MH , Rogers J , Tyler-Smith C , Durbin R
Ref : Nature , 483 :169 , 2012
Abstract : Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.
ESTHER : Scally_2012_Nature_483_169
PubMedSearch : Scally_2012_Nature_483_169
PubMedID: 22398555
Gene_locus related to this paper: gorgo-g3qfr8 , gorgo-g3qgi3 , gorgo-g3r1s1 , gorgo-g3r9p9 , gorgo-a0a2i2zrx6 , gorgo-g3re16 , gorgo-g3s122 , gorgo-a0a2i2y3x8

Title : Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis - Dalloul_2010_PLoS.Biol_8_E1000475
Author(s) : Dalloul RA , Long JA , Zimin AV , Aslam L , Beal K , Blomberg Le A , Bouffard P , Burt DW , Crasta O , Crooijmans RP , Cooper K , Coulombe RA , De S , Delany ME , Dodgson JB , Dong JJ , Evans C , Frederickson KM , Flicek P , Florea L , Folkerts O , Groenen MA , Harkins TT , Herrero J , Hoffmann S , Megens HJ , Jiang A , de Jong P , Kaiser P , Kim H , Kim KW , Kim S , Langenberger D , Lee MK , Lee T , Mane S , Marcais G , Marz M , McElroy AP , Modise T , Nefedov M , Notredame C , Paton IR , Payne WS , Pertea G , Prickett D , Puiu D , Qioa D , Raineri E , Ruffier M , Salzberg SL , Schatz MC , Scheuring C , Schmidt CJ , Schroeder S , Searle SM , Smith EJ , Smith J , Sonstegard TS , Stadler PF , Tafer H , Tu ZJ , Van Tassell CP , Vilella AJ , Williams KP , Yorke JA , Zhang L , Zhang HB , Zhang X , Zhang Y , Reed KM
Ref : PLoS Biol , 8 : , 2010
Abstract : A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly ( approximately 1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.
ESTHER : Dalloul_2010_PLoS.Biol_8_E1000475
PubMedSearch : Dalloul_2010_PLoS.Biol_8_E1000475
PubMedID: 20838655
Gene_locus related to this paper: melga-g1mv74 , melga-g1myh1 , melga-g1n3b6 , melga-g1n4i8 , melga-g1n8a7 , melga-g1nb53 , melga-g1ndd8 , melga-g1npu5 , melga-g3ur65 , melga-g3uur6 , melga-g1njn8 , melga-g1mrp7 , melga-g1mzw6 , melga-g1n2a7 , melga-g1n608 , melga-g1n2j6 , melga-g1n2k0 , melga-g1ncb6 , melga-g1nei5 , melga-g1n1j3 , melga-g1nfd3 , melga-g1nna9 , melga-h9h0c1 , melga-g1nnl1 , melga-g1nhb9 , melga-g1mtl7 , fical-u3jnn0 , melga-g1n332 , melga-g1mtx9 , melga-g1nns1

Title : The genome sequence of taurine cattle: a window to ruminant biology and evolution - Elsik_2009_Science_324_522
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
Ref : Science , 324 :522 , 2009
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.
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

Title : Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences - Mikkelsen_2007_Nature_447_167
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
Ref : Nature , 447 :167 , 2007
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.
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

Title : DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage - Zody_2006_Nature_440_1045
Author(s) : Zody MC , Garber M , Adams DJ , Sharpe T , Harrow J , Lupski JR , Nicholson C , Searle SM , Wilming L , Young SK , Abouelleil A , Allen NR , Bi W , Bloom T , Borowsky ML , Bugalter BE , Butler J , Chang JL , Chen CK , Cook A , Corum B , Cuomo CA , de Jong PJ , Decaprio D , Dewar K , FitzGerald M , Gilbert J , Gibson R , Gnerre S , Goldstein S , Grafham DV , Grocock R , Hafez N , Hagopian DS , Hart E , Norman CH , Humphray S , Jaffe DB , Jones M , Kamal M , Khodiyar VK , LaButti K , Laird G , Lehoczky J , Liu X , Lokyitsang T , Loveland J , Lui A , Macdonald P , Major JE , Matthews L , Mauceli E , McCarroll SA , Mihalev AH , Mudge J , Nguyen C , Nicol R , O'Leary SB , Osoegawa K , Schwartz DC , Shaw-Smith C , Stankiewicz P , Steward C , Swarbreck D , Venkataraman V , Whittaker CA , Yang X , Zimmer AR , Bradley A , Hubbard T , Birren BW , Rogers J , Lander ES , Nusbaum C
Ref : Nature , 440 :1045 , 2006
Abstract : Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome. It is also enriched in segmental duplications, ranking third in density among the autosomes. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome.
ESTHER : Zody_2006_Nature_440_1045
PubMedSearch : Zody_2006_Nature_440_1045
PubMedID: 16625196
Gene_locus related to this paper: human-NLGN2 , human-NOTUM

Title : Genome sequence, comparative analysis and haplotype structure of the domestic dog - Lindblad-Toh_2005_Nature_438_803
Author(s) : Lindblad-Toh K , Wade CM , Mikkelsen TS , Karlsson EK , Jaffe DB , Kamal M , Clamp M , Chang JL , Kulbokas EJ, 3rd , Zody MC , Mauceli E , Xie X , Breen M , Wayne RK , Ostrander EA , Ponting CP , Galibert F , Smith DR , deJong PJ , Kirkness E , Alvarez P , Biagi T , Brockman W , Butler J , Chin CW , Cook A , Cuff J , Daly MJ , Decaprio D , Gnerre S , Grabherr M , Kellis M , Kleber M , Bardeleben C , Goodstadt L , Heger A , Hitte C , Kim L , Koepfli KP , Parker HG , Pollinger JP , Searle SM , Sutter NB , Thomas R , Webber C , Baldwin J , Abebe A , Abouelleil A , Aftuck L , Ait-Zahra M , Aldredge T , Allen N , An P , Anderson S , Antoine C , Arachchi H , Aslam A , Ayotte L , Bachantsang P , Barry A , Bayul T , Benamara M , Berlin A , Bessette D , Blitshteyn B , Bloom T , Blye J , Boguslavskiy L , Bonnet C , Boukhgalter B , Brown A , Cahill P , Calixte N , Camarata J , Cheshatsang Y , Chu J , Citroen M , Collymore A , Cooke P , Dawoe T , Daza R , Decktor K , DeGray S , Dhargay N , Dooley K , Dorje P , Dorjee K , Dorris L , Duffey N , Dupes A , Egbiremolen O , Elong R , Falk J , Farina A , Faro S , Ferguson D , Ferreira P , Fisher S , FitzGerald M , Foley K , Foley C , Franke A , Friedrich D , Gage D , Garber M , Gearin G , Giannoukos G , Goode T , Goyette A , Graham J , Grandbois E , Gyaltsen K , Hafez N , Hagopian D , Hagos B , Hall J , Healy C , Hegarty R , Honan T , Horn A , Houde N , Hughes L , Hunnicutt L , Husby M , Jester B , Jones C , Kamat A , Kanga B , Kells C , Khazanovich D , Kieu AC , Kisner P , Kumar M , Lance K , Landers T , Lara M , Lee W , Leger JP , Lennon N , Leuper L , LeVine S , Liu J , Liu X , Lokyitsang Y , Lokyitsang T , Lui A , MacDonald J , Major J , Marabella R , Maru K , Matthews C , McDonough S , Mehta T , Meldrim J , Melnikov A , Meneus L , Mihalev A , Mihova T , Miller K , Mittelman R , Mlenga V , Mulrain L , Munson G , Navidi A , Naylor J , Nguyen T , Nguyen N , Nguyen C , Nicol R , Norbu N , Norbu C , Novod N , Nyima T , Olandt P , O'Neill B , O'Neill K , Osman S , Oyono L , Patti C , Perrin D , Phunkhang P , Pierre F , Priest M , Rachupka A , Raghuraman S , Rameau R , Ray V , Raymond C , Rege F , Rise C , Rogers J , Rogov P , Sahalie J , Settipalli S , Sharpe T , Shea T , Sheehan M , Sherpa N , Shi J , Shih D , Sloan J , Smith C , Sparrow T , Stalker J , Stange-Thomann N , Stavropoulos S , Stone C , Stone S , Sykes S , Tchuinga P , Tenzing P , Tesfaye S , Thoulutsang D , Thoulutsang Y , Topham K , Topping I , Tsamla T , Vassiliev H , Venkataraman V , Vo A , Wangchuk T , Wangdi T , Weiand M , Wilkinson J , Wilson A , Yadav S , Yang S , Yang X , Young G , Yu Q , Zainoun J , Zembek L , Zimmer A , Lander ES
Ref : Nature , 438 :803 , 2005
Abstract : Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
ESTHER : Lindblad-Toh_2005_Nature_438_803
PubMedSearch : Lindblad-Toh_2005_Nature_438_803
PubMedID: 16341006
Gene_locus related to this paper: canfa-1lipg , canfa-2neur , canfa-3neur , canfa-ACHE , canfa-BCHE , canfa-cauxin , canfa-CESDD1 , canfa-e2qsb1 , canfa-e2qsl3 , canfa-e2qsz2 , canfa-e2qvk3 , canfa-e2qw15 , canfa-e2qxs8 , canfa-e2qzs6 , canfa-e2r5t3 , canfa-e2r6f6 , canfa-e2r7e8 , canfa-e2r8v9 , canfa-e2r8z1 , canfa-e2r9h4 , canfa-e2r455 , canfa-e2rb70 , canfa-e2rcq9 , canfa-e2rd94 , canfa-e2rgi0 , canfa-e2rkq0 , canfa-e2rlz9 , canfa-e2rm00 , canfa-e2rqf1 , canfa-e2rss9 , canfa-f1p6w8 , canfa-f1p8b6 , canfa-f1p9d8 , canfa-f1p683 , canfa-f1pb79 , canfa-f1pgw0 , canfa-f1phd0 , canfa-f1phx2 , canfa-f1pke8 , canfa-f1pp08 , canfa-f1ppp9 , canfa-f1ps07 , canfa-f1ptf1 , canfa-f1pvp4 , canfa-f1pw93 , canfa-f1pwk3 , canfa-pafa , canfa-q1ert3 , canfa-q5jzr0 , canfa-e2rmb9 , canlf-f6v865 , canlf-e2rjg6 , canlf-e2r2h2 , canlf-f1p648 , canlf-f1pw90 , canlf-j9p8v6 , canlf-f1pcc4 , canlf-e2qxh0 , canlf-e2r774 , canlf-f1pf96 , canlf-e2rq56 , canlf-j9nwb1 , canlf-f1ptw2 , canlf-j9p8h1 , canlf-e2ree2 , canlf-f1prs1 , canlf-j9nus1 , canlf-e2rf91 , canlf-f1pg57 , canlf-f1q111

Title : Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution - Hillier_2004_Nature_432_695
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
Ref : Nature , 432 :695 , 2004
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.
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

Title : Genome sequence of the Brown Norway rat yields insights into mammalian evolution - Gibbs_2004_Nature_428_493
Author(s) : Gibbs RA , Weinstock GM , Metzker ML , Muzny DM , Sodergren EJ , Scherer S , Scott G , Steffen D , Worley KC , Burch PE , Okwuonu G , Hines S , Lewis L , DeRamo C , Delgado O , Dugan-Rocha S , Miner G , Morgan M , Hawes A , Gill R , Celera , Holt RA , Adams MD , Amanatides PG , Baden-Tillson H , Barnstead M , Chin S , Evans CA , Ferriera S , Fosler C , Glodek A , Gu Z , Jennings D , Kraft CL , Nguyen T , Pfannkoch CM , Sitter C , Sutton GG , Venter JC , Woodage T , Smith D , Lee HM , Gustafson E , Cahill P , Kana A , Doucette-Stamm L , Weinstock K , Fechtel K , Weiss RB , Dunn DM , Green ED , Blakesley RW , Bouffard GG , de Jong PJ , Osoegawa K , Zhu B , Marra M , Schein J , Bosdet I , Fjell C , Jones S , Krzywinski M , Mathewson C , Siddiqui A , Wye N , McPherson J , Zhao S , Fraser CM , Shetty J , Shatsman S , Geer K , Chen Y , Abramzon S , Nierman WC , Havlak PH , Chen R , Durbin KJ , Egan A , Ren Y , Song XZ , Li B , Liu Y , Qin X , Cawley S , Cooney AJ , D'Souza LM , Martin K , Wu JQ , Gonzalez-Garay ML , Jackson AR , Kalafus KJ , McLeod MP , Milosavljevic A , Virk D , Volkov A , Wheeler DA , Zhang Z , Bailey JA , Eichler EE , Tuzun E , Birney E , Mongin E , Ureta-Vidal A , Woodwark C , Zdobnov E , Bork P , Suyama M , Torrents D , Alexandersson M , Trask BJ , Young JM , Huang H , Wang H , Xing H , Daniels S , Gietzen D , Schmidt J , Stevens K , Vitt U , Wingrove J , Camara F , Mar Alba M , Abril JF , Guigo R , Smit A , Dubchak I , Rubin EM , Couronne O , Poliakov A , Hubner N , Ganten D , Goesele C , Hummel O , Kreitler T , Lee YA , Monti J , Schulz H , Zimdahl H , Himmelbauer H , Lehrach H , Jacob HJ , Bromberg S , Gullings-Handley J , Jensen-Seaman MI , Kwitek AE , Lazar J , Pasko D , Tonellato PJ , Twigger S , Ponting CP , Duarte JM , Rice S , Goodstadt L , Beatson SA , Emes RD , Winter EE , Webber C , Brandt P , Nyakatura G , Adetobi M , Chiaromonte F , Elnitski L , Eswara P , Hardison RC , Hou M , Kolbe D , Makova K , Miller W , Nekrutenko A , Riemer C , Schwartz S , Taylor J , Yang S , Zhang Y , Lindpaintner K , Andrews TD , Caccamo M , Clamp M , Clarke L , Curwen V , Durbin R , Eyras E , Searle SM , Cooper GM , Batzoglou S , Brudno M , Sidow A , Stone EA , Payseur BA , Bourque G , Lopez-Otin C , Puente XS , Chakrabarti K , Chatterji S , Dewey C , Pachter L , Bray N , Yap VB , Caspi A , Tesler G , Pevzner PA , Haussler D , Roskin KM , Baertsch R , Clawson H , Furey TS , Hinrichs AS , Karolchik D , Kent WJ , Rosenbloom KR , Trumbower H , Weirauch M , Cooper DN , Stenson PD , Ma B , Brent M , Arumugam M , Shteynberg D , Copley RR , Taylor MS , Riethman H , Mudunuri U , Peterson J , Guyer M , Felsenfeld A , Old S , Mockrin S , Collins F
Ref : Nature , 428 :493 , 2004
Abstract : The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
ESTHER : Gibbs_2004_Nature_428_493
PubMedSearch : Gibbs_2004_Nature_428_493
PubMedID: 15057822
Gene_locus related to this paper: rat-abhea , rat-abheb , rat-cd029 , rat-d3zaw4 , rat-dpp9 , rat-d3zhq1 , rat-d3zkp8 , rat-d3zuq1 , rat-d3zxw8 , rat-d4a4w4 , rat-d4a7w1 , rat-d4a9l7 , rat-d4a071 , rat-d4aa31 , rat-d4aa33 , rat-d4aa61 , rat-dglb , rat-f1lz91 , rat-Kansl3 , rat-nceh1 , rat-Tex30 , ratno-1hlip , ratno-1neur , ratno-1plip , ratno-2neur , ratno-3neur , ratno-3plip , ratno-ABH15 , ratno-ACHE , ratno-balip , ratno-BCHE , ratno-cauxin , ratno-Ces1d , ratno-Ces1e , ratno-Ces2f , ratno-d3ze31 , ratno-d3zp14 , ratno-d3zxi3 , ratno-d3zxq0 , ratno-d3zxq1 , ratno-d4a3d4 , ratno-d4aa05 , ratno-dpp4 , ratno-dpp6 , ratno-est8 , ratno-FAP , ratno-hyep , ratno-hyes , ratno-kmcxe , ratno-lmcxe , ratno-LOC246252 , ratno-MGLL , ratno-pbcxe , ratno-phebest , ratno-Ppgb , ratno-q4qr68 , ratno-q6ayr2 , ratno-q6q629 , ratno-SPG21 , ratno-thyro , rat-m0rc77 , rat-a0a0g2k9y7 , rat-a0a0g2kb83 , rat-d3zba8 , rat-d3zbj1 , rat-d3zcr8 , rat-d3zxw5 , rat-d4a340 , rat-f1lvg7 , rat-m0r509 , rat-m0r5d4 , rat-b5den3 , rat-d3zxk4 , rat-d4a1b6 , rat-d3zmg4 , rat-ab17c

Title : The DNA sequence and analysis of human chromosome 6 - Mungall_2003_Nature_425_805
Author(s) : Mungall AJ , Palmer SA , Sims SK , Edwards CA , Ashurst JL , Wilming L , Jones MC , Horton R , Hunt SE , Scott CE , Gilbert JG , Clamp ME , Bethel G , Milne S , Ainscough R , Almeida JP , Ambrose KD , Andrews TD , Ashwell RI , Babbage AK , Bagguley CL , Bailey J , Banerjee R , Barker DJ , Barlow KF , Bates K , Beare DM , Beasley H , Beasley O , Bird CP , Blakey S , Bray-Allen S , Brook J , Brown AJ , Brown JY , Burford DC , Burrill W , Burton J , Carder C , Carter NP , Chapman JC , Clark SY , Clark G , Clee CM , Clegg S , Cobley V , Collier RE , Collins JE , Colman LK , Corby NR , Coville GJ , Culley KM , Dhami P , Davies J , Dunn M , Earthrowl ME , Ellington AE , Evans KA , Faulkner L , Francis MD , Frankish A , Frankland J , French L , Garner P , Garnett J , Ghori MJ , Gilby LM , Gillson CJ , Glithero RJ , Grafham DV , Grant M , Gribble S , Griffiths C , Griffiths M , Hall R , Halls KS , Hammond S , Harley JL , Hart EA , Heath PD , Heathcott R , Holmes SJ , Howden PJ , Howe KL , Howell GR , Huckle E , Humphray SJ , Humphries MD , Hunt AR , Johnson CM , Joy AA , Kay M , Keenan SJ , Kimberley AM , King A , Laird GK , Langford C , Lawlor S , Leongamornlert DA , Leversha M , Lloyd CR , Lloyd DM , Loveland JE , Lovell J , Martin S , Mashreghi-Mohammadi M , Maslen GL , Matthews L , Mccann OT , McLaren SJ , McLay K , McMurray A , Moore MJ , Mullikin JC , Niblett D , Nickerson T , Novik KL , Oliver K , Overton-Larty EK , Parker A , Patel R , Pearce AV , Peck AI , Phillimore B , Phillips S , Plumb RW , Porter KM , Ramsey Y , Ranby SA , Rice CM , Ross MT , Searle SM , Sehra HK , Sheridan E , Skuce CD , Smith S , Smith M , Spraggon L , Squares SL , Steward CA , Sycamore N , Tamlyn-Hall G , Tester J , Theaker AJ , Thomas DW , Thorpe A , Tracey A , Tromans A , Tubby B , Wall M , Wallis JM , West AP , White SS , Whitehead SL , Whittaker H , Wild A , Willey DJ , Wilmer TE , Wood JM , Wray PW , Wyatt JC , Young L , Younger RM , Bentley DR , Coulson A , Durbin R , Hubbard T , Sulston JE , Dunham I , Rogers J , Beck S
Ref : Nature , 425 :805 , 2003
Abstract : Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.
ESTHER : Mungall_2003_Nature_425_805
PubMedSearch : Mungall_2003_Nature_425_805
PubMedID: 14574404
Gene_locus related to this paper: human-ABHD16A , human-BPHL , human-FAM135A , human-PRSS16 , human-SERAC1