Lander ES

References (20)

Title : Association of Rare and Common Variation in the Lipoprotein Lipase Gene With Coronary Artery Disease - Khera_2017_JAMA_317_937
Author(s) : Khera AV , Won HH , Peloso GM , O'Dushlaine C , Liu D , Stitziel NO , Natarajan P , Nomura A , Emdin CA , Gupta N , Borecki IB , Asselta R , Duga S , Merlini PA , Correa A , Kessler T , Wilson JG , Bown MJ , Hall AS , Braund PS , Carey DJ , Murray MF , Kirchner HL , Leader JB , Lavage DR , Manus JN , Hartzel DN , Samani NJ , Schunkert H , Marrugat J , Elosua R , McPherson R , Farrall M , Watkins H , Lander ES , Rader DJ , Danesh J , Ardissino D , Gabriel S , Willer C , Abecasis GR , Saleheen D , Dewey FE , Kathiresan S
Ref : Jama , 317 :937 , 2017
Abstract : Importance: The activity of lipoprotein lipase (LPL) is the rate-determining step in clearing triglyceride-rich lipoproteins from the circulation. Mutations that damage the LPL gene (LPL) lead to lifelong deficiency in enzymatic activity and can provide insight into the relationship of LPL to human disease. Objective: To determine whether rare and/or common variants in LPL are associated with early-onset coronary artery disease (CAD). Design, Setting, and Participants: In a cross-sectional study, LPL was sequenced in 10 CAD case-control cohorts of the multinational Myocardial Infarction Genetics Consortium and a nested CAD case-control cohort of the Geisinger Health System DiscovEHR cohort between 2010 and 2015. Common variants were genotyped in up to 305699 individuals of the Global Lipids Genetics Consortium and up to 120600 individuals of the CARDIoGRAM Exome Consortium between 2012 and 2014. Study-specific estimates were pooled via meta-analysis. Exposures: Rare damaging mutations in LPL included loss-of-function variants and missense variants annotated as pathogenic in a human genetics database or predicted to be damaging by computer prediction algorithms trained to identify mutations that impair protein function. Common variants in the LPL gene region included those independently associated with circulating triglyceride levels. Main Outcomes and Measures: Circulating lipid levels and CAD. Results: Among 46891 individuals with LPL gene sequencing data available, the mean (SD) age was 50 (12.6) years and 51% were female. A total of 188 participants (0.40%; 95% CI, 0.35%-0.46%) carried a damaging mutation in LPL, including 105 of 32646 control participants (0.32%) and 83 of 14245 participants with early-onset CAD (0.58%). Compared with 46703 noncarriers, the 188 heterozygous carriers of an LPL damaging mutation displayed higher plasma triglyceride levels (19.6 mg/dL; 95% CI, 4.6-34.6 mg/dL) and higher odds of CAD (odds ratio = 1.84; 95% CI, 1.35-2.51; P < .001). An analysis of 6 common LPL variants resulted in an odds ratio for CAD of 1.51 (95% CI, 1.39-1.64; P = 1.1 x 10-22) per 1-SD increase in triglycerides. Conclusions and Relevance: The presence of rare damaging mutations in LPL was significantly associated with higher triglyceride levels and presence of coronary artery disease. However, further research is needed to assess whether there are causal mechanisms by which heterozygous lipoprotein lipase deficiency could lead to coronary artery disease.
ESTHER : Khera_2017_JAMA_317_937
PubMedSearch : Khera_2017_JAMA_317_937
PubMedID: 28267856
Gene_locus related to this paper: human-LPL

Title : The genomic substrate for adaptive radiation in African cichlid fish - Brawand_2014_Nature_513_375
Author(s) : Brawand D , Wagner CE , Li YI , Malinsky M , Keller I , Fan S , Simakov O , Ng AY , Lim ZW , Bezault E , Turner-Maier J , Johnson J , Alcazar R , Noh HJ , Russell P , Aken B , Alfoldi J , Amemiya C , Azzouzi N , Baroiller JF , Barloy-Hubler F , Berlin A , Bloomquist R , Carleton KL , Conte MA , D'Cotta H , Eshel O , Gaffney L , Galibert F , Gante HF , Gnerre S , Greuter L , Guyon R , Haddad NS , Haerty W , Harris RM , Hofmann HA , Hourlier T , Hulata G , Jaffe DB , Lara M , Lee AP , MacCallum I , Mwaiko S , Nikaido M , Nishihara H , Ozouf-Costaz C , Penman DJ , Przybylski D , Rakotomanga M , Renn SC , Ribeiro FJ , Ron M , Salzburger W , Sanchez-Pulido L , Santos ME , Searle S , Sharpe T , Swofford R , Tan FJ , Williams L , Young S , Yin S , Okada N , Kocher TD , Miska EA , Lander ES , Venkatesh B , Fernald RD , Meyer A , Ponting CP , Streelman JT , Lindblad-Toh K , Seehausen O , Di Palma F
Ref : Nature , 513 :375 , 2014
Abstract : Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.
ESTHER : Brawand_2014_Nature_513_375
PubMedSearch : Brawand_2014_Nature_513_375
PubMedID: 25186727
Gene_locus related to this paper: oreni-i3j014 , oreni-i3iw22 , oreni-i3iwp5 , oreni-i3j6k7 , oreni-i3jhp1 , oreni-i3jeq5 , oreni-i3kf65 , oreni-i3j210 , oreni-i3j221 , oreni-i3k9y3 , oreni-i3k5p0 , oreni-i3jwi4 , oreni-i3jv26 , oreni-i3k9m0 , 9cich-a0a3p9d5c0 , oreni-i3knk8 , 9cich-a0a3b4hcr5 , 9cich-a0a3p9dbr8 , oreni-i3k1a6 , oreni-i3jq62 , 9cich-a0a3p9dgm2 , neobr-a0a3q4g2a1 , oreni-i3jdv9 , neobr-a0a3q4hk25 , oreni-i3jbm3 , oreni-i3jbm2 , oreni-i3jds8 , 9cich-a0a3b4hbf8 , 9cich-a0a3p9ars6 , neobr-a0a3q4ghw9 , oreni-i3kx89 , 9cich-a0a3p9d359 , oreni-i3kaa3 , 9cich-a0a3p9bvw3

Title : Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 - Grad_2012_Proc.Natl.Acad.Sci.U.S.A_109_3065
Author(s) : Grad YH , Lipsitch M , Feldgarden M , Arachchi HM , Cerqueira GC , FitzGerald M , Godfrey P , Haas BJ , Murphy CI , Russ C , Sykes S , Walker BJ , Wortman JR , Young S , Zeng Q , Abouelleil A , Bochicchio J , Chauvin S , Desmet T , Gujja S , McCowan C , Montmayeur A , Steelman S , Frimodt-Moller J , Petersen AM , Struve C , Krogfelt KA , Bingen E , Weill FX , Lander ES , Nusbaum C , Birren BW , Hung DT , Hanage WP
Ref : Proc Natl Acad Sci U S A , 109 :3065 , 2012
Abstract : The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.
ESTHER : Grad_2012_Proc.Natl.Acad.Sci.U.S.A_109_3065
PubMedSearch : Grad_2012_Proc.Natl.Acad.Sci.U.S.A_109_3065
PubMedID: 22315421
Gene_locus related to this paper: ecoli-fes , ecoli-MCMK , ecoli-yaim , ecoli-ycfp , ecoli-YFBB , ecoli-yhet , ecoli-yiel , ecoli-yqia , ecoli-YfhR

Title : A high-resolution map of human evolutionary constraint using 29 mammals - Lindblad-Toh_2011_Nature_478_476
Author(s) : Lindblad-Toh K , Garber M , Zuk O , Lin MF , Parker BJ , Washietl S , Kheradpour P , Ernst J , Jordan G , Mauceli E , Ward LD , Lowe CB , Holloway AK , Clamp M , Gnerre S , Alfoldi J , Beal K , Chang J , Clawson H , Cuff J , Di Palma F , Fitzgerald S , Flicek P , Guttman M , Hubisz MJ , Jaffe DB , Jungreis I , Kent WJ , Kostka D , Lara M , Martins AL , Massingham T , Moltke I , Raney BJ , Rasmussen MD , Robinson J , Stark A , Vilella AJ , Wen J , Xie X , Zody MC , Baldwin J , Bloom T , Chin CW , Heiman D , Nicol R , Nusbaum C , Young S , Wilkinson J , Worley KC , Kovar CL , Muzny DM , Gibbs RA , Cree A , Dihn HH , Fowler G , Jhangiani S , Joshi V , Lee S , Lewis LR , Nazareth LV , Okwuonu G , Santibanez J , Warren WC , Mardis ER , Weinstock GM , Wilson RK , Delehaunty K , Dooling D , Fronik C , Fulton L , Fulton B , Graves T , Minx P , Sodergren E , Birney E , Margulies EH , Herrero J , Green ED , Haussler D , Siepel A , Goldman N , Pollard KS , Pedersen JS , Lander ES , Kellis M
Ref : Nature , 478 :476 , 2011
Abstract : The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.
ESTHER : Lindblad-Toh_2011_Nature_478_476
PubMedSearch : Lindblad-Toh_2011_Nature_478_476
PubMedID: 21993624
Gene_locus related to this paper: cavpo-1plip , cavpo-2plrp , cavpo-h0v1b7 , cavpo-h0v5v8 , cavpo-h0vj36 , cavpo-lipli , rabit-1hlip , rabit-1plip , rabit-g1t6x7 , rabit-LIPH , myolu-l7n1c2 , myolu-g1pqd9 , cavpo-h0uyz6 , cavpo-h0vi56 , rabit-g1tbj4 , myolu-g1p5c0 , rabit-g1sds3 , rabit-g1sye0 , cavpo-h0v0r2 , cavpo-h0v7s5 , rabit-g1sp43 , myolu-g1p4p3 , cavpo-h0vw09 , rabit-g1ssu3 , myolu-g1pds0 , rabit-g1sic4 , cavpo-h0v2c4 , myolu-g1pg61 , myolu-g1pnb1 , myolu-g1pu06 , myolu-g1qa15 , myolu-g1qfu0 , rabit-g1sn99 , rabit-g1snq9 , rabit-g1sns7 , rabit-g1tuu8 , rabit-g1tzq7 , cavpo-h0v2i2 , cavpo-h0v2j0 , cavpo-h0vsf5 , cavpo-a0a286x8d3 , cavpo-a0a286xbr3 , cavpo-a0a286y0i8 , cavpo-a0a286y4p3 , myolu-g1q2n9 , cavpo-h0v1p4 , myolu-g1pan8 , myolu-g1paq0 , myolu-g1par4 , myolu-g1prn3 , myolu-g1q3i0 , myolu-g1q463 , myolu-g1pat6 , myolu-g1q859 , rabit-g1sul9 , rabit-g1sun0 , rabit-g1sup0 , myolu-l7n125 , myolu-g1pan2 , rabit-g1sxd0 , cavpo-h0v8j4 , rabit-d5fit0 , rabit-g1tkr5 , myolu-g1nty6 , myolu-g1p1p3 , cavpo-h0vdd5 , myolu-g1pdp2 , rabit-g1tmm5 , cavpo-h0vhq3 , myolu-g1nth4 , cavpo-h0vqx6 , rabit-g1tqr7 , myolu-g1p1e9 , cavpo-h0v8y6 , rabit-g1skt3 , myolu-g1nzg3 , cavpo-h0v5z0 , rabit-g1sgz5 , myolu-g1pkg5 , rabit-g1tmw5 , rabit-g1t134 , cavpo-a0a286x9v5 , myolu-g1qc57 , myolu-g1q061 , rabit-g1tnp4 , rabit-g1tyf7 , cavpo-h0w2w1 , rabit-g1ta36 , cavpo-h0w342 , myolu-g1q4e3 , rabit-g1sqa1 , cavpo-h0uxk7 , myolu-g1p353 , cavpo-h0vpm0 , rabit-a0a5f9cru6 , cavpo-a0a286xtc0

Title : The genome of the green anole lizard and a comparative analysis with birds and mammals - Alfoldi_2011_Nature_477_587
Author(s) : Alfoldi J , Di Palma F , Grabherr M , Williams C , Kong L , Mauceli E , Russell P , Lowe CB , Glor RE , Jaffe JD , Ray DA , Boissinot S , Shedlock AM , Botka C , Castoe TA , Colbourne JK , Fujita MK , Moreno RG , ten Hallers BF , Haussler D , Heger A , Heiman D , Janes DE , Johnson J , de Jong PJ , Koriabine MY , Lara M , Novick PA , Organ CL , Peach SE , Poe S , Pollock DD , de Queiroz K , Sanger T , Searle S , Smith JD , Smith Z , Swofford R , Turner-Maier J , Wade J , Young S , Zadissa A , Edwards SV , Glenn TC , Schneider CJ , Losos JB , Lander ES , Breen M , Ponting CP , Lindblad-Toh K
Ref : Nature , 477 :587 , 2011
Abstract : The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments. Among amniotes, genome sequences are available for mammals and birds, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes. Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.
ESTHER : Alfoldi_2011_Nature_477_587
PubMedSearch : Alfoldi_2011_Nature_477_587
PubMedID: 21881562
Gene_locus related to this paper: anoca-h9g670 , anoca-h9g675 , anoca-h9g680 , anoca-h9gbf2 , anoca-h9gl37 , anoca-h9gq07 , anoca-h9gqa2 , anoca-h9gqv4 , anoca-h9gr08 , anoca-h9glr3 , anoca-h9gfq0 , anoca-h9gfy1 , anoca-h9g7n4 , anoca-h9gpa2 , anoca-h9g3p8

Title : Genome sequence, comparative analysis, and population genetics of the domestic horse - Wade_2009_Science_326_865
Author(s) : Wade CM , Giulotto E , Sigurdsson S , Zoli M , Gnerre S , Imsland F , Lear TL , Adelson DL , Bailey E , Bellone RR , Blocker H , Distl O , Edgar RC , Garber M , Leeb T , Mauceli E , MacLeod JN , Penedo MC , Raison JM , Sharpe T , Vogel J , Andersson L , Antczak DF , Biagi T , Binns MM , Chowdhary BP , Coleman SJ , Della Valle G , Fryc S , Guerin G , Hasegawa T , Hill EW , Jurka J , Kiialainen A , Lindgren G , Liu J , Magnani E , Mickelson JR , Murray J , Nergadze SG , Onofrio R , Pedroni S , Piras MF , Raudsepp T , Rocchi M , Roed KH , Ryder OA , Searle S , Skow L , Swinburne JE , Syvanen AC , Tozaki T , Valberg SJ , Vaudin M , White JR , Zody MC , Lander ES , Lindblad-Toh K
Ref : Science , 326 :865 , 2009
Abstract : We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.
ESTHER : Wade_2009_Science_326_865
PubMedSearch : Wade_2009_Science_326_865
PubMedID: 19892987
Gene_locus related to this paper: horse-1plip , horse-2plrp , horse-ACHE , horse-BCHE , horse-f6pri5 , horse-f6qlk6 , horse-f6qsc5 , horse-f6r958 , horse-f6sfg0 , horse-f6uif6 , horse-f6un85 , horse-f6vxp7 , horse-f6wfs9 , horse-f6wzv8 , horse-f6x0i7 , horse-f6x5e5 , horse-f6zmg7 , horse-f7afw6 , horse-f7agv7 , horse-f7bj10 , horse-f7bk45 , horse-f7bvl6 , horse-f7c7a8 , horse-f7cdt1 , horse-f7cxj0 , horse-f6ut17 , horse-f6svq9 , horse-f6xgj6 , horse-f6s101 , horse-f6wfa7 , horse-f7cpx3 , horse-f7adj7 , horse-f6r609 , horse-f6y0j2 , horse-f6zvb2 , horse-f7e4g0 , horse-f6ti02 , horse-f6re01 , horse-f6xmp6 , horse-f6vts1 , horse-f6quf7 , horse-f6tn81 , horse-f7bm46 , horse-f6q1u3 , horse-f6zna7 , horse-f6q208 , horse-f7cuh0 , horse-f6tq73 , horse-f6xa70 , horse-f6qj19 , horse-f6wgf3 , horse-f7d8t6 , horse-f6ul42 , horse-f7am73 , horse-f7dme2

Title : cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism - Freeman_2008_Biological.Bulletin_214_284
Author(s) : Freeman RM, Jr. , Wu M , Cordonnier-Pratt MM , Pratt LH , Gruber CE , Smith M , Lander ES , Stange-Thomann N , Lowe CJ , Gerhart J , Kirschner M
Ref : Biol Bull , 214 :284 , 2008
Abstract : We describe a collection of expressed sequence tags (ESTs) for Saccoglossus kowalevskii, a direct-developing hemichordate valuable for evolutionary comparisons with chordates. The 202,175 ESTs represent 163,633 arrayed clones carrying cDNAs prepared from embryonic libraries, and they assemble into 13,677 continuous sequences (contigs), leaving 10,896 singletons (excluding mitochondrial sequences). Of the contigs, 53% had significant matches when BLAST was used to query the NCBI databases (< or = 10(-10)), as did 51% of the singletons. Contigs most frequently matched sequences from amphioxus (29%), chordates (67%), and deuterostomes (87%). From the clone array, we isolated 400 full-length sequences for transcription factors and signaling proteins of use for evolutionary and developmental studies. The set includes sequences for fox, pax, tbx, hox, and other homeobox-containing factors, and for ligands and receptors of the TGFbeta, Wnt, Hh, Delta/Notch, and RTK pathways. At least 80% of key sequences have been obtained, when judged against gene lists of model organisms. The median length of these cDNAs is 2.3 kb, including 1.05 kb of 3' untranslated region (UTR). Only 30% are entirely matched by single contigs assembled from ESTs. We conclude that an EST collection based on 150,000 clones is a rich source of sequences for molecular developmental work, and that the EST approach is an efficient way to initiate comparative studies of a new organism.
ESTHER : Freeman_2008_Biological.Bulletin_214_284
PubMedSearch : Freeman_2008_Biological.Bulletin_214_284
PubMedID: 18574105
Gene_locus related to this paper: sacko-a0a1l7h7f0 , sacko-a0a1l7h7f2

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 : Human chromosome 11 DNA sequence and analysis including novel gene identification - Taylor_2006_Nature_440_497
Author(s) : Taylor TD , Noguchi H , Totoki Y , Toyoda A , Kuroki Y , Dewar K , Lloyd C , Itoh T , Takeda T , Kim DW , She X , Barlow KF , Bloom T , Bruford E , Chang JL , Cuomo CA , Eichler E , Fitzgerald MG , Jaffe DB , LaButti K , Nicol R , Park HS , Seaman C , Sougnez C , Yang X , Zimmer AR , Zody MC , Birren BW , Nusbaum C , Fujiyama A , Hattori M , Rogers J , Lander ES , Sakaki Y
Ref : Nature , 440 :497 , 2006
Abstract : Chromosome 11, although average in size, is one of the most gene- and disease-rich chromosomes in the human genome. Initial gene annotation indicates an average gene density of 11.6 genes per megabase, including 1,524 protein-coding genes, some of which were identified using novel methods, and 765 pseudogenes. One-quarter of the protein-coding genes shows overlap with other genes. Of the 856 olfactory receptor genes in the human genome, more than 40% are located in 28 single- and multi-gene clusters along this chromosome. Out of the 171 disorders currently attributed to the chromosome, 86 remain for which the underlying molecular basis is not yet known, including several mendelian traits, cancer and susceptibility loci. The high-quality data presented here--nearly 134.5 million base pairs representing 99.8% coverage of the euchromatic sequence--provide scientists with a solid foundation for understanding the genetic basis of these disorders and other biological phenomena.
ESTHER : Taylor_2006_Nature_440_497
PubMedSearch : Taylor_2006_Nature_440_497
PubMedID: 16554811
Gene_locus related to this paper: human-PRCP

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 : Analysis of the DNA sequence and duplication history of human chromosome 15 - Zody_2006_Nature_440_671
Author(s) : Zody MC , Garber M , Sharpe T , Young SK , Rowen L , O'Neill K , Whittaker CA , Kamal M , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Kodira CD , Madan A , Qin S , Yang X , Abbasi N , Abouelleil A , Arachchi HM , Baradarani L , Birditt B , Bloom S , Bloom T , Borowsky ML , Burke J , Butler J , Cook A , DeArellano K , Decaprio D , Dorris L, 3rd , Dors M , Eichler EE , Engels R , Fahey J , Fleetwood P , Friedman C , Gearin G , Hall JL , Hensley G , Johnson E , Jones C , Kamat A , Kaur A , Locke DP , Munson G , Jaffe DB , Lui A , Macdonald P , Mauceli E , Naylor JW , Nesbitt R , Nicol R , O'Leary SB , Ratcliffe A , Rounsley S , She X , Sneddon KM , Stewart S , Sougnez C , Stone SM , Topham K , Vincent D , Wang S , Zimmer AR , Birren BW , Hood L , Lander ES , Nusbaum C
Ref : Nature , 440 :671 , 2006
Abstract : Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.
ESTHER : Zody_2006_Nature_440_671
PubMedSearch : Zody_2006_Nature_440_671
PubMedID: 16572171
Gene_locus related to this paper: human-DPP8 , human-LIPC , human-SPG21

Title : DNA sequence and analysis of human chromosome 8 - Nusbaum_2006_Nature_439_331
Author(s) : Nusbaum C , Mikkelsen TS , Zody MC , Asakawa S , Taudien S , Garber M , Kodira CD , Schueler MG , Shimizu A , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Allen NR , Anderson S , Asakawa T , Blechschmidt K , Bloom T , Borowsky ML , Butler J , Cook A , Corum B , DeArellano K , Decaprio D , Dooley KT , Dorris L, 3rd , Engels R , Glockner G , Hafez N , Hagopian DS , Hall JL , Ishikawa SK , Jaffe DB , Kamat A , Kudoh J , Lehmann R , Lokitsang T , Macdonald P , Major JE , Matthews CD , Mauceli E , Menzel U , Mihalev AH , Minoshima S , Murayama Y , Naylor JW , Nicol R , Nguyen C , O'Leary SB , O'Neill K , Parker SC , Polley A , Raymond CK , Reichwald K , Rodriguez J , Sasaki T , Schilhabel M , Siddiqui R , Smith CL , Sneddon TP , Talamas JA , Tenzin P , Topham K , Venkataraman V , Wen G , Yamazaki S , Young SK , Zeng Q , Zimmer AR , Rosenthal A , Birren BW , Platzer M , Shimizu N , Lander ES
Ref : Nature , 439 :331 , 2006
Abstract : The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.
ESTHER : Nusbaum_2006_Nature_439_331
PubMedSearch : Nusbaum_2006_Nature_439_331
PubMedID: 16421571
Gene_locus related to this paper: human-TG

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 : DNA sequence and analysis of human chromosome 18 - Nusbaum_2005_Nature_437_551
Author(s) : Nusbaum C , Zody MC , Borowsky ML , Kamal M , Kodira CD , Taylor TD , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Abouelleil A , Allen NR , Anderson S , Bloom T , Bugalter B , Butler J , Cook A , Decaprio D , Engels R , Garber M , Gnirke A , Hafez N , Hall JL , Norman CH , Itoh T , Jaffe DB , Kuroki Y , Lehoczky J , Lui A , Macdonald P , Mauceli E , Mikkelsen TS , Naylor JW , Nicol R , Nguyen C , Noguchi H , O'Leary SB , O'Neill K , Piqani B , Smith CL , Talamas JA , Topham K , Totoki Y , Toyoda A , Wain HM , Young SK , Zeng Q , Zimmer AR , Fujiyama A , Hattori M , Birren BW , Sakaki Y , Lander ES
Ref : Nature , 437 :551 , 2005
Abstract : Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.
ESTHER : Nusbaum_2005_Nature_437_551
PubMedSearch : Nusbaum_2005_Nature_437_551
PubMedID: 16177791
Gene_locus related to this paper: human-LIPG

Title : Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype - Jaillon_2004_Nature_431_946
Author(s) : Jaillon O , Aury JM , Brunet F , Petit JL , Stange-Thomann N , Mauceli E , Bouneau L , Fischer C , Ozouf-Costaz C , Bernot A , Nicaud S , Jaffe D , Fisher S , Lutfalla G , Dossat C , Segurens B , Dasilva C , Salanoubat M , Levy M , Boudet N , Castellano S , Anthouard V , Jubin C , Castelli V , Katinka M , Vacherie B , Biemont C , Skalli Z , Cattolico L , Poulain J , de Berardinis V , Cruaud C , Duprat S , Brottier P , Coutanceau JP , Gouzy J , Parra G , Lardier G , Chapple C , McKernan KJ , McEwan P , Bosak S , Kellis M , Volff JN , Guigo R , Zody MC , Mesirov J , Lindblad-Toh K , Birren B , Nusbaum C , Kahn D , Robinson-Rechavi M , Laudet V , Schachter V , Quetier F , Saurin W , Scarpelli C , Wincker P , Lander ES , Weissenbach J , Roest Crollius H
Ref : Nature , 431 :946 , 2004
Abstract : Tetraodon nigroviridis is a freshwater puffer fish with the smallest known vertebrate genome. Here, we report a draft genome sequence with long-range linkage and substantial anchoring to the 21 Tetraodon chromosomes. Genome analysis provides a greatly improved fish gene catalogue, including identifying key genes previously thought to be absent in fish. Comparison with other vertebrates and a urochordate indicates that fish proteins have diverged markedly faster than their mammalian homologues. Comparison with the human genome suggests approximately 900 previously unannotated human genes. Analysis of the Tetraodon and human genomes shows that whole-genome duplication occurred in the teleost fish lineage, subsequent to its divergence from mammals. The analysis also makes it possible to infer the basic structure of the ancestral bony vertebrate genome, which was composed of 12 chromosomes, and to reconstruct much of the evolutionary history of ancient and recent chromosome rearrangements leading to the modern human karyotype.
ESTHER : Jaillon_2004_Nature_431_946
PubMedSearch : Jaillon_2004_Nature_431_946
PubMedID: 15496914
Gene_locus related to this paper: tetng-3neur , tetng-4neur , tetng-ACHE , tetng-BCHE , tetng-h3cfz4 , tetng-h3ci57 , tetng-h3cl30 , tetng-h3cnh2 , tetng-nlgn2b , tetng-h3czr1 , tetng-h3dbr5 , tetng-nlgn2a , tetng-nlgn3b , tetng-q4ref8 , tetng-q4rjp3 , tetng-q4rjy3 , tetng-q4rk53 , tetng-q4rk63 , tetng-q4rk66 , tetng-q4rkk3 , tetng-q4rli3 , tetng-q4rn09 , tetng-q4rqj4 , tetng-q4rqz6 , tetng-q4rr22 , tetng-q4rru9 , tetng-q4rtq6 , tetng-q4rvf8 , tetng-q4rwa0 , tetng-q4rx90 , tetng-q4ryv8 , tetng-q4ryz3 , tetng-q4s0h8 , tetng-q4s5x0 , tetng-q4s6r1 , tetng-q4s6t6 , tetng-q4s7e3 , tetng-q4s7x6 , tetng-q4s8t5 , tetng-q4s9w9 , tetng-q4s050 , tetng-q4s091 , tetng-q4s144 , tetng-q4s309 , tetng-q4s578 , tetng-q4sal4 , tetng-q4sbm6 , tetng-q4sbp0 , tetng-q4sbu0 , tetng-q4sd49 , tetng-q4ser6 , tetng-q4sfm7 , tetng-q4sgm5 , tetng-q4sgv2 , tetng-q4sh74 , tetng-q4shl7 , tetng-q4si60 , tetng-q4sie5 , tetng-q4sku6 , tetng-q4smu0 , tetng-q4smy3 , tetng-q4snp0 , tetng-q4snq3 , tetng-q4spa7 , tetng-q4spq0 , tetng-q4sqr3 , tetng-q4sty0 , tetng-q4suu2 , tetng-q4suz1 , tetng-q4sxh3 , tetng-q4syn6 , tetng-q4szk0 , tetng-q4szy0 , tetng-q4t3m9 , tetng-q4t4a1 , tetng-q4t6m1 , tetng-q4t7r6 , tetng-q4t173 , tetng-q4t826 , tetng-q4t920 , tetng-q4ta33 , tetng-q4tab8 , tetng-q4tb62 , tetng-q4tbe2 , tetng-h3dbw2 , tetng-h3cpc8 , tetng-h3cjy0 , tetng-h3d966 , tetng-h3d3e3 , tetng-h3d961 , tetng-h3ctg6 , tetng-h3dde8 , tetng-h3dde9 , tetng-h3det9 , tetng-h3cre8 , tetng-h3dfb4 , tetng-h3clj8

Title : The genome sequence of the filamentous fungus Neurospora crassa - Galagan_2003_Nature_422_859
Author(s) : Galagan JE , Calvo SE , Borkovich KA , Selker EU , Read ND , Jaffe D , FitzHugh W , Ma LJ , Smirnov S , Purcell S , Rehman B , Elkins T , Engels R , Wang S , Nielsen CB , Butler J , Endrizzi M , Qui D , Ianakiev P , Bell-Pedersen D , Nelson MA , Werner-Washburne M , Selitrennikoff CP , Kinsey JA , Braun EL , Zelter A , Schulte U , Kothe GO , Jedd G , Mewes W , Staben C , Marcotte E , Greenberg D , Roy A , Foley K , Naylor J , Stange-Thomann N , Barrett R , Gnerre S , Kamal M , Kamvysselis M , Mauceli E , Bielke C , Rudd S , Frishman D , Krystofova S , Rasmussen C , Metzenberg RL , Perkins DD , Kroken S , Cogoni C , Macino G , Catcheside D , Li W , Pratt RJ , Osmani SA , DeSouza CP , Glass L , Orbach MJ , Berglund JA , Voelker R , Yarden O , Plamann M , Seiler S , Dunlap J , Radford A , Aramayo R , Natvig DO , Alex LA , Mannhaupt G , Ebbole DJ , Freitag M , Paulsen I , Sachs MS , Lander ES , Nusbaum C , Birren B
Ref : Nature , 422 :859 , 2003
Abstract : Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many as in the fission yeast Schizosaccharomyces pombe and only about 25% fewer than in the fruitfly Drosophila melanogaster. Analysis of the gene set yields insights into unexpected aspects of Neurospora biology including the identification of genes potentially associated with red light photobiology, genes implicated in secondary metabolism, and important differences in Ca2+ signalling as compared with plants and animals. Neurospora possesses the widest array of genome defence mechanisms known for any eukaryotic organism, including a process unique to fungi called repeat-induced point mutation (RIP). Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
ESTHER : Galagan_2003_Nature_422_859
PubMedSearch : Galagan_2003_Nature_422_859
PubMedID: 12712197
Gene_locus related to this paper: neucr-5E6.090 , neucr-64C2.080 , neucr-90C4.300 , neucr-a7uw78 , neucr-a7uwh6 , neucr-a7uwy7 , neucr-apth1 , neucr-ATG15 , neucr-B7H23.190 , neucr-B11O8.160 , neucr-B13B3.090 , neucr-B14D6.130 , neucr-B18E6.050 , neucr-B19A17.360 , neucr-B23G1.090 , neucr-CBPYA , neucr-MET5 , neucr-NCU00292.1 , neucr-NCU00350.1 , neucr-NCU00536.1 , neucr-NCU00825.1 , neucr-NCU02148.1 , neucr-NCU02679.1 , neucr-NCU02904.1 , neucr-NCU02924.1 , neucr-NCU03158.1 , neucr-NCU04930.1 , neucr-NCU06332.1 , neucr-NCU06573.1 , neucr-NCU07081.1 , neucr-NCU07415.1 , neucr-NCU07909.1 , neucr-NCU08752.1 , neucr-NCU09575.1 , neucr-NCU10022.1 , neucr-ppme1 , neucr-q6mfs7 , neucr-q7rxb4 , neucr-q7rxv5 , neucr-q7ry06 , neucr-q7ryd2 , neucr-q7rzk2 , neucr-q7s0g7 , neucr-q7s1x0 , neucr-q7s2b3 , neucr-q7s2c5 , neucr-q7s2p4 , neucr-q7s2u9 , neucr-q7s3c6 , neucr-q7s3c8 , neucr-q7s3m2 , neucr-q7s4e3 , neucr-q7s4f8 , neucr-q7s4j4 , neucr-q7s5d6 , neucr-q7s5m2 , neucr-q7s5v8 , neucr-q7s6c5 , neucr-q7s8h2 , neucr-q7s070 , neucr-q7s082 , neucr-q7s134 , neucr-q7s216 , neucr-q7s259 , neucr-q7s260 , neucr-q7s283 , neucr-q7s512 , neucr-q7s736 , neucr-q7s828 , neucr-q7s897 , neucr-q7sbf9 , neucr-q7sbn0 , neucr-q7scr4 , neucr-q7sdw5 , neucr-q7sdx9 , neucr-q7se51 , neucr-q7sea3 , neucr-q7sez8 , neucr-q7sff7 , neucr-q7sga3 , neucr-q7sgj0 , neucr-q7sgp3 , neucr-q7sha3 , neucr-q7sha5 , neucr-q7shu8 , neucr-q9p6a7 , neucr-q872l1 , neucr-f5hbr2 , neucr-q7ry64

Title : Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs - Okazaki_2002_Nature_420_563
Author(s) : Okazaki Y , Furuno M , Kasukawa T , Adachi J , Bono H , Kondo S , Nikaido I , Osato N , Saito R , Suzuki H , Yamanaka I , Kiyosawa H , Yagi K , Tomaru Y , Hasegawa Y , Nogami A , Schonbach C , Gojobori T , Baldarelli R , Hill DP , Bult C , Hume DA , Quackenbush J , Schriml LM , Kanapin A , Matsuda H , Batalov S , Beisel KW , Blake JA , Bradt D , Brusic V , Chothia C , Corbani LE , Cousins S , Dalla E , Dragani TA , Fletcher CF , Forrest A , Frazer KS , Gaasterland T , Gariboldi M , Gissi C , Godzik A , Gough J , Grimmond S , Gustincich S , Hirokawa N , Jackson IJ , Jarvis ED , Kanai A , Kawaji H , Kawasawa Y , Kedzierski RM , King BL , Konagaya A , Kurochkin IV , Lee Y , Lenhard B , Lyons PA , Maglott DR , Maltais L , Marchionni L , McKenzie L , Miki H , Nagashima T , Numata K , Okido T , Pavan WJ , Pertea G , Pesole G , Petrovsky N , Pillai R , Pontius JU , Qi D , Ramachandran S , Ravasi T , Reed JC , Reed DJ , Reid J , Ring BZ , Ringwald M , Sandelin A , Schneider C , Semple CA , Setou M , Shimada K , Sultana R , Takenaka Y , Taylor MS , Teasdale RD , Tomita M , Verardo R , Wagner L , Wahlestedt C , Wang Y , Watanabe Y , Wells C , Wilming LG , Wynshaw-Boris A , Yanagisawa M , Yang I , Yang L , Yuan Z , Zavolan M , Zhu Y , Zimmer A , Carninci P , Hayatsu N , Hirozane-Kishikawa T , Konno H , Nakamura M , Sakazume N , Sato K , Shiraki T , Waki K , Kawai J , Aizawa K , Arakawa T , Fukuda S , Hara A , Hashizume W , Imotani K , Ishii Y , Itoh M , Kagawa I , Miyazaki A , Sakai K , Sasaki D , Shibata K , Shinagawa A , Yasunishi A , Yoshino M , Waterston R , Lander ES , Rogers J , Birney E , Hayashizaki Y
Ref : Nature , 420 :563 , 2002
Abstract : Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
ESTHER : Okazaki_2002_Nature_420_563
PubMedSearch : Okazaki_2002_Nature_420_563
PubMedID: 12466851
Gene_locus related to this paper: mouse-1lipg , mouse-1llip , mouse-1plrp , mouse-3neur , mouse-ABH15 , mouse-abhd4 , mouse-abhd5 , mouse-Abhd8 , mouse-Abhd11 , mouse-abhda , mouse-acot4 , mouse-adcl4 , mouse-AI607300 , mouse-BAAT , mouse-bphl , mouse-C87498 , mouse-Ldah , mouse-Ces1d , mouse-Ces2e , mouse-CMBL , mouse-DGLB , mouse-dpp9 , mouse-ES10 , mouse-F135A , mouse-FASN , mouse-hslip , mouse-hyes , mouse-Kansl3 , mouse-LIPH , mouse-LIPK , mouse-lipli , mouse-LIPM , mouse-lypla1 , mouse-lypla2 , mouse-MEST , mouse-MGLL , mouse-ndr4 , mouse-OVCA2 , mouse-pafa , mouse-pcp , mouse-ppce , mouse-Ppgb , mouse-PPME1 , mouse-q3uuq7 , mouse-Q8BLF1 , mouse-ACOT6 , mouse-Q8C1A9 , mouse-Q9DAI6 , mouse-Q80UX8 , mouse-Q8BGG9 , mouse-Q8C167 , mouse-rbbp9 , mouse-SERHL , mouse-tssp

Title : Characterization of single-nucleotide polymorphisms in coding regions of human genes - Cargill_1999_Nat.Genet_22_231
Author(s) : Cargill M , Altshuler D , Ireland J , Sklar P , Ardlie K , Patil N , Shaw N , Lane CR , Lim EP , Kalyanaraman N , Nemesh J , Ziaugra L , Friedland L , Rolfe A , Warrington J , Lipshutz R , Daley GQ , Lander ES
Ref : Nat Genet , 22 :231 , 1999
Abstract : A major goal in human genetics is to understand the role of common genetic variants in susceptibility to common diseases. This will require characterizing the nature of gene variation in human populations, assembling an extensive catalogue of single-nucleotide polymorphisms (SNPs) in candidate genes and performing association studies for particular diseases. At present, our knowledge of human gene variation remains rudimentary. Here we describe a systematic survey of SNPs in the coding regions of human genes. We identified SNPs in 106 genes relevant to cardiovascular disease, endocrinology and neuropsychiatry by screening an average of 114 independent alleles using 2 independent screening methods. To ensure high accuracy, all reported SNPs were confirmed by DNA sequencing. We identified 560 SNPs, including 392 coding-region SNPs (cSNPs) divided roughly equally between those causing synonymous and non-synonymous changes. We observed different rates of polymorphism among classes of sites within genes (non-coding, degenerate and non-degenerate) as well as between genes. The cSNPs most likely to influence disease, those that alter the amino acid sequence of the encoded protein, are found at a lower rate and with lower allele frequencies than silent substitutions. This likely reflects selection acting against deleterious alleles during human evolution. The lower allele frequency of missense cSNPs has implications for the compilation of a comprehensive catalogue, as well as for the subsequent application to disease association.
ESTHER : Cargill_1999_Nat.Genet_22_231
PubMedSearch : Cargill_1999_Nat.Genet_22_231
PubMedID: 10391209
Gene_locus related to this paper: human-LIPC

Title : Genome-wide search for asthma susceptibility loci in a founder population. The Collaborative Study on the Genetics of Asthma - Ober_1998_Hum.Mol.Genet_7_1393
Author(s) : Ober C , Cox NJ , Abney M , Di Rienzo A , Lander ES , Changyaleket B , Gidley H , Kurtz B , Lee J , Nance M , Pettersson A , Prescott J , Richardson A , Schlenker E , Summerhill E , Willadsen S , Parry R
Ref : Hum Mol Genet , 7 :1393 , 1998
Abstract : Founder populations offer many advantages for mapping genetic traits, particularly complex traits that are likely to be genetically heterogeneous. To identify genes that influence asthma and asthma-associated phenotypes, we conducted a genome-wide screen in the Hutterites, a religious isolate of European ancestry. A primary sample of 361 individuals and a replication sample of 292 individuals were evaluated for asthma phenotypes according to a standardized protocol. A genome-wide screen has been completed using 292 autosomal and three X-Y pseudoautosomal markers. Using the semi-parametric likelihood ratio chi2 test and the transmission-disequilibrium test, we identified 12 markers in 10 regions that showed possible linkage to asthma or an associated phenotype (likelihood ratio P < 0.01). Markers in four regions (5q23-31, 12q15-24.1, 19q13 and 21q21) showed possible linkage in both the primary and replication samples and have also shown linkage to asthma phenotypes in other samples; two adjacent markers in one additional region (3p24.2-22) showing possible linkage is reported for the first time in the Hutterites. The results suggest that even in founder populations with a relatively small number of independent genomes, susceptibility alleles at many loci may influence asthma phenotypes and that these susceptibility alleles are likely to be common polymorphisms in the population.
ESTHER : Ober_1998_Hum.Mol.Genet_7_1393
PubMedSearch : Ober_1998_Hum.Mol.Genet_7_1393
PubMedID: 9700192
Gene_locus related to this paper: human-PLA2G7

Title : Identification of polymorphic simple sequence repeats in the genome of the zebrafish - Goff_1992_Genomics_14_200
Author(s) : Goff DJ , Galvin K , Katz H , Westerfield M , Lander ES , Tabin CJ
Ref : Genomics , 14 :200 , 1992
Abstract : The zebrafish has drawn a great deal of attention as a developmental system because it offers the ability to combine excellent embryology and genetics. Here, we report that simple sequence repeats are abundant in the zebrafish genome and are highly polymorphic between two outbred lines, making them useful markers for the construction of a genetic map of this organism.
ESTHER : Goff_1992_Genomics_14_200
PubMedSearch : Goff_1992_Genomics_14_200
PubMedID: 1427829