Clarke L

References (7)

Title : A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin - Holt_2011_Genome.Biol.Evol_3_881
Author(s) : Holt DC , Holden MT , Tong SY , Castillo-Ramirez S , Clarke L , Quail MA , Currie BJ , Parkhill J , Bentley SD , Feil EJ , Giffard PM
Ref : Genome Biol Evol , 3 :881 , 2011
Abstract : Here we discuss the evolution of the northern Australian Staphylococcus aureus isolate MSHR1132 genome. MSHR1132 belongs to the divergent clonal complex 75 lineage. The average nucleotide divergence between orthologous genes in MSHR1132 and typical S. aureus is approximately sevenfold greater than the maximum divergence observed in this species to date. MSHR1132 has a small accessory genome, which includes the well-characterized genomic islands, nuSAalpha and nuSabeta, suggesting that these elements were acquired well before the expansion of the typical S. aureus population. Other mobile elements show mosaic structure (the prophage varphiSa3) or evidence of recent acquisition from a typical S. aureus lineage (SCCmec, ICE6013 and plasmid pMSHR1132). There are two differences in gene repertoire compared with typical S. aureus that may be significant clues as to the genetic basis underlying the successful emergence of S. aureus as a pathogen. First, MSHR1132 lacks the genes for production of staphyloxanthin, the carotenoid pigment that confers upon S. aureus its characteristic golden color and protects against oxidative stress. The lack of pigment was demonstrated in 126 of 126 CC75 isolates. Second, a mobile clustered regularly interspaced short palindromic repeat (CRISPR) element is inserted into orfX of MSHR1132. Although common in other staphylococcal species, these elements are very rare within S. aureus and may impact accessory genome acquisition. The CRISPR spacer sequences reveal a history of attempted invasion by known S. aureus mobile elements. There is a case for the creation of a new taxon to accommodate this and related isolates.
ESTHER : Holt_2011_Genome.Biol.Evol_3_881
PubMedSearch : Holt_2011_Genome.Biol.Evol_3_881
PubMedID: 21813488
Gene_locus related to this paper: staau-SA0897 , staau-SA2240

Title : Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype - Kingsley_2009_Genome.Res_19_2279
Author(s) : Kingsley RA , Msefula CL , Thomson NR , Kariuki S , Holt KE , Gordon MA , Harris D , Clarke L , Whitehead S , Sangal V , Marsh K , Achtman M , Molyneux ME , Cormican M , Parkhill J , MacLennan CA , Heyderman RS , Dougan G
Ref : Genome Res , 19 :2279 , 2009
Abstract : Whereas most nontyphoidal Salmonella (NTS) are associated with gastroenteritis, there has been a dramatic increase in reports of NTS-associated invasive disease in sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multilocus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, which currently is rarely reported outside of Africa. Whole-genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid. Further, there was evidence of genome degradation, including pseudogene formation and chromosomal deletions, when compared with other S. Typhimurium genome sequences. Some of this genome degradation involved genes previously implicated in virulence of S. Typhimurium or genes for which the orthologs in S. Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for microevolution and clonal replacement in the field.
ESTHER : Kingsley_2009_Genome.Res_19_2279
PubMedSearch : Kingsley_2009_Genome.Res_19_2279
PubMedID: 19901036
Gene_locus related to this paper: salen-OPDB , salti-q8z717 , salty-AES , salty-BIOH , salty-DLHH , salty-ENTF , salty-FES , salty-IROD , salty-IROE , salty-P74847 , salty-PLDB , salty-STM0332 , salty-STM4506 , salty-STY1441 , salty-STY2428 , salty-STY3846 , salty-yafa , salty-YBFF , salty-ycfp , salty-YFBB , salty-YHET , salty-YQIA

Title : Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa - Winstanley_2009_Genome.Res_19_12
Author(s) : Winstanley C , Langille MG , Fothergill JL , Kukavica-Ibrulj I , Paradis-Bleau C , Sanschagrin F , Thomson NR , Winsor GL , Quail MA , Lennard N , Bignell A , Clarke L , Seeger K , Saunders D , Harris D , Parkhill J , Hancock RE , Brinkman FS , Levesque RC
Ref : Genome Res , 19 :12 , 2009
Abstract : Pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. The identification of the Liverpool Epidemic Strain (LES) in a children's cystic fibrosis (CF) unit in 1996 and its subsequent observation in several centers in the United Kingdom challenged the previous widespread assumption that CF patients acquire only unique strains of P. aeruginosa from the environment. To learn about the forces that shaped the development of this important epidemic strain, the genome of the earliest archived LES isolate, LESB58, was sequenced. The sequence revealed the presence of many large genomic islands, including five prophage clusters, one defective (pyocin) prophage cluster, and five non-phage islands. To determine the role of these clusters, an unbiased signature tagged mutagenesis study was performed, followed by selection in the chronic rat lung infection model. Forty-seven mutants were identified by sequencing, including mutants in several genes known to be involved in Pseudomonas infection. Furthermore, genes from four prophage clusters and one genomic island were identified and in direct competition studies with the parent isolate; four were demonstrated to strongly impact on competitiveness in the chronic rat lung infection model. This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes.
ESTHER : Winstanley_2009_Genome.Res_19_12
PubMedSearch : Winstanley_2009_Genome.Res_19_12
PubMedID: 19047519
Gene_locus related to this paper: pseae-clipa , pseae-CPO , pseae-llipa , pseae-metx , pseae-PA0201 , pseae-PA0231 , pseae-PA0308 , pseae-PA0368 , pseae-PA0480 , pseae-PA0502 , pseae-PA0543 , pseae-PA0599 , pseae-PA1166 , pseae-PA1291 , pseae-PA1304 , pseae-PA1510 , pseae-PA1558 , pseae-PA1597 , pseae-PA1907 , pseae-PA2086 , pseae-PA2098 , pseae-PA2302 , pseae-PA2425 , pseae-PA2451 , pseae-PA2540 , pseae-PA2682 , pseae-PA2689 , pseae-PA2745 , pseae-PA2764 , pseae-PA2927 , pseae-PA2934 , pseae-PA2949 , pseae-PA3132 , pseae-PA3301 , pseae-PA3324 , pseae-PA3327 , pseae-PA3429 , pseae-PA3586 , pseae-PA3628 , pseae-PA3695 , pseae-PA3859 , pseae-PA3994 , pseae-PA4152 , pseae-PA4968 , pseae-PA5080 , pseae-PCHC , pseae-PCHF , pseae-PHAC2 , pseae-phaD , pseae-phag , pseae-Q9APW4 , pseae-rhla , pseae-q9i252

Title : Genome analysis of the platypus reveals unique signatures of evolution - Warren_2008_Nature_453_175
Author(s) : Warren WC , Hillier LW , Marshall Graves JA , Birney E , Ponting CP , Grutzner F , Belov K , Miller W , Clarke L , Chinwalla AT , Yang SP , Heger A , Locke DP , Miethke P , Waters PD , Veyrunes F , Fulton L , Fulton B , Graves T , Wallis J , Puente XS , Lopez-Otin C , Ordonez GR , Eichler EE , Chen L , Cheng Z , Deakin JE , Alsop A , Thompson K , Kirby P , Papenfuss AT , Wakefield MJ , Olender T , Lancet D , Huttley GA , Smit AF , Pask A , Temple-Smith P , Batzer MA , Walker JA , Konkel MK , Harris RS , Whittington CM , Wong ES , Gemmell NJ , Buschiazzo E , Vargas Jentzsch IM , Merkel A , Schmitz J , Zemann A , Churakov G , Kriegs JO , Brosius J , Murchison EP , Sachidanandam R , Smith C , Hannon GJ , Tsend-Ayush E , McMillan D , Attenborough R , Rens W , Ferguson-Smith M , Lefevre CM , Sharp JA , Nicholas KR , Ray DA , Kube M , Reinhardt R , Pringle TH , Taylor J , Jones RC , Nixon B , Dacheux JL , Niwa H , Sekita Y , Huang X , Stark A , Kheradpour P , Kellis M , Flicek P , Chen Y , Webber C , Hardison R , Nelson J , Hallsworth-Pepin K , Delehaunty K , Markovic C , Minx P , Feng Y , Kremitzki C , Mitreva M , Glasscock J , Wylie T , Wohldmann P , Thiru P , Nhan MN , Pohl CS , Smith SM , Hou S , Nefedov M , de Jong PJ , Renfree MB , Mardis ER , Wilson RK
Ref : Nature , 453 :175 , 2008
Abstract : We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
ESTHER : Warren_2008_Nature_453_175
PubMedSearch : Warren_2008_Nature_453_175
PubMedID: 18464734
Gene_locus related to this paper: ornan-f6s0q0 , ornan-f6ty74 , ornan-f6u2k2 , ornan-f6uve1 , ornan-f6vpb6 , ornan-f6ybp3 , ornan-f7bgu8 , ornan-f7ct41 , ornan-f7cza1 , ornan-f7ejp8 , ornan-f7exu1 , ornan-f7f392 , ornan-f7f9y6 , ornan-f6ve87 , ornan-f7f1d9 , ornan-f6z3l1 , ornan-f6r3f9 , ornan-f6r3g8 , ornan-f6vs71 , ornan-f7g4v8

Title : Evolutionary and biomedical insights from the rhesus macaque genome - Gibbs_2007_Science_316_222
Author(s) : Gibbs RA , Rogers J , Katze MG , Bumgarner R , Weinstock GM , Mardis ER , Remington KA , Strausberg RL , Venter JC , Wilson RK , Batzer MA , Bustamante CD , Eichler EE , Hahn MW , Hardison RC , Makova KD , Miller W , Milosavljevic A , Palermo RE , Siepel A , Sikela JM , Attaway T , Bell S , Bernard KE , Buhay CJ , Chandrabose MN , Dao M , Davis C , Delehaunty KD , Ding Y , Dinh HH , Dugan-Rocha S , Fulton LA , Gabisi RA , Garner TT , Godfrey J , Hawes AC , Hernandez J , Hines S , Holder M , Hume J , Jhangiani SN , Joshi V , Khan ZM , Kirkness EF , Cree A , Fowler RG , Lee S , Lewis LR , Li Z , Liu YS , Moore SM , Muzny D , Nazareth LV , Ngo DN , Okwuonu GO , Pai G , Parker D , Paul HA , Pfannkoch C , Pohl CS , Rogers YH , Ruiz SJ , Sabo A , Santibanez J , Schneider BW , Smith SM , Sodergren E , Svatek AF , Utterback TR , Vattathil S , Warren W , White CS , Chinwalla AT , Feng Y , Halpern AL , Hillier LW , Huang X , Minx P , Nelson JO , Pepin KH , Qin X , Sutton GG , Venter E , Walenz BP , Wallis JW , Worley KC , Yang SP , Jones SM , Marra MA , Rocchi M , Schein JE , Baertsch R , Clarke L , Csuros M , Glasscock J , Harris RA , Havlak P , Jackson AR , Jiang H , Liu Y , Messina DN , Shen Y , Song HX , Wylie T , Zhang L , Birney E , Han K , Konkel MK , Lee J , Smit AF , Ullmer B , Wang H , Xing J , Burhans R , Cheng Z , Karro JE , Ma J , Raney B , She X , Cox MJ , Demuth JP , Dumas LJ , Han SG , Hopkins J , Karimpour-Fard A , Kim YH , Pollack JR , Vinar T , Addo-Quaye C , Degenhardt J , Denby A , Hubisz MJ , Indap A , Kosiol C , Lahn BT , Lawson HA , Marklein A , Nielsen R , Vallender EJ , Clark AG , Ferguson B , Hernandez RD , Hirani K , Kehrer-Sawatzki H , Kolb J , Patil S , Pu LL , Ren Y , Smith DG , Wheeler DA , Schenck I , Ball EV , Chen R , Cooper DN , Giardine B , Hsu F , Kent WJ , Lesk A , Nelson DL , O'Brien W E , Prufer K , Stenson PD , Wallace JC , Ke H , Liu XM , Wang P , Xiang AP , Yang F , Barber GP , Haussler D , Karolchik D , Kern AD , Kuhn RM , Smith KE , Zwieg AS
Ref : Science , 316 :222 , 2007
Abstract : The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.
ESTHER : Gibbs_2007_Science_316_222
PubMedSearch : Gibbs_2007_Science_316_222
PubMedID: 17431167
Gene_locus related to this paper: macmu-3neur , macmu-ACHE , macmu-BCHE , macmu-f6rul6 , macmu-f6sz31 , macmu-f6the6 , macmu-f6unj2 , macmu-f6wtx1 , macmu-f6zkq5 , macmu-f7aa58 , macmu-f7ai42 , macmu-f7aim4 , macmu-f7buk8 , macmu-f7cfi8 , macmu-f7cnr2 , macmu-f7cu68 , macmu-f7flv1 , macmu-f7ggk1 , macmu-f7hir7 , macmu-g7n054 , macmu-KANSL3 , macmu-TEX30 , macmu-Y4neur , macmu-g7n4x3 , macmu-i2cy02 , macmu-f7ba84 , macmu-CES2 , macmu-h9er02 , macmu-a0a1d5rbr3 , macmu-a0a1d5q4k5 , macmu-g7mxj6 , macmu-f7dn71 , macmu-f7hkw9 , macmu-f7hm08 , macmu-g7mke4 , macmu-a0a1d5rh04 , macmu-h9fud6 , macmu-f6qwx1 , macmu-f7h4t2 , macmu-h9zaw9 , macmu-f7h550 , macmu-a0a1d5q9w1 , macmu-f7gkb9 , macmu-f7hp78 , macmu-a0a1d5qvu5

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 genome sequence of Caenorhabditis briggsae: a platform for comparative genomics - Stein_2003_PLoS.Biol_1_E45
Author(s) : Stein LD , Bao Z , Blasiar D , Blumenthal T , Brent MR , Chen N , Chinwalla A , Clarke L , Clee C , Coghlan A , Coulson A , D'Eustachio P , Fitch DH , Fulton LA , Fulton RE , Griffiths-Jones S , Harris TW , Hillier LW , Kamath R , Kuwabara PE , Mardis ER , Marra MA , Miner TL , Minx P , Mullikin JC , Plumb RW , Rogers J , Schein JE , Sohrmann M , Spieth J , Stajich JE , Wei C , Willey D , Wilson RK , Durbin R , Waterston RH
Ref : PLoS Biol , 1 :E45 , 2003
Abstract : The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.
ESTHER : Stein_2003_PLoS.Biol_1_E45
PubMedSearch : Stein_2003_PLoS.Biol_1_E45
PubMedID: 14624247
Gene_locus related to this paper: caebr-a8wl70 , caebr-a8wm66 , caebr-a8wny7 , caebr-a8wpj6 , caebr-a8wpy7.1 , caebr-a8wq91 , caebr-a8wr10 , caebr-A8WSQ5 , caebr-a8wta1 , caebr-A8WTU9 , caebr-a8wux6 , caebr-A8WX49 , caebr-a8wxx0 , caebr-a8wyd4 , caebr-a8wye8 , caebr-a8wz10 , caebr-a8wz31.1 , caebr-a8wz31.2 , caebr-a8wz31.4 , caebr-a8wzp9 , caebr-a8wzr9.1 , caebr-a8wzr9.2 , caebr-a8wzs0 , caebr-a8wzs1 , caebr-a8x0r9 , caebr-a8x0z5 , caebr-a8x1l6 , caebr-a8x1r6 , caebr-a8x3t6 , caebr-a8x4h0 , caebr-a8x4u8 , caebr-a8x4w8 , caebr-a8x5l4 , caebr-a8x5l5 , caebr-a8x5r5 , caebr-a8x5s6 , caebr-a8x5t4 , caebr-a8x6s0 , caebr-a8x6s1 , caebr-a8x7d1 , caebr-a8x7h0 , caebr-a8x7v6 , caebr-A8X8P2 , caebr-a8x8q5 , caebr-a8x8y6 , caebr-a8x9s4 , caebr-a8x324.1 , caebr-a8x324.2 , caebr-a8x622 , caebr-a8xac7 , caebr-a8xag5 , caebr-a8xb07 , caebr-a8xb88 , caebr-a8xby0 , caebr-a8xdz0 , caebr-a8xf42 , caebr-a8xfd1 , caebr-a8xfe6 , caebr-a8xgi0 , caebr-a8xgz4 , caebr-a8xgz5 , caebr-a8xh38 , caebr-a8xhp8 , caebr-a8xhx9 , caebr-a8xjw4 , caebr-a8xk02 , caebr-a8xk46 , caebr-a8xk76 , caebr-a8xke1 , caebr-A8XLQ2 , caebr-a8xns2.1 , caebr-a8xns2.2 , caebr-a8xq21 , caebr-a8xub3 , caebr-a8xuc2 , caebr-a8xuc8 , caebr-a8xug3 , caebr-a8xuh6 , caebr-a8xui4 , caebr-a8xui5 , caebr-a8xui6 , caebr-a8xui7 , caebr-a8xum8 , caebr-a8y0h0.1 , caebr-a8y0h0.2 , caebr-a8y0h1.1 , caebr-a8y0h1.2 , caebr-a8y1b5 , caebr-a8y1r7 , caebr-a8y2v4 , caebr-a8y3e3 , caebr-a8y3i5 , caebr-a8y3j9 , caebr-a8y4p9 , caebr-a8y100 , caebr-a8y101 , caebr-ACHE1 , caebr-ACHE2 , caebr-ACHE3 , caebr-ACHE4 , caebr-b6ii84 , caebr-G01D9.5 , caebr-ges1e , caebr-a8y4l4 , caebr-A8Y1T9 , caebr-A8Y168 , caebr-A8Y0Z5 , caebr-A8XYQ5 , caebr-A8XXK4 , caebr-A8XWZ8 , caebr-A8XUF0 , caebr-A8XUB6 , caebr-A8XSV2 , caebr-A8XJ37 , caebr-A8XG15 , caebr-A8XFE8 , caebr-A8XEY7 , caebr-A8XEU8 , caebr-A8XDT6 , caebr-A8XDV3 , caebr-A8XDQ3 , caebr-A8XDK8 , caebr-A8XBW4 , caebr-A8XAG3 , caebr-A8X8H5 , caebr-A8X6Z9 , caebr-A8X6H9 , caebr-A8X629 , caebr-A8X438 , caebr-A8X4G2 , caebr-A8X4H8 , caebr-A8X4W2 , caebr-A8X3P4 , caebr-A8X3R1 , caebr-A8X2Z4 , caebr-A8X0N2 , caebr-A8X0B3 , caebr-A8WW80 , caebr-U483 , caebr-A8XPH6 , caebr-A8XNJ0 , caebr-A8XNA2 , caebr-A8XLP0 , caebr-A8XK33 , caebr-A8WTK6 , caebr-A8WU44 , caebr-A8WPJ2 , caebr-A8WNE5 , caebr-A8WMB3 , caebr-a8x1r2