Volff JN

References (6)

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 : Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle - Chen_2014_Nat.Genet_46_253
Author(s) : Chen S , Zhang G , Shao C , Huang Q , Liu G , Zhang P , Song W , An N , Chalopin D , Volff JN , Hong Y , Li Q , Sha Z , Zhou H , Xie M , Yu Q , Liu Y , Xiang H , Wang N , Wu K , Yang C , Zhou Q , Liao X , Yang L , Hu Q , Zhang J , Meng L , Jin L , Tian Y , Lian J , Yang J , Miao G , Liu S , Liang Z , Yan F , Li Y , Sun B , Zhang H , Zhu Y , Du M , Zhao Y , Schartl M , Tang Q , Wang J
Ref : Nat Genet , 46 :253 , 2014
Abstract : Genetic sex determination by W and Z chromosomes has developed independently in different groups of organisms. To better understand the evolution of sex chromosomes and the plasticity of sex-determination mechanisms, we sequenced the whole genomes of a male (ZZ) and a female (ZW) half-smooth tongue sole (Cynoglossus semilaevis). In addition to insights into adaptation to a benthic lifestyle, we find that the sex chromosomes of these fish are derived from the same ancestral vertebrate protochromosome as the avian W and Z chromosomes. Notably, the same gene on the Z chromosome, dmrt1, which is the male-determining gene in birds, showed convergent evolution of features that are compatible with a similar function in tongue sole. Comparison of the relatively young tongue sole sex chromosomes with those of mammals and birds identified events that occurred during the early phase of sex-chromosome evolution. Pertinent to the current debate about heterogametic sex-chromosome decay, we find that massive gene loss occurred in the wake of sex-chromosome 'birth'.
ESTHER : Chen_2014_Nat.Genet_46_253
PubMedSearch : Chen_2014_Nat.Genet_46_253
PubMedID: 24487278
Gene_locus related to this paper: cynse-a0a3p8wch2 , cynse-a0a3p8vd14 , cynse-a0a3p8w747 , cynse-a0a3p8wq40 , cynse-a0a3p8wul3 , cynse-a0a3p8vqr4 , cynse-a0a3p8vmz4

Title : The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates - Berthelot_2014_Nat.Commun_5_3657
Author(s) : Berthelot C , Brunet F , Chalopin D , Juanchich A , Bernard M , Noel B , Bento P , Da Silva C , Labadie K , Alberti A , Aury JM , Louis A , Dehais P , Bardou P , Montfort J , Klopp C , Cabau C , Gaspin C , Thorgaard GH , Boussaha M , Quillet E , Guyomard R , Galiana D , Bobe J , Volff JN , Genet C , Wincker P , Jaillon O , Roest Crollius H , Guiguen Y
Ref : Nat Commun , 5 :3657 , 2014
Abstract : Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions.
ESTHER : Berthelot_2014_Nat.Commun_5_3657
PubMedSearch : Berthelot_2014_Nat.Commun_5_3657
PubMedID: 24755649
Gene_locus related to this paper: oncmy-a0a060yri0 , oncmy-a0a060.1 , oncmy-a0a060.2 , oncmy-a0a060wwk7 , oncmy-a0a060wr62 , oncmy-a0a060wae0 , oncmy-a0a060wcy0 , oncmy-a0a060wwk2 , oncmy-a0a060wxj2 , oncmy-a0a060y4g9 , oncmy-a0a060w9c6 , oncmy-a0a060y4c5 , oncmy-a0a060yjg0 , oncmy-a0a060yqr9 , oncmy-a0a060w5s8 , oncmy-a0a060vy20 , oncmy-a0a060w006 , oncmy-a0a060y788 , oncmy-a0a060yt95 , oncmy-a0a060xce0 , oncmy-a0a060yqu0 , oncmy-a0a060xjp0 , oncmy-a0a060xym5 , oncmy-a0a060xqc7 , oncmy-a0a060xjn9 , oncmy-a0a060wwr6 , oncmy-a0a060xgb0 , oncmy-a0a060xey2 , oncmy-a0a060yle3 , oncmy-a0a060y6u5

Title : The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits - Schartl_2013_Nat.Genet_45_567
Author(s) : Schartl M , Walter RB , Shen Y , Garcia T , Catchen J , Amores A , Braasch I , Chalopin D , Volff JN , Lesch KP , Bisazza A , Minx P , Hillier L , Wilson RK , Fuerstenberg S , Boore J , Searle S , Postlethwait JH , Warren WC
Ref : Nat Genet , 45 :567 , 2013
Abstract : Several attributes intuitively considered to be typical mammalian features, such as complex behavior, live birth and malignant disease such as cancer, also appeared several times independently in lower vertebrates. The genetic mechanisms underlying the evolution of these elaborate traits are poorly understood. The platyfish, X. maculatus, offers a unique model to better understand the molecular biology of such traits. We report here the sequencing of the platyfish genome. Integrating genome assembly with extensive genetic maps identified an unexpected evolutionary stability of chromosomes in fish, in contrast to in mammals. Genes associated with viviparity show signatures of positive selection, identifying new putative functional domains and rare cases of parallel evolution. We also find that genes implicated in cognition show an unexpectedly high rate of duplicate gene retention after the teleost genome duplication event, suggesting a hypothesis for the evolution of the behavioral complexity in fish, which exceeds that found in amphibians and reptiles.
ESTHER : Schartl_2013_Nat.Genet_45_567
PubMedSearch : Schartl_2013_Nat.Genet_45_567
PubMedID: 23542700
Gene_locus related to this paper: xipma-m4a796 , xipma-a0a3b5r0c8 , xipma-m3zmg6 , xipma-m3zml4 , xipma-m4a704 , xipma-a0a3b5r3p5 , xipma-a0a3b5rfa0 , xipma-m3zns4 , xipma-m4a5i1 , xipma-m3zxe7 , xipma-a0a3b5r7u3 , xipma-m3zyp9 , xipma-m4a7a2 , xipma-m4a1z8 , xipma-a0a3b5qbj2 , xipma-m4azu0 , xipma-a0a3b5q4l7

Title : Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate - Denoeud_2010_Science_330_1381
Author(s) : Denoeud F , Henriet S , Mungpakdee S , Aury JM , Da Silva C , Brinkmann H , Mikhaleva J , Olsen LC , Jubin C , Canestro C , Bouquet JM , Danks G , Poulain J , Campsteijn C , Adamski M , Cross I , Yadetie F , Muffato M , Louis A , Butcher S , Tsagkogeorga G , Konrad A , Singh S , Jensen MF , Huynh Cong E , Eikeseth-Otteraa H , Noel B , Anthouard V , Porcel BM , Kachouri-Lafond R , Nishino A , Ugolini M , Chourrout P , Nishida H , Aasland R , Huzurbazar S , Westhof E , Delsuc F , Lehrach H , Reinhardt R , Weissenbach J , Roy SW , Artiguenave F , Postlethwait JH , Manak JR , Thompson EM , Jaillon O , Du Pasquier L , Boudinot P , Liberles DA , Volff JN , Philippe H , Lenhard B , Roest Crollius H , Wincker P , Chourrout D
Ref : Science , 330 :1381 , 2010
Abstract : Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.
ESTHER : Denoeud_2010_Science_330_1381
PubMedSearch : Denoeud_2010_Science_330_1381
PubMedID: 21097902
Gene_locus related to this paper: oikdi-ACHE , oikdi-cholike.1 , oikdi-cholike.2 , oikdi-e4wug8 , oikdi-e4ww04 , oikdi-e4wxm9 , oikdi-e4x0y9 , oikdi-e4x1t6 , oikdi-e4x2c7.1 , oikdi-e4x2c7.2 , oikdi-e4x4v7 , oikdi-e4x5i7 , oikdi-e4x5s6 , oikdi-e4x6c7 , oikdi-e4x6i0 , oikdi-e4x7y6 , oikdi-e4xa91 , oikdi-e4xe86 , oikdi-e4xeg3 , oikdi-e4xgg8 , oikdi-e4xiw0 , oikdi-e4xk51 , oikdi-e4xl53 , oikdi-e4xm24 , oikdi-e4xm43 , oikdi-e4xn79 , oikdi-e4xp62 , oikdi-e4xpy1 , oikdi-e4xqm4 , oikdi-e4xtm1 , oikdi-e4xug7 , oikdi-e4xv59 , oikdi-e4xw55 , oikdi-e4xwt6 , oikdi-e4xxh8 , oikdi-e4y5n1 , oikdi-e4y7j8 , oikdi-e4y8s7 , oikdi-e4ya76 , oikdi-e4ydw0 , oikdi-e4yi65 , oikdi-e4yp15 , oikdi-e4yp69 , oikdi-e4yst1 , oikdi-e4yvr0 , oikdi-e4yvu0 , oikdi-e4x630 , oikdi-e4ykb2 , oikdi-e4wt97 , oikdi-e4ws23

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