Backstrom N

References (3)

Title : The genomic landscape of species divergence in Ficedula flycatchers - Ellegren_2012_Nature_491_756
Author(s) : Ellegren H , Smeds L , Burri R , Olason PI , Backstrom N , Kawakami T , Kunstner A , Makinen H , Nadachowska-Brzyska K , Qvarnstrom A , Uebbing S , Wolf JB
Ref : Nature , 491 :756 , 2012
Abstract : Unravelling the genomic landscape of divergence between lineages is key to understanding speciation. The naturally hybridizing collared flycatcher and pied flycatcher are important avian speciation models that show pre- as well as postzygotic isolation. We sequenced and assembled the 1.1-Gb flycatcher genome, physically mapped the assembly to chromosomes using a low-density linkage map and re-sequenced population samples of each species. Here we show that the genomic landscape of species differentiation is highly heterogeneous with approximately 50 'divergence islands' showing up to 50-fold higher sequence divergence than the genomic background. These non-randomly distributed islands, with between one and three regions of elevated divergence per chromosome irrespective of chromosome size, are characterized by reduced levels of nucleotide diversity, skewed allele-frequency spectra, elevated levels of linkage disequilibrium and reduced proportions of shared polymorphisms in both species, indicative of parallel episodes of selection. Proximity of divergence peaks to genomic regions resistant to sequence assembly, potentially including centromeres and telomeres, indicate that complex repeat structures may drive species divergence. A much higher background level of species divergence of the Z chromosome, and a lower proportion of shared polymorphisms, indicate that sex chromosomes and autosomes are at different stages of speciation. This study provides a roadmap to the emerging field of speciation genomics.
ESTHER : Ellegren_2012_Nature_491_756
PubMedSearch : Ellegren_2012_Nature_491_756
PubMedID: 23103876
Gene_locus related to this paper: fical-u3kcg8 , fical-u3jzm0 , fical-u3jdg9 , fical-u3k1a7 , fical-u3k5s8 , fical-u3k5t1

Title : The genome of a songbird - Warren_2010_Nature_464_757
Author(s) : Warren WC , Clayton DF , Ellegren H , Arnold AP , Hillier LW , Kunstner A , Searle S , White S , Vilella AJ , Fairley S , Heger A , Kong L , Ponting CP , Jarvis ED , Mello CV , Minx P , Lovell P , Velho TA , Ferris M , Balakrishnan CN , Sinha S , Blatti C , London SE , Li Y , Lin YC , George J , Sweedler J , Southey B , Gunaratne P , Watson M , Nam K , Backstrom N , Smeds L , Nabholz B , Itoh Y , Whitney O , Pfenning AR , Howard J , Volker M , Skinner BM , Griffin DK , Ye L , McLaren WM , Flicek P , Quesada V , Velasco G , Lopez-Otin C , Puente XS , Olender T , Lancet D , Smit AF , Hubley R , Konkel MK , Walker JA , Batzer MA , Gu W , Pollock DD , Chen L , Cheng Z , Eichler EE , Stapley J , Slate J , Ekblom R , Birkhead T , Burke T , Burt D , Scharff C , Adam I , Richard H , Sultan M , Soldatov A , Lehrach H , Edwards SV , Yang SP , Li X , Graves T , Fulton L , Nelson J , Chinwalla A , Hou S , Mardis ER , Wilson RK
Ref : Nature , 464 :757 , 2010
Abstract : The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.
ESTHER : Warren_2010_Nature_464_757
PubMedSearch : Warren_2010_Nature_464_757
PubMedID: 20360741
Gene_locus related to this paper: taegu-b5fyu7 , taegu-BCHE , taegu-h0z4h9 , taegu-h0z9w8 , taegu-h0zat6 , taegu-h0ze48 , taegu-h0zha8 , taegu-h0zkr8 , taegu-h0zqp3 , taegu-h0zz82 , taegu-h0zqs1 , taegu-h0yy64 , taegu-h0yv40 , taegu-h0yyt1 , taegu-h0zcc8 , taegu-h0z3k5 , taegu-h0yw95 , taegu-h0zkm7 , taegu-h1a198 , taegu-h0z6w2 , taegu-h0zl93 , taegu-h0zt33 , taegu-h0yp71 , taegu-h0ypu5 , taegu-h1a048 , taegu-h0ztq1 , fical-u3kau2 , 9pass-a0a093qu66 , taegu-h0z7g0 , fical-u3jnn0 , taegu-h0zb80 , taegu-h0zb89 , taegu-h0z994 , taegu-h0ztj6

Title : Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution - Hillier_2004_Nature_432_695
Author(s) : Hillier LW , Miller W , Birney E , Warren W , Hardison RC , Ponting CP , Bork P , Burt DW , Groenen MA , Delany ME , Dodgson JB , Chinwalla AT , Cliften PF , Clifton SW , Delehaunty KD , Fronick C , Fulton RS , Graves TA , Kremitzki C , Layman D , Magrini V , McPherson JD , Miner TL , Minx P , Nash WE , Nhan MN , Nelson JO , Oddy LG , Pohl CS , Randall-Maher J , Smith SM , Wallis JW , Yang SP , Romanov MN , Rondelli CM , Paton B , Smith J , Morrice D , Daniels L , Tempest HG , Robertson L , Masabanda JS , Griffin DK , Vignal A , Fillon V , Jacobbson L , Kerje S , Andersson L , Crooijmans RP , Aerts J , van der Poel JJ , Ellegren H , Caldwell RB , Hubbard SJ , Grafham DV , Kierzek AM , McLaren SR , Overton IM , Arakawa H , Beattie KJ , Bezzubov Y , Boardman PE , Bonfield JK , Croning MD , Davies RM , Francis MD , Humphray SJ , Scott CE , Taylor RG , Tickle C , Brown WR , Rogers J , Buerstedde JM , Wilson SA , Stubbs L , Ovcharenko I , Gordon L , Lucas S , Miller MM , Inoko H , Shiina T , Kaufman J , Salomonsen J , Skjoedt K , Ka-Shu Wong G , Wang J , Liu B , Yu J , Yang H , Nefedov M , Koriabine M , deJong PJ , Goodstadt L , Webber C , Dickens NJ , Letunic I , Suyama M , Torrents D , von Mering C , Zdobnov EM , Makova K , Nekrutenko A , Elnitski L , Eswara P , King DC , Yang S , Tyekucheva S , Radakrishnan A , Harris RS , Chiaromonte F , Taylor J , He J , Rijnkels M , Griffiths-Jones S , Ureta-Vidal A , Hoffman MM , Severin J , Searle SM , Law AS , Speed D , Waddington D , Cheng Z , Tuzun E , Eichler E , Bao Z , Flicek P , Shteynberg DD , Brent MR , Bye JM , Huckle EJ , Chatterji S , Dewey C , Pachter L , Kouranov A , Mourelatos Z , Hatzigeorgiou AG , Paterson AH , Ivarie R , Brandstrom M , Axelsson E , Backstrom N , Berlin S , Webster MT , Pourquie O , Reymond A , Ucla C , Antonarakis SE , Long M , Emerson JJ , Betran E , Dupanloup I , Kaessmann H , Hinrichs AS , Bejerano G , Furey TS , Harte RA , Raney B , Siepel A , Kent WJ , Haussler D , Eyras E , Castelo R , Abril JF , Castellano S , Camara F , Parra G , Guigo R , Bourque G , Tesler G , Pevzner PA , Smit A , Fulton LA , Mardis ER , Wilson RK
Ref : Nature , 432 :695 , 2004
Abstract : We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
ESTHER : Hillier_2004_Nature_432_695
PubMedSearch : Hillier_2004_Nature_432_695
PubMedID: 15592404
Gene_locus related to this paper: chick-a0a1d5pmd9 , chick-b3tzb3 , chick-BCHE , chick-cb043 , chick-d3wgl5 , chick-e1bsm0 , chick-e1bvq6 , chick-e1bwz0 , chick-e1bwz1 , chick-e1byn1 , chick-e1bz81 , chick-e1c0z8 , chick-e1c7p7 , chick-f1nby4 , chick-f1ncz8 , chick-f1ndp3 , chick-f1nep4 , chick-f1nj68 , chick-f1njg6 , chick-f1njk4 , chick-f1njs4 , chick-f1njs5 , chick-f1nk87 , chick-f1nmx9 , chick-f1ntp8 , chick-f1nvg7 , chick-f1nwf2 , chick-f1p1l1 , chick-f1p3j5 , chick-f1p4c6 , chick-f1p508 , chick-fas , chick-h9l0k6 , chick-nlgn1 , chick-NLGN3 , chick-q5f3h8 , chick-q5zhm0 , chick-q5zi81 , chick-q5zij5 , chick-q5zin0 , chick-thyro , chick-f1nrq2 , chick-e1byd4 , chick-e1c2h6 , chick-a0a1d5pk92 , chick-a0a1d5pzg7 , chick-f1nbc2 , chick-f1nf25 , chick-f1nly5 , chick-f1p4h5 , chick-f1nzi7 , chick-f1p5k3 , chick-f1nm35 , chick-a0a1d5pl11 , chick-a0a1d5pj73 , chick-f1nxu6 , chick-a0a1d5nwc0 , chick-e1bxs8 , chick-f1p2g7 , chick-f1nd96