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Sökning: onr:"swepub:oai:DiVA.org:uu-351064" > Natural selection b...

  • Craig, Rory J.Uppsala universitet,Evolutionsbiologi,Univ Edinburgh, Sch Biol Sci, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland. (författare)

Natural selection beyond genes : Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)

  • Artikel/kapitelEngelska2018

Förlag, utgivningsår, omfång ...

  • 2018-01-09
  • WILEY,2018
  • electronicrdacarrier

Nummerbeteckningar

  • LIBRIS-ID:oai:DiVA.org:uu-351064
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-351064URI
  • https://doi.org/10.1111/mec.14462DOI

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  • Språk:engelska
  • Sammanfattning på:engelska

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  • Ämneskategori:ref swepub-contenttype
  • Ämneskategori:art swepub-publicationtype

Anmärkningar

  • It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence are particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts. We report that similar to 6.6% of the collared flycatcher genome (74.0Mb) is spanned by similar to 1.28 million CEs, a higher proportion of the genome but a lower total amount of conserved sequence than has been reported in mammals. We identified >200,000 CEs specific to either the archosaur, avian, neoavian or passeridan lineages, constituting candidates for lineage-specific adaptations. Importantly, no less than similar to 71% of CE sites were nonexonic (52.6Mb), and conserved nonexonic sequence density was negatively correlated with functional exonic density at local genomic scales. Additionally, nucleotide diversity was strongly reduced at nonexonic conserved sites (0.00153) relative to intergenic nonconserved sites (0.00427). By integrating deep transcriptome sequencing and additional genome annotation, we identified novel protein-coding genes, long noncoding RNA genes and transposon-derived (exapted) CEs. The approach taken here based on the use of a progressive cactus whole-genome alignment to identify CEs should be readily applicable to nonmodel organisms in general and help to reveal the rich repertoire of putatively functional noncoding sequence as targets for selection.

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Biuppslag (personer, institutioner, konferenser, titlar ...)

  • Suh, AlexanderUppsala universitet,Evolutionsbiologi(Swepub:uu)alesu519 (författare)
  • Wang, MiUppsala universitet,Evolutionsbiologi(Swepub:uu)miawa118 (författare)
  • Ellegren, HansUppsala universitet,Evolutionsbiologi(Swepub:uu)hanselle (författare)
  • Uppsala universitetEvolutionsbiologi (creator_code:org_t)

Sammanhörande titlar

  • Ingår i:Molecular Ecology: WILEY27:2, s. 476-4920962-10831365-294X

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Av författaren/redakt...
Craig, Rory J.
Suh, Alexander
Wang, Mi
Ellegren, Hans
Om ämnet
NATURVETENSKAP
NATURVETENSKAP
och Biologi
och Evolutionsbiolog ...
Artiklar i publikationen
Molecular Ecolog ...
Av lärosätet
Uppsala universitet

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Rory_J_Craig
Craig, Rory J.
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