000265252 001__ 265252
000265252 005__ 20190630102129.0
000265252 0247_ $$2doi$$a10.1111/1755-0998.12991
000265252 02470 $$2DOI$$a10.1111/1755-0998.12991
000265252 037__ $$aARTICLE
000265252 245__ $$aGenome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina  (Brassicaceae)
000265252 260__ $$c2019-01-13
000265252 269__ $$a2019-01-13
000265252 336__ $$aJournal Articles
000265252 520__ $$aAdvances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e. presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population‐specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as non‐synonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented dataset, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.
000265252 542__ $$fCC BY-ND
000265252 6531_ $$aArabis alpina
000265252 6531_ $$aGenome‐wide diversity
000265252 6531_ $$aLinkage disequilibrium
000265252 6531_ $$aSingle‐nucleotide polymorphisms
000265252 6531_ $$aTransposable elements
000265252 6531_ $$aGenescale
000265252 6531_ $$aVaud Prealps
000265252 700__ $$aRogivue, Aude
000265252 700__ $$aChoudhury, Rimjhim R.
000265252 700__ $$aZoller, Stefan
000265252 700__ $$aJoost, Stéphane
000265252 700__ $$aFelber, François
000265252 700__ $$aKasser, Michel
000265252 700__ $$aParisod, Christian
000265252 700__ $$aGugerli, Felix
000265252 773__ $$j19$$tMolecular Ecology Resources$$k3$$q773-787
000265252 8560_ $$fstephane.joost@epfl.ch
000265252 85641 $$uhttps://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12991$$yMolecular Ecology Resources website
000265252 909CO $$particle$$pENAC$$ooai:infoscience.epfl.ch:265252
000265252 909C0 $$zCharbonnier, Valérie$$xU10244$$pLASIG$$mfrancois.golay@epfl.ch$$0252045
000265252 960__ $$astephane.joost@epfl.ch
000265252 961__ $$apierre.devaud@epfl.ch
000265252 973__ $$rREVIEWED$$sPUBLISHED$$aOTHER
000265252 980__ $$aARTICLE
000265252 981__ $$aoverwrite