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  4. Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina  (Brassicaceae)
 
research article

Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina  (Brassicaceae)

Rogivue, Aude
•
Choudhury, Rimjhim R.
•
Zoller, Stefan
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January 13, 2019
Molecular Ecology Resources

Advances 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.

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Type
research article
DOI
10.1111/1755-0998.12991
Author(s)
Rogivue, Aude
Choudhury, Rimjhim R.
Zoller, Stefan
Joost, Stéphane  
Felber, François
Kasser, Michel
Parisod, Christian
Gugerli, Felix
Date Issued

2019-01-13

Published in
Molecular Ecology Resources
Volume

19

Issue

3

Start page

773

End page

787

Subjects

Arabis alpina

•

Genome‐wide diversity

•

Linkage disequilibrium

•

Single‐nucleotide polymorphisms

•

Transposable elements

•

Genescale

•

Vaud Prealps

URL

Molecular Ecology Resources website

https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12991
Editorial or Peer reviewed

REVIEWED

Written at

OTHER

EPFL units
LASIG  
Available on Infoscience
April 11, 2019
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/155994
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