Atlas of telomeric repeat diversity in Arabidopsis thaliana.
Arabidopsis
Long reads
Satellite repeats
Telomere
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
16 Sep 2024
16 Sep 2024
Historique:
received:
29
01
2024
accepted:
03
09
2024
medline:
17
9
2024
pubmed:
17
9
2024
entrez:
16
9
2024
Statut:
epublish
Résumé
Telomeric repeat arrays at the ends of chromosomes are highly dynamic in composition, but their repetitive nature and technological limitations have made it difficult to assess their true variation in genome diversity surveys. We have comprehensively characterized the sequence variation immediately adjacent to the canonical telomeric repeat arrays at the very ends of chromosomes in 74 genetically diverse Arabidopsis thaliana accessions. We first describe several types of distinct telomeric repeat units and then identify evolutionary processes such as local homogenization and higher-order repeat formation that shape diversity of chromosome ends. By comparing largely isogenic samples, we also determine repeat number variation of the degenerate and variant telomeric repeat array at both the germline and somatic levels. Finally, our analysis of haplotype structure uncovers chromosome end-specific patterns in the distribution of variant telomeric repeats, and their linkage to the more proximal non-coding region. Our findings illustrate the spectrum of telomeric repeat variation at multiple levels in A. thaliana-in germline and soma, across all chromosome ends, and across genetic groups-thereby expanding our knowledge of the evolution of chromosome ends.
Sections du résumé
BACKGROUND
BACKGROUND
Telomeric repeat arrays at the ends of chromosomes are highly dynamic in composition, but their repetitive nature and technological limitations have made it difficult to assess their true variation in genome diversity surveys.
RESULTS
RESULTS
We have comprehensively characterized the sequence variation immediately adjacent to the canonical telomeric repeat arrays at the very ends of chromosomes in 74 genetically diverse Arabidopsis thaliana accessions. We first describe several types of distinct telomeric repeat units and then identify evolutionary processes such as local homogenization and higher-order repeat formation that shape diversity of chromosome ends. By comparing largely isogenic samples, we also determine repeat number variation of the degenerate and variant telomeric repeat array at both the germline and somatic levels. Finally, our analysis of haplotype structure uncovers chromosome end-specific patterns in the distribution of variant telomeric repeats, and their linkage to the more proximal non-coding region.
CONCLUSIONS
CONCLUSIONS
Our findings illustrate the spectrum of telomeric repeat variation at multiple levels in A. thaliana-in germline and soma, across all chromosome ends, and across genetic groups-thereby expanding our knowledge of the evolution of chromosome ends.
Identifiants
pubmed: 39285474
doi: 10.1186/s13059-024-03388-3
pii: 10.1186/s13059-024-03388-3
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
244Subventions
Organisme : Novo Nordisk Fonden
ID : Novozymes Prize
Informations de copyright
© 2024. The Author(s).
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