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Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest

  • Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes ofSiberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.show moreshow less

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Author details:Luise SchulteORCiDGND, Nadine BernhardtORCiD, Kathleen Rosemarie Stoof-LeichsenringORCiDGND, Heike Hildegard ZimmermannORCiDGND, Luidmila Agafyevna PestryakovaORCiD, Laura S. EppORCiD, Ulrike HerzschuhORCiDGND
DOI:https://doi.org/10.1111/1755-0998.13311
ISSN:1755-098X
ISSN:1755-0998
Pubmed ID:https://pubmed.ncbi.nlm.nih.gov/33319428
Title of parent work (English):Molecular ecology resources
Publisher:Wiley
Place of publishing:Hoboken
Publication type:Article
Language:English
Date of first publication:2020/12/15
Publication year:2020
Release date:2023/03/27
Tag:Larix; chloroplast genome; hybridization capture; sediment core; sedimentary ancient DNA; target enrichment
Volume:21
Issue:3
Number of pages:15
First page:801
Last Page:815
Funding institution:European Research CouncilEuropean Research Council (ERC)European Commission [772852]; German Research FoundationGerman Research Foundation (DFG) [EP98/2-1]
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie
DDC classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Peer review:Referiert
Publishing method:Open Access / Hybrid Open-Access
License (German):License LogoCC-BY - Namensnennung 4.0 International
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