Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly
Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are theref...
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PUBLIC LIBRARY SCIENCE
2019
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Online Access: | https://epic.awi.de/id/eprint/49843/ https://epic.awi.de/id/eprint/49843/2/journalpone0216966.pdf https://doi.org/10.1371/journal.pone.0216966 https://hdl.handle.net/10013/epic.35cbeb05-050d-4140-a6ca-0cc3d5bf0c66 https://hdl.handle.net/ |
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ftawi:oai:epic.awi.de:49843 2023-05-15T17:05:09+02:00 Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly Zimmermann, Heike Harms, Lars Epp, Laura Mewes, Nick Bernhardt, Nadine Kruse, Stefan Stoof-Leichsenring, Kathleen Pestryakova, Luidmila A. Wieczorek, Mareike Trense, Daronja Herzschuh, Ulrike 2019-07-10 application/pdf https://epic.awi.de/id/eprint/49843/ https://epic.awi.de/id/eprint/49843/2/journalpone0216966.pdf https://doi.org/10.1371/journal.pone.0216966 https://hdl.handle.net/10013/epic.35cbeb05-050d-4140-a6ca-0cc3d5bf0c66 https://hdl.handle.net/ unknown PUBLIC LIBRARY SCIENCE https://epic.awi.de/id/eprint/49843/2/journalpone0216966.pdf https://hdl.handle.net/ Zimmermann, H. orcid:0000-0002-0225-5176 , Harms, L. orcid:0000-0001-7620-0613 , Epp, L. orcid:0000-0002-2230-9477 , Mewes, N. , Bernhardt, N. , Kruse, S. orcid:0000-0003-1107-1958 , Stoof-Leichsenring, K. orcid:0000-0002-6609-3217 , Pestryakova, L. A. , Wieczorek, M. orcid:0000-0002-3180-1607 , Trense, D. and Herzschuh, U. orcid:0000-0003-0999-1261 (2019) Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly , PLoS ONE, 14 (7), e0216966 . doi:10.1371/journal.pone.0216966 <https://doi.org/10.1371/journal.pone.0216966> , hdl:10013/epic.35cbeb05-050d-4140-a6ca-0cc3d5bf0c66 info:eu-repo/semantics/openAccess EPIC3PLoS ONE, PUBLIC LIBRARY SCIENCE, 14(7), pp. e0216966, ISSN: 1932-6203 Article isiRev info:eu-repo/semantics/article 2019 ftawi https://doi.org/10.1371/journal.pone.0216966 2022-06-19T23:12:19Z Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix. Article in Journal/Newspaper kolyma river taiga Taymyr Taymyr Peninsula Tundra Siberia Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) Kolyma ENVELOPE(161.000,161.000,69.500,69.500) Taymyr ENVELOPE(89.987,89.987,68.219,68.219) PLOS ONE 14 7 e0216966 |
institution |
Open Polar |
collection |
Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) |
op_collection_id |
ftawi |
language |
unknown |
description |
Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix. |
format |
Article in Journal/Newspaper |
author |
Zimmermann, Heike Harms, Lars Epp, Laura Mewes, Nick Bernhardt, Nadine Kruse, Stefan Stoof-Leichsenring, Kathleen Pestryakova, Luidmila A. Wieczorek, Mareike Trense, Daronja Herzschuh, Ulrike |
spellingShingle |
Zimmermann, Heike Harms, Lars Epp, Laura Mewes, Nick Bernhardt, Nadine Kruse, Stefan Stoof-Leichsenring, Kathleen Pestryakova, Luidmila A. Wieczorek, Mareike Trense, Daronja Herzschuh, Ulrike Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly |
author_facet |
Zimmermann, Heike Harms, Lars Epp, Laura Mewes, Nick Bernhardt, Nadine Kruse, Stefan Stoof-Leichsenring, Kathleen Pestryakova, Luidmila A. Wieczorek, Mareike Trense, Daronja Herzschuh, Ulrike |
author_sort |
Zimmermann, Heike |
title |
Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly |
title_short |
Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly |
title_full |
Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly |
title_fullStr |
Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly |
title_full_unstemmed |
Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly |
title_sort |
chloroplast and mitochondrial genetic variation of larches at the siberian tundra-taiga ecotone revealed by de novo assembly |
publisher |
PUBLIC LIBRARY SCIENCE |
publishDate |
2019 |
url |
https://epic.awi.de/id/eprint/49843/ https://epic.awi.de/id/eprint/49843/2/journalpone0216966.pdf https://doi.org/10.1371/journal.pone.0216966 https://hdl.handle.net/10013/epic.35cbeb05-050d-4140-a6ca-0cc3d5bf0c66 https://hdl.handle.net/ |
long_lat |
ENVELOPE(161.000,161.000,69.500,69.500) ENVELOPE(89.987,89.987,68.219,68.219) |
geographic |
Kolyma Taymyr |
geographic_facet |
Kolyma Taymyr |
genre |
kolyma river taiga Taymyr Taymyr Peninsula Tundra Siberia |
genre_facet |
kolyma river taiga Taymyr Taymyr Peninsula Tundra Siberia |
op_source |
EPIC3PLoS ONE, PUBLIC LIBRARY SCIENCE, 14(7), pp. e0216966, ISSN: 1932-6203 |
op_relation |
https://epic.awi.de/id/eprint/49843/2/journalpone0216966.pdf https://hdl.handle.net/ Zimmermann, H. orcid:0000-0002-0225-5176 , Harms, L. orcid:0000-0001-7620-0613 , Epp, L. orcid:0000-0002-2230-9477 , Mewes, N. , Bernhardt, N. , Kruse, S. orcid:0000-0003-1107-1958 , Stoof-Leichsenring, K. orcid:0000-0002-6609-3217 , Pestryakova, L. A. , Wieczorek, M. orcid:0000-0002-3180-1607 , Trense, D. and Herzschuh, U. orcid:0000-0003-0999-1261 (2019) Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly , PLoS ONE, 14 (7), e0216966 . doi:10.1371/journal.pone.0216966 <https://doi.org/10.1371/journal.pone.0216966> , hdl:10013/epic.35cbeb05-050d-4140-a6ca-0cc3d5bf0c66 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1371/journal.pone.0216966 |
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14 |
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7 |
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