scholarly journals Hybridization capture of larch (Larix Mill) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forests

2020 ◽  
Author(s):  
Luise Schulte ◽  
Nadine Bernhardt ◽  
Kathleen R. Stoof-Leichsenring ◽  
Heike H. Zimmermann ◽  
Luidmila A. Pestryakova ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Sediment Cores ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Hybridization Capture ◽  
Chloroplast Genomes ◽  
Dna Metabarcoding ◽  
Long Range Pcr ◽  
Northern Russia ◽  
Genome Scale

AbstractSiberian 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 the 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 up to 6700 years in age from the Taymyr region in northern Siberia. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborate 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 to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.

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

2020 ◽  
Author(s):  
Luise Schulte ◽  
Nadine Bernhardt ◽  
Kathleen Stoof-Leichsenring ◽  
Heike Zimmermann ◽  
Luidmila Pestryakova ◽  
...  
Keyword(s):  
Lake Sediment ◽  
Ancient Dna ◽  
Sediment Cores ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Hybridization Capture ◽  
Chloroplast Genomes ◽  
Long Range Pcr ◽  
Northern Russia ◽  
Genome Scale

<p>Siberian larch (<em>Larix</em> Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the earth. To be able to predict future responses of these forests to a changing climate, it is important to understand also past dynamics of larch populations. One well-preserved archive to study vegetation changes of the past is sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores. We studied a lake sediment core covering 6700 calibrated years BP, from the Taymyr region in northern Siberia. To enrich the sedaDNA for DNA of our focal species <em>Larix</em>, we combine shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete <em>Larix</em> chloroplast genome. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes of <em>Larix</em>. Variation in the chloroplast reads confirm an invasion of <em>Larix gmelinii</em> into the range of <em>Larix sibirica</em> before 6700 years ago. In this time span, both species can be detected at the site, although larch populations have decreased from a forested area to a single-tree tundra at present. This study demonstrates for the first time that hybridization capture applied to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.</p>

Hybridization capture of Larix candidate adaptive genes from sedimentary ancient DNA.

2021 ◽  
Author(s):  
Stefano Meucci ◽  
Luise Schulte ◽  
Kathleen R. Stoof-Leichsenring ◽  
Stefan Kruse ◽  
Konstantin Krutovsky ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Environmental Changes ◽  
Genetic Material ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Adaptive Genetic Variation ◽  
Hybridization Capture ◽  
Sequencing Method ◽  
Larch Species

<p>Siberian larch forests dominate large areas of northern Russia and contribute important roles for the world´s ecosystem. In order to understand the past dynamics of larches and their adaptive genetic variation, sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores is a crucial source of genetic material. The difficulty of retrieving extremely rare DNA sequences from samples reaching back up to 25000 years in age, is challenging. Previous studies (Schulte et al.) showed that the hybridization capture allowed an enrichment of targeted sequences by several orders of magnitude in comparison to shotgun sequencing method. Therefore, we established for the first time, a hybridization capture method targeting 65 candidate adaptive genes laying on the Larix nuclear genome. Our preliminary results showed the ability of our newly established method to enrich extremely rare DNA sequences of the targeted Larix candidate adaptive genes, which were not retrieved by shotgun sequencing method applied on the same samples. Furthermore, the results allowed to detect and compare specific nucleotide polymorphism of adaptive candidate genes among sedaDNA samples distributed in space and time. The establishment of this new method is laying the basis to investigate possible adaptive variation of larch species acquired across the dry and cold conditions of the Last Glacial Maximum (LGM); as well as their possible advantages or disadvantages in relation to the current environmental changes toward dry and warm conditions.</p>

Fungi and plant co-variation in Arctic Siberia inferred from sedimentary ancient DNA metabarcoding during the last 45.000 years

2021 ◽  
Author(s):  
Barbara von Hippel ◽  
Kathleen R. Stoof-Leichsenring ◽  
Luise Schulte ◽  
Peter Seeber ◽  
Laura S. Epp ◽  
...  
Keyword(s):  
Climate Change ◽  
Ancient Dna ◽  
Mycorrhizal Fungi ◽  
Vegetation Change ◽  
Sediment Cores ◽  
Siberian Larch ◽  
Biotic Interactions ◽  
Arctic Ecosystems ◽  
Arctic Regions ◽  
Arctic Siberia

<p>Climate change has a great impact on boreal ecosystems including Siberian larch forests. As a consequence of warming, larch grow is possible in areas where climate used to be too cold, leading to a shift of the tree line into more arctic regions. Most plants co-exist in symbiosis with heterotrophic organisms surrounding their root system. In arctic ecosystems, mycorrhizal fungi are a prerequisite for plant establishment and survival because they support nutrient uptake from nutrient-poor soils and maintain the water supply. Until now, however, knowledge about the co-variation of vegetation and fungi is poor. Certainly, the understanding of dynamic changes in biotic interactions is important to understand adaptation mechanisms of ecosystems to climate change.</p><p>We investigated sedimentary ancient DNA from Lake Levinson Lessing, Taymyr Peninsula (Arctic Siberia, tundra), Lake Lama, Lake Kyutyunda (both northern Siberia, tundra-taiga transition zone) and Lake Bolshoe Toko (southern Siberia, forest area) covering the last about 45.000 years using ITS primers for fungi along with the chloroplast P6 loop marker for vegetation metabarcoding. We found changes in the fungal communities that are in broad agreement with vegetation turnover. To our knowledge, this is the first broad ecological study on lake sediment cores to analyze fungal biodiversity in relation to vegetation change on millennial time scales.</p>

scholarly journals Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel

2016 ◽  
Vol 17 (2) ◽  
pp. 300-313 ◽  
Author(s):  
Elmira Mohandesan ◽  
Camilla F. Speller ◽  
Joris Peters ◽  
Hans-Peter Uerpmann ◽  
Margarethe Uerpmann ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Dna Analysis ◽  
Shotgun Sequencing ◽  
Dromedary Camel ◽  
Hybridization Capture ◽  
Ancient Dna Analysis

scholarly journals Long-fragment targeted capture for long read sequencing of plastomes

2018 ◽  
Author(s):  
Kevin Bethune ◽  
Cédric Mariac ◽  
Marie Couderc ◽  
Nora Scarcelli ◽  
Sylvian Santoni ◽  
...  
Keyword(s):  
Cost Effective ◽  
Hybridization Capture ◽  
Third Generation Sequencing ◽  
Chloroplast Genomes ◽  
Palm Species ◽  
Long Read ◽  
Enrichment Rate ◽  
Targeted Capture ◽  
Long Range Pcr ◽  
Generation Sequencing

Third generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities to better study biodiversity, phylogeography and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete chloroplast genomes. The protocol uses cost effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silicagel dried leaves. Our protocol successfully captured long read chloroplast fragments (up to 4264 bp median) with an enrichment rate ranging from 15% to 98%. DNA extracted from silicagel dried leaves led to low quality plastome assemblies when compared to freshly extracted DNA. Our protocol could also be generalized to capture long sequences from specific nuclear fragments.

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

Authorea ◽  
2020 ◽  
Author(s):  
Luise Schulte ◽  
Nadine Bernhardt ◽  
Heike Zimmermann ◽  
Kathleen Stoof Leichsenring ◽  
Luidmila Pestryakova ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Hybridization Capture ◽  
Chloroplast Genomes

scholarly journals Long-fragment targeted capture for long read sequencing of plastomes

2018 ◽  
Author(s):  
Kevin Bethune ◽  
Cédric Mariac ◽  
Marie Couderc ◽  
Nora Scarcelli ◽  
Sylvian Santoni ◽  
...  
Keyword(s):  
Cost Effective ◽  
Hybridization Capture ◽  
Third Generation Sequencing ◽  
Chloroplast Genomes ◽  
Palm Species ◽  
Long Read ◽  
Enrichment Rate ◽  
Targeted Capture ◽  
Long Range Pcr ◽  
Generation Sequencing

Third generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities to better study biodiversity, phylogeography and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete chloroplast genomes. The protocol uses cost effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silicagel dried leaves. Our protocol successfully captured long read chloroplast fragments (up to 4264 bp median) with an enrichment rate ranging from 15% to 98%. DNA extracted from silicagel dried leaves led to low quality plastome assemblies when compared to freshly extracted DNA. Our protocol could also be generalized to capture long sequences from specific nuclear fragments.

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

2020 ◽  
Author(s):  
Luise Schulte ◽  
Nadine Bernhardt ◽  
Kathleen Stoof‐Leichsenring ◽  
Heike H. Zimmermann ◽  
Luidmila A. Pestryakova ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Hybridization Capture ◽  
Chloroplast Genomes

scholarly journals Ancient plant DNA, macro- and microfossil studies of the lake sediments from the High Arctic lake Tenndammen, Svalbard

2020 ◽  
Author(s):  
Anastasia Poliakova ◽  
Lena M. Håkansson ◽  
Anders Schomacker ◽  
Sandra Garces Pastor ◽  
Inger Greve Alsos
Keyword(s):  
Ancient Dna ◽  
Vegetation History ◽  
Sediment Cores ◽  
Local Environment ◽  
Plant Macrofossils ◽  
High Arctic ◽  
Arctic Ecosystems ◽  
Dna Metabarcoding ◽  
History Of ◽  
Shallow Water Body

<p>Ancient DNA metabarcoding applied together with the investigations of the plant macro-remains, pollen, spores and non-pollen palynomorphs (NPP), open new perspectives and give better taxonomical resolution, allowing to obtain more precise and specific data on the local environment conditions and their changes. So far, only three multiproxy studies that involve both molecular and palaeobotanical/palynological methods are available for the high Arctic archipelago Svalbard. We intend to contribute filling this gap. Therefore, a field trip to Svalbard was undertaken in September, 2019, and three sediment cores were retrieved from the Tenndammen lake (N 78°06.118; E 15°02.024, 7 m asl) which is a small and shallow water body (ca 2.5 m depth). The lake is located in the valley of Colesdalen, a well-known Svalbard’s biodiversity hot spots and a home for about seven to ten thermophilic plant species.</p><p>To investigate the Holocene to modern vegetation history of this place, the 85cm core Te2019 was chosen, it was described for lithology, X-rayed, µXRF-scanned, line-scan photographed with high resolution and sampled for sedaDNA, pollen, spores and NPP studies as well as for studies on plant macrofossils. Ten 14C AMS dates were taken in order to establish an age-depth model. The DNA record contains around 100 taxa, most findings of those are supported by pollen studies (Asteraceae, <em>Betula</em>, Brassicaceae, <em>Salix, Saxifraga, Vaccinium</em>/Ericaceae) and by spores (<em>Equisetum</em> and Bryophyta). In addition, various fungi spores were identified. Investigations of plant macro-remains well support findings of the aquatic (i.e. Warnstorfia fluitans) and terrestrial mosses (e.g. <em>Aulacomnium</em> conf. <em>turgidum, Bryum</em> spp., <em>Distichium capillaceum, Calliergon richardsonii, Scorpidium cossonii, Sphagnum</em> spp., <em>Rhizomnium</em> spp.). Besides, fragments of <em>Salix</em> and <em>Betula</em> leaves and fruit parts, various leaf, stem tissues and flower fragments of <em>Saxifraga</em> species were found within the samples from the same depths with the correspondence to DNA records. Three DNA zones (SvDNA 1 – SvDNA3) and  one subzone within the earliest zone (SvDNA-1a – SvDNA-1b) were established. Relations between DNA, pollen and macrofossil zones were studied. This study is performed within the “Future ArcTic Ecosystems” (FATE) research program: Initiative for investigation on drivers of diversity and future scenarios from ethnoecology, contemporary ecology and ancient DNA.</p>

scholarly journals Three Reagents for in-Solution Enrichment of Ancient Human DNA at More than a Million SNPs

2022 ◽  
Author(s):  
Nadin Rohland ◽  
Swapan Mallick ◽  
Matthew Mah ◽  
Robert M Maier ◽  
Nick J Patterson ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Cost Effective ◽  
Shotgun Sequencing ◽  
Joint Analysis ◽  
Nucleotide Polymorphisms ◽  
Data Types ◽  
Human Dna ◽  
Dna Libraries ◽  
Wide Range ◽  
Genome Scale

In-solution enrichment for hundreds of thousands of single nucleotide polymorphisms (SNPs) has been the source of >70% of all genome-scale ancient human DNA data published to date. This approach has made it possible to generate data for one to two orders of magnitude lower cost than random shotgun sequencing, making it economical to study ancient samples with low proportions of human DNA, and increasing the rate of conversion of sampled remains into working data thereby facilitating ethical stewardship of human remains. So far, nearly all ancient DNA data obtained using in-solution enrichment has been generated using a set of bait sequences targeting about 1.24 million SNPs (the 1240k reagent). These sequences were published in 2015, but synthesis of the reagent has been cost-effective for only a few laboratories. In 2021, two companies made available reagents that target the same core set of SNPs along with supplementary content. Here, we test the properties of the three reagents on a common set of 27 ancient DNA libraries across a range of richness of DNA content and percentages of human molecules. All three reagents are highly effective at enriching many hundreds of thousands of SNPs. For all three reagents and a wide range of conditions, one round of enrichment produces data that is as useful as two rounds when tens of millions of sequences are read out as is typical for such experiments. In our testing, the Twist Ancient DNA reagent produces the highest coverages, greatest uniformity on targeted positions, and almost no bias toward enriching one allele more than another relative to shotgun sequencing. Allelic bias in 1240k enrichment has made it challenging to carry out joint analysis of these data with shotgun data, creating a situation where the ancient DNA community has been publishing two important bodes of data that cannot easily be co-analyzed by population genetic methods. To address this challenge, we introduce a subset of hundreds of thousands of SNPs for which 1240k data can be effectively co-analyzed with all other major data types.

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