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 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>

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 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.

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>

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 Comparison of target enrichment strategies for ancient pathogen DNA

2020 ◽  
Author(s):  
Anja Furtwängler ◽  
Judith Neukamm ◽  
Lisa Böhme ◽  
Ella Reiter ◽  
Melanie Vollstedt ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Treponema Pallidum ◽  
Mycobacterium Leprae ◽  
Target Enrichment ◽  
Hybridization Capture ◽  
Research Outcomes ◽  
Pathogen Dna ◽  
Different Characteristics ◽  
Rna And Dna ◽  
Better Than

AbstractIn ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA, and targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – (1) array-based hybridization capture and in-solution capture using either (2) RNA or (3) DNA baits – have different characteristics that may influence the capture efficiency, specificity, and reproducibility. Here, we compared their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum of 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens, and RNA baits usually perform better than DNA baits.Method summaryWe compared three targeted DNA enrichment strategies used in ancient DNA research for the specific enrichment of pathogen DNA regarding their efficiency, specificity, and reproducibility for ancient and modern Mycobacterium leprae and Treponema pallidum samples. Array-based capture and in-solution capture with RNA and DNA baits were all tested in three independent replicates.

scholarly journals Comparison of target enrichment strategies for ancient pathogen DNA

BioTechniques ◽  
2020 ◽  
Vol 69 (6) ◽  
pp. 455-459
Author(s):  
Anja Furtwängler ◽  
Judith Neukamm ◽  
Lisa Böhme ◽  
Ella Reiter ◽  
Melanie Vollstedt ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Treponema Pallidum ◽  
Mycobacterium Leprae ◽  
Capture Efficiency ◽  
Target Enrichment ◽  
Hybridization Capture ◽  
Research Outcomes ◽  
Pathogen Dna ◽  
Different Characteristics ◽  
Better Than

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – array-based hybridization capture and in-solution capture using either RNA or DNA baits – have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.

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 Ancient DNA and microfossils reveal dynamics of three harmful dinoflagellate species off Eastern Tasmania, Australia, over the last 9,000 years

2021 ◽  
Author(s):  
Linda Armbrecht ◽  
Bradley Paine ◽  
Christopher J.S. Bolch ◽  
Alan Cooper ◽  
Andrew McMinn ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Algal Blooms ◽  
Surface Sediments ◽  
Reference Sequence ◽  
List Type ◽  
Noctiluca Scintillans ◽  
Alexandrium Catenella ◽  
Hybridization Capture ◽  
Recent Climate ◽  
Gymnodinium Catenatum

AbstractHarmful algal blooms (HABs) have significantly impacted the seafood industry along the Tasmanian east coast over the past three decades, and are expected to change in frequency and magnitude due to climate change induced changing oceanographic conditions. To investigate the long-term history of regional HABs, a combination of palynological and sedimentary ancient DNA (sedaDNA) analyses was applied to marine sediment cores from inshore (up to 145 years old) and offshore (up to ~9,000 years) sites at Maria Island, southeast Tasmania. Analyses focused Paralytic Shellfish Toxin (PST) producing dinoflagellates Alexandrium catenella and Gymnodinium catenatum, and the red-tide dinoflagellate Noctiluca scintillans, which were specifically targeted using a hybridization capture sedaDNA technique. Identification of primulin-stained A. catenella cysts throughout the inshore sediment core, together with sedaDNA evidence of a bloom-phase of Alexandrium ~15 years ago, indicates recent stimulation of a cryptic endemic population. Morphologically similar but unstained Alexandrium cysts were observed throughout the offshore core, with sedaDNA confirming the presence of A. catenella from ~8,300 years ago to present. Gymnodinium catenatum cysts were detected only in inshore surface sediments from 30 years ago to present, supporting previous evidence of a 1970s introduction via shipping ballast water. sedaDNA confirmed the presence of G. catenatum-related sequences in the inshore and offshore cores, however, unambiguous species identification could not be achieved due to limited reference sequence coverage of Gymnodinium. Our hybridization capture sedaDNA data also confirmed the historically recent dispersal of the non-fossilizing dinoflagellate Noctiluca scintillans, detected inshore from ~30 years ago, matching first observations of this species in Tasmanian waters in 1994. At the offshore site, N. scintillans sedaDNA was detected only in surface sediments, confirming a recent climate-driven range expansion this species. This study provides new insights into the distribution and abundance of three HAB species in the Tasmanian region, including clues to past bloom phases. Further research into paleo-environmental conditions and paleo-community structure are required to identify the factors driving bloom phases through time and predict plankton community responses under different future climate scenarios.HighlightsDinocyst and sedaDNA analyses were applied to marine sediments off TasmaniaAlexandrium catenella has been endemic to Australia for at least ~9,000 yearsRecent A. catenella blooms are likely induced by climate and oceanographic changeGymnodinium catenatum cysts in recent (~30y) sediments confirm a 1970s introductionNoctiluca scintillans sedaDNAin recent (~30y) sediments matches a 1994 introduction

scholarly journals Recovery of Chloroplast Genomes from Medieval Millet Grains Excavated from the Areni-1 Cave in Southern Armenia

2021 ◽  
Author(s):  
Stephen M. Richards ◽  
Leiting Li ◽  
James Breen ◽  
Nelli Hovhannisyan ◽  
Oscar Estrada ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Demographic History ◽  
Northern China ◽  
Haplotype Network ◽  
Bootstrap Support ◽  
Hybridization Capture ◽  
Chloroplast Genomes ◽  
Broomcorn Millet ◽  
Strong Bootstrap Support ◽  
The Rich

Abstract Broomcorn millet (Panicum miliaceum L.) was domesticated in northern China at least 7,000 years ago and was subsequentially adopted as a cereal in many areas throughout Eurasia. One such locale is Areni-1 an archaeological cave site in Southern Armenia, a region that has an important history in crop domestication. The rich botanical material found at Areni-1 includes grains identified by morphology as broomcorn millet that were 14C dated to the medieval era (873 ± 36 CE and 1118 ± 35 CE). To retrace the demographic history of these broomcorn millet samples, we used ancient DNA extraction and hybridization capture enrichment to sequence and assemble three chloroplast genomes from the Areni-1 grains and then compared these sequences to 50 modern chloroplast genomes. Overall, the chloroplast genomes contained a low amount of diversity and little inference on broomcorn demography could be made. However, in a phylogeny the chloroplast genomes separated into two clades with strong bootstrap support, similar to what has been reported for nuclear DNA from broomcorn millet. In a haplotype network, the chloroplast genomes of two accessions of wild (undomesticated) broomcorn millet contained a relatively large number of variants, 11 SNPs. These SNPs were not present in the domesticated varieties, suggesting these wild accessions may not be directly related to the lineages that underwent domestication or that broomcorn millet may have undergone a domestication bottleneck resulting in lost diversity in the chloroplast genome. These results demonstrate that broomcorn millet from archaeological sites can preserve DNA for at least 1000 years and serve as a genetic resource to study the domestication of this cereal crop.

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