scholarly journals Conservation genomics: applying whole genome studies to species conservation efforts

2004 ◽  
Vol 108 (1-3) ◽  
pp. 6-15 ◽  
Author(s):  
O.A. Ryder
Keyword(s):  
Species Conservation ◽  
Whole Genome ◽  
Conservation Genomics

High throughput crop genome genotyping by a combination of pool next generation sequencing and haplotype-based data processing

2021 ◽  
Author(s):  
Michael Schneider ◽  
Asis Shrestha ◽  
Agim Ballvora ◽  
Jens Leon
Keyword(s):  
Next Generation Sequencing ◽  
Allele Frequency ◽  
Frequency Estimation ◽  
Whole Genome ◽  
Next Generation ◽  
Conservation Genomics ◽  
High Coverage ◽  
Allele Frequency Estimation ◽  
Low Coverage ◽  
Generation Sequencing

Abstract BackgroundThe identification of environmentally specific alleles and the observation of evolutional processes is a goal of conservation genomics. By generational changes of allele frequencies in populations, questions regarding effective population size, gene flow, drift, and selection can be addressed. The observation of such effects often is a trade-off of costs and resolution, when a decent sample of genotypes should be genotyped for many loci. Pool genotyping approaches can derive a high resolution and precision in allele frequency estimation, when high coverage sequencing is utilized. Still, pool high coverage pool sequencing of big genomes comes along with high costs.ResultsHere we present a reliable method to estimate a barley population’s allele frequency at low coverage sequencing. Three hundred genotypes were sampled from a barley backcross population to estimate the entire population’s allele frequency. The allele frequency estimation accuracy and yield were compared for three next generation sequencing methods. To reveal accurate allele frequency estimates on a low coverage sequencing level, a haplotyping approach was performed. Low coverage allele frequency of positional connected single polymorphisms were aggregated to a single haplotype allele frequency, resulting in two to 271 times higher depth and increased precision. We compared different haplotyping tactics, showing that gene and chip marker-based haplotypes perform on par or better than simple contig haplotype windows. The comparison of multiple pool samples and the referencing against an individual sequencing approach revealed whole genome pool resequencing having the highest correlation to individual genotyping (up to 0.97), while transcriptomics and genotyping by sequencing indicated higher error rates and lower correlations.ConclusionUsing the proposed method allows to identify the allele frequency of populations with high accuracy at low cost. This is particularly interesting for conservation genomics in species with big genomes, like barley or wheat. Whole genome low coverage resequencing at 10x coverage can deliver a highly accurate estimation of the allele frequency, when a loci-based haplotyping approach is applied. Using annotated haplotypes allows to capitalize from biological background and statistical robustness.

scholarly journals Comment on “Individual heterozygosity predicts translocation success in threatened desert tortoises”

Science ◽  
2021 ◽  
Vol 372 (6546) ◽  
pp. eabh1105
Author(s):  
Bengt Hansson ◽  
Hernán E. Morales ◽  
Cock van Oosterhout
Keyword(s):  
Decision Rule ◽  
Conservation Management ◽  
Species Conservation ◽  
Genetic Load ◽  
Conservation Genomics

Scott et al. (Reports, 27 November 2020, p. 1086) bring much-needed attention to species conservation by demonstrating heterozygote superiority among translocated tortoises. However, we believe that their recommended heterozygosity decision rule risks taking conservation genomics backward. We argue that their advice could misguide conservation management aimed at establishing viable populations, and that it can be improved by also assessing the genetic load.

scholarly journals Whole genome sequences from non-invasively collected caribou faecal samples

2021 ◽  
Author(s):  
Rebecca S. Taylor ◽  
Micheline Manseau ◽  
Bridget Redquest ◽  
Sonesinh Keobouasone ◽  
Patrick Gagné ◽  
...  
Keyword(s):  
Demographic History ◽  
Primate Species ◽  
Whole Genome ◽  
Faecal Dna ◽  
Conservation Genomics ◽  
High Coverage ◽  
Tissue Samples ◽  
Non Invasive ◽  
Faecal Samples ◽  
Whole Genomes

AbstractConservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.

scholarly journals LI-Seq: A Cost-Effective, Low Input DNA method for Whole Genome Library Preparation

2021 ◽  
Author(s):  
Teia M Schweizer ◽  
Kristen C Ruegg ◽  
Matthew G DeSaix
Keyword(s):  
Species Conservation ◽  
Population Level ◽  
Cost Effective ◽  
Whole Genome ◽  
High Quality ◽  
Library Size ◽  
Low Input ◽  
Cost Effective Method ◽  
Sequencing Quality ◽  
Conservation Concern

Samples from species of high conservation concern are often low in total genomic DNA. Whole Genome Sequencing (WGS) can provide many insights that can be used to aid in species conservation, but current methods for working with low quality and low input samples can be cost prohibitive for population level genomic analyses. Thus, there is an urgent need for a cost-effective method of preparing WGS libraries from low input DNA samples. To bridge the gap between sampling techniques commonly used in conservation genetics that yield low quality and low input DNA and the powerful tool of WGS, we developed LI-Seq, a more efficient method that successfully produces libraries from low quality DNA with as low input as 0.48 ng of DNA, with an average final library size of 300-500 base pairs. Sequencing results suggest no difference in sequencing quality or coverage between low quality, low input and high quality, high input starting material using our protocol. We conclude that our new method will facilitate high-throughput WGS on low quality, low input samples, thus expanding the power of genomic tools beyond traditional high quality samples.

scholarly journals Whole genome approach in conservation biology and its perspectives

2021 ◽  
Vol 19 (3) ◽  
pp. 281-298
Author(s):  
Sergei F. Kliver
Keyword(s):  
Conservation Biology ◽  
Conservation Planning ◽  
Biological Diversity ◽  
Demographic History ◽  
National Level ◽  
Whole Genome ◽  
Total Abundance ◽  
Conservation Genomics ◽  
Reliable Assessment ◽  
The Status

Conservation biology aims to maintain biological diversity and to defend species from extinction. The number of endangered species is constantly increasing from year to year, reflecting both a deteriorating situation and an increasing number of studied species. In order to obtain a reliable assessment of the status and conservation planning of threatened species, not only an estimate of current total abundance, but also data on population structure, demographic history, and genetic diversity are needed. The development of new approaches and lower costs of sequencing have made it possible to solve these problems at a level previously inaccessible and have led to the formation of conservation genomics. This review discusses the opportunities and prospects offered by the use of whole genome sequencing in conservation biology, features of sample gathering for sequencing, as well as some features of planning whole genome studies. In addition, emphasis is placed on the importance of the formation of open biobanks of samples and cell cultures at the national level.

Whole genome scan identifies several chromosomal regions linked to equine sarcoids

2012 ◽  
Vol 154 (1) ◽  
pp. 19-25 ◽  
Author(s):  
V. Jandova ◽  
J. Klukowska-Rötzler ◽  
G. Dolf ◽  
J. Janda ◽  
P. Roosje ◽  
...  
Keyword(s):  
Genome Scan ◽  
Whole Genome ◽  
Whole Genome Scan

Genetische Untersuchungen während der Schwangerschaft und beim Kind

2013 ◽  
Vol 70 (11) ◽  
pp. 621-631 ◽  
Author(s):  
Deborah Bartholdi ◽  
Peter Miny
Keyword(s):  
Array Cgh ◽  
Neuromuskuläre Erkrankungen ◽  
Whole Genome ◽  
Klinische Diagnostik ◽  
Molekulare Karyotypisierung ◽  
Monogene Erkrankungen ◽  
Genetische Untersuchungen

Neue Schlüsseltechnologien führen gegenwärtig zu einem grundlegenden Wandel im klinischen Einsatz genetischer Labordiagnostik. In der Pränataldiagnostik hat die nicht invasive Abklärung von Aneuploidien im mütterliche Blut Fuß gefasst (NIPT) und dieser Ansatz wird in Zukunft auch bei anderen Chromosomenstörungen und Fragestellungen (monogene Erkrankungen) zum Einsatz kommen. Im postnatalen Bereich hat die Microarray Analyse (Array-CGH, molekulare Karyotypisierung) die konventionelle Chromosomenanalyse bei der Abklärung von Kindern mit Fehlbildungen, einer nicht-syndromalen geistigen Behinderung oder Autismusspektrumstörung abgelöst. Die neuen Hochdurchsatzsequenziermethoden erlauben die effiziente Abklärung von genetisch sehr heterogenen Krankheitsbildern wie z. B. Epilepsien, neuromuskuläre Erkrankungen und Schwerhörigkeit, durch Diagnostik-Panels, bei welchen Dutzende von Genen parallel analysiert werden können. Der Einsatz der Exom oder whole genome Sequenzierung als wissenschaftliche Methode zur Identifizierung von neuen Krankheitsgenen wird auch in der Diagnostik von schweren ungeklärten Erkrankungen oder Entwicklungsstörungen, die genetisch extrem heterogen sind, zum Einsatz kommen. Die neuen Methoden werden die klinische Diagnostik in der Pädiatrie und anderen Bereichen der Medizin über kurz oder lang verändern, indem die genetische Labordiagnostik eher früher im Abklärungsprozess zur Anwendung kommen wird (genetics first).

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