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.

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 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.

scholarly journals Non-Invasive Molecular Survey of Sarcoptic Mange in Wildlife: Diagnostic Performance in Wolf Faecal Samples Evaluated by Multi-Event Capture–Recapture Models

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 243
Author(s):  
Julieta Rousseau ◽  
Mónia Nakamura ◽  
Helena Rio-Maior ◽  
Francisco Álvares ◽  
Rémi Choquet ◽  
...  
Keyword(s):  
Molecular Detection ◽  
High Specificity ◽  
Sarcoptes Scabiei ◽  
Sarcoptic Mange ◽  
Diagnostic Specificity ◽  
Non Invasive ◽  
Faecal Samples ◽  
Capture Recapture ◽  
The Mean ◽  
Event Capture

Sarcoptic mange is globally enzootic, and non-invasive methods with high diagnostic specificity for its surveillance in wildlife are lacking. We describe the molecular detection of Sarcoptes scabiei in non-invasively collected faecal samples, targeting the 16S rDNA gene. We applied this method to 843 Iberian wolf Canis lupus signatus faecal samples collected in north-western Portugal (2006–2018). We further integrated this with serological data (61 samples from wolf and 20 from red fox Vulpes vulpes, 1997–2019) in multi-event capture–recapture models. The mean predicted prevalence by the molecular analysis of wolf faecal samples from 2006–2018 was 7.2% (CI95 5.0–9.4%; range: 2.6–11.7%), highest in 2009. The mean predicted seroprevalence in wolves was 24.5% (CI95 18.5–30.6%; range: 13.0–55.0%), peaking in 2006–2009. Multi-event capture–recapture models estimated 100% diagnostic specificity and moderate diagnostic sensitivity (30.0%, CI95 14.0–53.0%) for the molecular method. Mange-infected individually identified wolves showed a tendency for higher mortality versus uninfected wolves (ΔMortality 0.150, CI95 −0.165–0.458). Long-term serology data highlights the endemicity of sarcoptic mange in wild canids but uncovers multi-year epidemics. This study developed and evaluated a novel method for surveying sarcoptic mange in wildlife populations by the molecular detection of S. scabiei in faecal samples, which stands out for its high specificity and non-invasive character.

scholarly journals Panel of serum miRNAs as potential non-invasive biomarkers for pancreatic ductal adenocarcinoma

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Imteyaz Ahmad Khan ◽  
Safoora Rashid ◽  
Nidhi Singh ◽  
Sumaira Rashid ◽  
Vishwajeet Singh ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pancreatic Ductal Adenocarcinoma ◽  
Early Stage ◽  
Ductal Adenocarcinoma ◽  
Next Generation ◽  
Serum Samples ◽  
Tissue Samples ◽  
Non Invasive ◽  
Specific Symptoms ◽  
Generation Sequencing

AbstractEarly-stage diagnosis of pancreatic ductal adenocarcinoma (PDAC) is difficult due to non-specific symptoms. Circulating miRNAs in body fluids have been emerging as potential non-invasive biomarkers for diagnosis of many cancers. Thus, this study aimed to assess a panel of miRNAs for their ability to differentiate PDAC from chronic pancreatitis (CP), a benign inflammatory condition of the pancreas. Next-generation sequencing was performed to identify miRNAs present in 60 FFPE tissue samples (27 PDAC, 23 CP and 10 normal pancreatic tissues). Four up-regulated miRNAs (miR-215-5p, miR-122-5p, miR-192-5p, and miR-181a-2-3p) and four down-regulated miRNAs (miR-30b-5p, miR-216b-5p, miR-320b, and miR-214-5p) in PDAC compared to CP were selected based on next-generation sequencing results. The levels of these 8 differentially expressed miRNAs were measured by qRT-PCR in 125 serum samples (50 PDAC, 50 CP, and 25 healthy controls (HC)). The results showed significant upregulation of miR-215-5p, miR-122-5p, and miR-192-5p in PDAC serum samples. In contrast, levels of miR-30b-5p and miR-320b were significantly lower in PDAC as compared to CP and HC. ROC analysis showed that these 5 miRNAs can distinguish PDAC from both CP and HC. Hence, this panel can serve as a non-invasive biomarker for the early detection of PDAC.

Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises

2021 ◽  
Author(s):  
Evelyn L. Jensen ◽  
Stephen J. Gaughran ◽  
Ryan C. Garrick ◽  
Michael A. Russello ◽  
Adalgisa Caccone
Keyword(s):  
Molecular Evolution ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Demographic History ◽  
Whole Genome

scholarly journals A curated dataset of modern and ancient high-coverage shotgun human genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Pierpaolo Maisano Delser ◽  
Eppie R. Jones ◽  
Anahit Hovhannisyan ◽  
Lara Cassidy ◽  
Ron Pinhasi ◽  
...  
Keyword(s):  
Sequence Data ◽  
Whole Genome ◽  
Reference Dataset ◽  
High Coverage ◽  
Sample Distribution ◽  
Human Samples ◽  
Human Genomes ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Computationally Intensive

AbstractOver the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10–18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.

scholarly journals Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Fan Jiang ◽  
Ruiyi Lin ◽  
Changyi Xiao ◽  
Tanghui Xie ◽  
Yaoxin Jiang ◽  
...  
Keyword(s):  
Gene Flow ◽  
South Asia ◽  
South Asian ◽  
Demographic History ◽  
Nervous System Development ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Chinese Populations ◽  
Asian Populations ◽  
History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

Whole genome transcriptome analysis of the stomach resected in human vertical sleeve gastrectomy: cutting more than calories

2021 ◽  
Author(s):  
William C Dungan ◽  
Michael R Garrett ◽  
Bradley A. Welch ◽  
William J Lawson ◽  
Alexandra R Himel ◽  
...  
Keyword(s):  
Body Weight ◽  
Sleeve Gastrectomy ◽  
Transcriptome Analysis ◽  
Gene Signature ◽  
Whole Genome ◽  
Vertical Sleeve Gastrectomy ◽  
Data Set ◽  
Tissue Samples ◽  
Highly Expressed Genes ◽  
A Prospective Study

Background. Vertical sleeve gastrectomy (VSG) is a surgical weight loss procedure that resects 80% of the stomach, creating a tube linking the esophagus to the duodenum. Because of the efficacy and relative simplicity of VSG, it is preferred in the U.S with VSG currently at >61% of bariatric surgeries performed. Surprisingly, there has never been a complete molecular characterization of the human stomach fundus and corpus. Here we compare and contrast the molecular make-up of these regions. Methods. We performed a prospective study to obtain gastric tissue samples from patients undergoing VSG. Paired fundus and corpus samples were obtained Whole genome transcriptome analysis was performed by RNA sequencing, with key findings validated by qPCR. Results. Participants were primarily female (95.8%) and white (79.15%). Mean BMI, body weight, and age were 46.1 kg/m2, 121.6 kg, and 43.29 years, respectively. Overall, 432 gene transcripts were significantly different between the fundus and corpus (p<0.05). A significant correlation was found between the RNAseq data set and qPCR validation, demonstrating robust gene expression differences. Significant genes included: progastricsin, acid chitinase, gastokine 1 and 2 in both fundus and corpus. Of the very highly expressed genes in both regions, 87% were present in both the stomach's fundus and corpus, indicating substantial overlap. Conclusions. Despite significant overlap in the greater curvature gene signature, regional differences exist. Given that the mechanism of VSG is partly unresolved, the potential that the resected tissue may express genes that influence long-term body weight regulation is unknown and could influence VSG outcomes.

scholarly journals Using reliable predator identification to investigate feeding habits of Neotropical carnivores (Mammalia, Carnivora) in a deforestation frontier of the Brazilian Amazon

Mammalia ◽  
2019 ◽  
Vol 83 (5) ◽  
pp. 415-427 ◽  
Author(s):  
Flávia P. Tirelli ◽  
Thales R.O. de Freitas ◽  
Fernanda Michalski ◽  
Alexandre R. Percequillo ◽  
Eduardo Eizirik
Keyword(s):  
Feeding Habits ◽  
Brazilian Amazon ◽  
Ecological Studies ◽  
Accurate Identification ◽  
Predator Species ◽  
Non Invasive ◽  
Carnivore Species ◽  
Faecal Samples ◽  
Critical Requirement ◽  
Better Than

Abstract Accurate identification of predator species is a critical requirement to investigate their diet using faecal samples. We used non-invasive sampling and two methods of predator identification to investigate the diets of sympatric carnivores in a highly deforested region of the Brazilian Amazon. Of 108 scats, 81 could be identified at the species level using DNA sequencing and/or trichology. The former performed better than the latter (81.5% vs. 54.3% of the identified samples), and results were quite congruent (89.7% concordance in the 29 samples that could be assessed with both approaches). Nine species were identified, out of which four (crab-eating fox, ocelot, puma and jaguar) presented a sufficient number of samples to allow dietary analyses. The crab-eating fox was the most generalist (BA=0.92); ocelots focused on small- to medium-sized prey; pumas fed mostly on medium-sized items; and jaguars mostly targeted large-sized prey. A considerable overlap was observed between ocelots and pumas in all estimations (O=0.47–0.83). The presence of jaguars in the same region could be driving pumas to select medium- and small-sized prey. The results of this study highlight the importance of reliable predator identification and the need for in-depth ecological studies in areas where carnivore species are sympatric.

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