Conservation of biodiversity in the genomics era

Supple, Megan A.; Shapiro, Beth

doi:10.1186/s13059-018-1520-3

Cited by 264 publications

(227 citation statements)

References 109 publications

Supporting

Mentioning

226

Contrasting

Order By: Relevance

“…Fluctuations at the molecular and cellular level are sensitive indicators of environmental change (36,37); they are analogous to veterinary medicine where blood transcriptomes serve as proxies for identifying health status, disease, and exposures to environmental toxicants (38)(39)(40)(41). Changes at the transcriptome level may also be useful indicators of ecological specialization, and therefore useful to design strategies for species management and conservation (42). However, existing approaches to generate transcriptome data from whole blood RNA are either specifically designed for short-read sequencing (DASH) or human samples (commercial hemoglobin depletion kit like GLOBINclear) and therefore lack a cost-effective approach for analyzing isoform-level transcriptomes of non-model organisms.…”

Section: Discussionmentioning

confidence: 99%

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Byrne

Supple

Volden

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance. This issue is more pronounced when using long-read sequencing technologies for isoform-level transcriptome analysis, as they have relatively lower throughput compared to short-read sequencers. As a result long-read based transcriptome analysis is prohibitively expensive for non-model organisms. While there are off-the-shelf kits available for select model organisms capable of depleting highly abundant transcripts for alpha (HBA) and beta (HBB) hemoglobin, they are unsuitable for non-model organisms. To address this, we have adapted the recent CRISPR/Cas9 based depletion method (Depletion of Abundant Sequences by Hybridization) for long-read full-length cDNA sequencing approaches that we call Long-DASH. Using a recombinant Cas9 protein with appropriate guide RNAs, full-length hemoglobin transcripts can be depleted in-vitro prior to performing any short-and long-read sequencing library preparations. Using this method, we sequenced depleted full-length cDNA in parallel using both our Oxford Nanopore Technology (ONT) based R2C2 long-read approach, as well as the Illumina short-read based Smart-seq2 approach. To showcase this, we have applied our methods to create an isoform-level transcriptome from whole blood samples derived from three polar bears (Ursus maritimus). Using Long-DASH, we succeeded in depleting hemoglobin transcripts and generated deep Smart-seq2 Illumina datasets and 3.8 million R2C2 full-length cDNA consensus reads. Applying Long-DASH with our isoform identification pipeline, Mandalorion we discovered ~6,000 high-confidence isoforms and a number of novel genes. This indicates there is a high diversity of gene isoforms within Ursus maritimus not yet reported. This reproducible and straightforward approach has not only improved the polar bear transcriptome annotations but will serve as the foundation for future efforts to investigate transcriptional dynamics within the 19 polar bear subpopulations around the Arctic.

show abstract

Section: Discussionmentioning

confidence: 99%

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Byrne

Supple

Volden

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Many of these investigations have focused on a relatively small number of neutral genetic markers. Sampling across the entire genome using next generation sequencing can help conservation efforts by identifying adaptive alleles and phenotype-associated variants 9 . While genomic approaches are useful for elephant conservation, the few elephant functional genomic studies currently available are limited to a small number of individuals and species [10][11][12][13] and the etiologies of many elephant traits with profound fitness (and therefore conservation-oriented) consequences have not yet been discovered.…”

Section: Introductionmentioning

confidence: 99%

Elephant Genomes Elucidate Disease Defenses and Other Traits

Tollis

Ferris

Ms.

et al. 2020

Preprint

View full text Add to dashboard Cite

Disease susceptibility and defense are important factors in conservation, particularly for elephants. We report that in addition to endotheliotropic herpesvirus and tuberculosis, Asian elephants are also more susceptible to cancer than African elephants. To determine mechanisms underlying elephant traits including disease resistance, we analyzed genomic datasets from multiple individuals and species. We report a draft genome assembly for the Asian elephant and an improved African elephant assembly. We found 862 and 1,017 potential regulatory elements in Asian and African elephants, respectively, that are enriched near 5,034 differentially expressed genes in peripheral blood mononuclear cells between the two species.These genes are enriched in immunity pathways, including tumor-necrosis factor which plays a role in the elephant response to endotheliotropic herpesvirus. Some elephant TP53 retrogenes are being maintained by purifying selection and may contribute to cancer resistance in elephants. Positive selection scans revealed genes that may control tusk development, memory, and somatic maintenance. Our study provides an example of how genomics can inform functional immunological studies, which may improve conservation and medical care for elephants and translate into human therapies.

show abstract

“…Sequencing whole (Prado-Martinez et al, 2013) or partial (e.g. RADseq, Baird et al, (2008)) genomes are now standards in molecular ecology and conservation genetic research (Ekblom & Galindo, 2010;Fuentes-Pardo & Ruzzante, 2017;Supple & Shapiro, 2018). Although sequencing costs per sample and per base-pair are decreasing, expenses to generate sufficient genotypic data still impose serious constraints on the number of individuals or populations sampled .…”

Section: Introductionmentioning

confidence: 99%

Leveraging targeted sequencing for non-model species: a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica

Pavinato

Wijeratne

Spacht

et al. 2019

Preprint

View full text Add to dashboard Cite

The sequencing of whole or partial (e.g. reduced representation) genomes are commonly employed in molecular ecology and conservation genetics studies. However, due to sequencing costs, a trade-off between the number of samples and genome coverage can hinder research for non-model organisms. Furthermore, the processing of raw sequences requires familiarity with coding and bioinformatic tools that are not always available. Here, we present a guide for isolating a set of short, SNP-containing genomic regions for use with targeted amplicon sequencing protocols. We also present a python pipeline--PypeAmplicon--that facilitates processing of reads to individual genotypes. We demonstrate the applicability of our method by generating an informative set of amplicons for genotyping of the Antarctic midge, Belgica antarctica, an endemic dipteran species of the Antarctic Peninsula. Our pipeline analyzed raw sequences produced by a combination of high-multiplexed PCR and next-generation sequencing. A total of 38 out of 47 (81%) amplicons designed by our panel were recovered, allowing successful genotyping of 42 out of 55 (76%) targeted SNPs. The sequencing of ~150 bp around the targeted SNPs also uncovered 80 new SNPs, which complemented our analyses. By comparing overall patterns of genetic diversity and population structure of amplicon data with the low-coverage, whole-genome re-sequencing (lcWGR) data used to isolate the informative amplicons, we were able to demonstrate that amplicon sequencing produces information and results similar to that of lcWGR. Our methods will benefit other research programs where rapid development of population genetic data is needed but yet prevented due to high expense and a lack of bioinformatic experience.

show abstract

Conservation of biodiversity in the genomics era

Cited by 264 publications

References 109 publications

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Depletion of hemoglobin transcripts and long read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Elephant Genomes Elucidate Disease Defenses and Other Traits

Leveraging targeted sequencing for non-model species: a step-by-step guide to obtain a reduced SNP set and a pipeline to automate data processing in the Antarctic Midge, Belgica antarctica

Contact Info

Product

Resources

About