NDLI: Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Content Provider	Springer Nature : BioMed Central
Author	Samaha, Georgina Wade, Claire M. Mazrier, Hamutal Grueber, Catherine E. Haase, Bianca
Abstract	Background While recent advances in genomics has enabled vast improvements in the quantification of genome-wide diversity and the identification of adaptive and deleterious alleles in model species, wildlife and non-model species have largely not reaped the same benefits. This has been attributed to the resources and infrastructure required to develop essential genomic datasets such as reference genomes. In the absence of a high-quality reference genome, cross-species alignments can provide reliable, cost-effective methods for single nucleotide variant (SNV) discovery. Here, we demonstrated the utility of cross-species genome alignment methods in gaining insights into population structure and functional genomic features in cheetah (Acinonyx jubatas), snow leopard (Panthera uncia) and Sumatran tiger (Panthera tigris sumatrae), relative to the domestic cat (Felis catus). Results Alignment of big cats to the domestic cat reference assembly yielded nearly complete sequence coverage of the reference genome. From this, 38,839,061 variants in cheetah, 15,504,143 in snow leopard and 13,414,953 in Sumatran tiger were discovered and annotated. This method was able to delineate population structure but limited in its ability to adequately detect rare variants. Enrichment analysis of fixed and species-specific SNVs revealed insights into adaptive traits, evolutionary history and the pathogenesis of heritable diseases. Conclusions The high degree of synteny among felid genomes enabled the successful application of the domestic cat reference in high-quality SNV detection. The datasets presented here provide a useful resource for future studies into population dynamics, evolutionary history and genetic and disease management of big cats. This cross-species method of variant discovery provides genomic context for identifying annotated gene regions essential to understanding adaptive and deleterious variants that can improve conservation outcomes.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-021-07899-2.pdf
Ending Page	13
Page Count	13
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-021-07899-2
Journal	BMC Genomics
Issue Number	1
Volume Number	22
Language	English
Publisher	BioMed Central
Publisher Date	2021-08-06
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genomics Conservation Felids Cheetah Tiger Snow leopard Cat Cross-species SNV WGS
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation

Synteny of Prunus and other model plant species

Ancestral gene synteny reconstruction improves extant species scaffolding

Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance

Refining borders of genome-rearrangements including repetitions

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

An In silico approach for the evaluation of DNA barcodes

Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management

Similar Documents

Rice pseudomolecule-anchored cross-species DNA sequence alignments indicate regional genomic variation in expressed sequence conservation

Synteny of Prunus and other model plant species

Ancestral gene synteny reconstruction improves extant species scaffolding

Using genotype imputation to integrate Canola populations for genome-wide association and genomic prediction of blackleg resistance

Refining borders of genome-rearrangements including repetitions

Chloroplast genomes of five Oedogonium species: genome structure, phylogenetic analysis and adaptive evolution

An In silico approach for the evaluation of DNA barcodes

Synteny conservation between the Prunus genome and both the present and ancestral Arabidopsis genomes

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management