Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management
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 attr...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2021-08-01
|
| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-021-07899-2 |
| _version_ | 1828920684924895232 |
|---|---|
| author | Georgina Samaha Claire M. Wade Hamutal Mazrier Catherine E. Grueber Bianca Haase |
| author_facet | Georgina Samaha Claire M. Wade Hamutal Mazrier Catherine E. Grueber Bianca Haase |
| author_sort | Georgina Samaha |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T21:50:35Z |
| format | Article |
| id | doaj.art-787f27249abb4d63bf2541a6a3b61945 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T21:50:35Z |
| publishDate | 2021-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-787f27249abb4d63bf2541a6a3b619452022-12-21T23:30:18ZengBMCBMC Genomics1471-21642021-08-0122111310.1186/s12864-021-07899-2Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation managementGeorgina Samaha0Claire M. Wade1Hamutal Mazrier2Catherine E. Grueber3Bianca Haase4Sydney School of Veterinary Science, Faculty of Science, The University of SydneySchool of Life and Environmental Sciences, The University of SydneySydney School of Veterinary Science, Faculty of Science, The University of SydneySchool of Life and Environmental Sciences, The University of SydneySydney School of Veterinary Science, Faculty of Science, The University of SydneyAbstract 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.https://doi.org/10.1186/s12864-021-07899-2GenomicsConservationFelidsCheetahTigerSnow leopard |
| spellingShingle | Georgina Samaha Claire M. Wade Hamutal Mazrier Catherine E. Grueber Bianca Haase Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management BMC Genomics Genomics Conservation Felids Cheetah Tiger Snow leopard |
| title | Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management |
| title_full | Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management |
| title_fullStr | Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management |
| title_full_unstemmed | Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management |
| title_short | Exploiting genomic synteny in Felidae: cross-species genome alignments and SNV discovery can aid conservation management |
| title_sort | exploiting genomic synteny in felidae cross species genome alignments and snv discovery can aid conservation management |
| topic | Genomics Conservation Felids Cheetah Tiger Snow leopard |
| url | https://doi.org/10.1186/s12864-021-07899-2 |
| work_keys_str_mv | AT georginasamaha exploitinggenomicsyntenyinfelidaecrossspeciesgenomealignmentsandsnvdiscoverycanaidconservationmanagement AT clairemwade exploitinggenomicsyntenyinfelidaecrossspeciesgenomealignmentsandsnvdiscoverycanaidconservationmanagement AT hamutalmazrier exploitinggenomicsyntenyinfelidaecrossspeciesgenomealignmentsandsnvdiscoverycanaidconservationmanagement AT catherineegrueber exploitinggenomicsyntenyinfelidaecrossspeciesgenomealignmentsandsnvdiscoverycanaidconservationmanagement AT biancahaase exploitinggenomicsyntenyinfelidaecrossspeciesgenomealignmentsandsnvdiscoverycanaidconservationmanagement |