The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
<p>Background: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - th...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Journal article |
| Published: |
BioMed Central
2017
|
| _version_ | 1797079301750784000 |
|---|---|
| author | Gopalakrishnan, S Samaniego Castruita, J Sinding, M Kuderna, L Raikkonen, J Petersen, B Sicheritz-Ponten, T Larson, G Orlando, L Marques-Bonet, T Hansen, A Dalen, L Gilbert, M |
| author_facet | Gopalakrishnan, S Samaniego Castruita, J Sinding, M Kuderna, L Raikkonen, J Petersen, B Sicheritz-Ponten, T Larson, G Orlando, L Marques-Bonet, T Hansen, A Dalen, L Gilbert, M |
| author_sort | Gopalakrishnan, S |
| collection | OXFORD |
| description | <p>Background: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference.</p><p> Results: Reassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples.</p><p> Conclusion: In conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome.</p> |
| first_indexed | 2024-03-07T00:43:52Z |
| format | Journal article |
| id | oxford-uuid:83f832fa-8072-4d8c-b51d-3df940cf3e26 |
| institution | University of Oxford |
| last_indexed | 2024-03-07T00:43:52Z |
| publishDate | 2017 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | oxford-uuid:83f832fa-8072-4d8c-b51d-3df940cf3e262022-03-26T21:47:56ZThe wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomicsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:83f832fa-8072-4d8c-b51d-3df940cf3e26Symplectic Elements at OxfordBioMed Central2017Gopalakrishnan, SSamaniego Castruita, JSinding, MKuderna, LRaikkonen, JPetersen, BSicheritz-Ponten, TLarson, GOrlando, LMarques-Bonet, THansen, ADalen, LGilbert, M<p>Background: An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a boxer dog (Canis lupus familiaris). We generated the first de novo wolf genome (Canis lupus lupus) as an additional choice of reference, and explored what implications may arise when previously published dog and wolf resequencing data are remapped to this reference.</p><p> Results: Reassuringly, we find that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped samples, the number of variants discovered, and heterozygosity estimates of the samples.</p><p> Conclusion: In conclusion, the choice of reference is dictated by the aims of the study being undertaken; if the study focuses on the differences between the different dog breeds or the fine structure among dogs, then using the boxer reference genome is appropriate, but if the aim of the study is to look at the variation within wolves and their relationships to dogs, then there are clear benefits to using the de novo assembled wolf reference genome.</p> |
| spellingShingle | Gopalakrishnan, S Samaniego Castruita, J Sinding, M Kuderna, L Raikkonen, J Petersen, B Sicheritz-Ponten, T Larson, G Orlando, L Marques-Bonet, T Hansen, A Dalen, L Gilbert, M The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics |
| title | The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics |
| title_full | The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics |
| title_fullStr | The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics |
| title_full_unstemmed | The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics |
| title_short | The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics |
| title_sort | wolf reference genome sequence canis lupus lupus and its implications for canis spp population genomics |
| work_keys_str_mv | AT gopalakrishnans thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT samaniegocastruitaj thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT sindingm thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT kudernal thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT raikkonenj thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT petersenb thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT sicheritzpontent thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT larsong thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT orlandol thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT marquesbonett thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT hansena thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT dalenl thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT gilbertm thewolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT gopalakrishnans wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT samaniegocastruitaj wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT sindingm wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT kudernal wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT raikkonenj wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT petersenb wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT sicheritzpontent wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT larsong wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT orlandol wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT marquesbonett wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT hansena wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT dalenl wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics AT gilbertm wolfreferencegenomesequencecanislupuslupusanditsimplicationsforcanisspppopulationgenomics |