The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics
Abstract 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 - tha...
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ftdatacite:10.6084/m9.figshare.c.3815656.v1 2023-05-15T15:49:35+02:00 The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics Gopalakrishnan, Shyam Castruita, Jose Samaniego Mikkel-Holger Sinding Kuderna, Lukas Jannikke RäIkkÜnen Petersen, Bent Sicheritz-Ponten, Thomas Larson, Greger Orlando, Ludovic Marques-Bonet, Tomas Hansen, Anders DalÊn, Love M. Gilbert 2017 https://dx.doi.org/10.6084/m9.figshare.c.3815656.v1 https://figshare.com/collections/The_wolf_reference_genome_sequence_Canis_lupus_lupus_and_its_implications_for_Canis_spp_population_genomics/3815656/1 unknown Figshare https://dx.doi.org/10.1186/s12864-017-3883-3 https://dx.doi.org/10.6084/m9.figshare.c.3815656 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Science Policy Computational Biology Collection article 2017 ftdatacite https://doi.org/10.6084/m9.figshare.c.3815656.v1 https://doi.org/10.1186/s12864-017-3883-3 https://doi.org/10.6084/m9.figshare.c.3815656 2021-11-05T12:55:41Z Abstract 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. 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. 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. Article in Journal/Newspaper Canis lupus DataCite Metadata Store (German National Library of Science and Technology) |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Science Policy Computational Biology |
spellingShingle |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Science Policy Computational Biology Gopalakrishnan, Shyam Castruita, Jose Samaniego Mikkel-Holger Sinding Kuderna, Lukas Jannikke RäIkkÜnen Petersen, Bent Sicheritz-Ponten, Thomas Larson, Greger Orlando, Ludovic Marques-Bonet, Tomas Hansen, Anders DalÊn, Love M. Gilbert The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics |
topic_facet |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Science Policy Computational Biology |
description |
Abstract 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. 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. 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. |
format |
Article in Journal/Newspaper |
author |
Gopalakrishnan, Shyam Castruita, Jose Samaniego Mikkel-Holger Sinding Kuderna, Lukas Jannikke RäIkkÜnen Petersen, Bent Sicheritz-Ponten, Thomas Larson, Greger Orlando, Ludovic Marques-Bonet, Tomas Hansen, Anders DalÊn, Love M. Gilbert |
author_facet |
Gopalakrishnan, Shyam Castruita, Jose Samaniego Mikkel-Holger Sinding Kuderna, Lukas Jannikke RäIkkÜnen Petersen, Bent Sicheritz-Ponten, Thomas Larson, Greger Orlando, Ludovic Marques-Bonet, Tomas Hansen, Anders DalÊn, Love M. Gilbert |
author_sort |
Gopalakrishnan, Shyam |
title |
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_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_sort |
wolf reference genome sequence (canis lupus lupus) and its implications for canis spp. population genomics |
publisher |
Figshare |
publishDate |
2017 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.3815656.v1 https://figshare.com/collections/The_wolf_reference_genome_sequence_Canis_lupus_lupus_and_its_implications_for_Canis_spp_population_genomics/3815656/1 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_relation |
https://dx.doi.org/10.1186/s12864-017-3883-3 https://dx.doi.org/10.6084/m9.figshare.c.3815656 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3815656.v1 https://doi.org/10.1186/s12864-017-3883-3 https://doi.org/10.6084/m9.figshare.c.3815656 |
_version_ |
1766384608296828928 |