Data from: An annotated draft genome of the mountain hare (Lepus timidus)
Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draf...
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ftzenodo:oai:zenodo.org:4147956 2024-09-15T18:17:46+00:00 Data from: An annotated draft genome of the mountain hare (Lepus timidus) Marques, João Pedro Seixas, Fernando A. Good, Jeffrey M. Farelo, Liliana Callahan, Colin M. Montgomery, W. Ian Reid, Neil Alves, Paulo C. Boursot, Pierre Melo-Ferreira, José 2020-12-18 https://doi.org/10.5061/dryad.j0zpc86bk unknown Zenodo https://doi.org/10.1093/gbe/evz273 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.j0zpc86bk oai:zenodo.org:4147956 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode whole-genome sequencing de novo Assembly annotation Hares Leporids Lagomorpha info:eu-repo/semantics/other 2020 ftzenodo https://doi.org/10.5061/dryad.j0zpc86bk10.1093/gbe/evz273 2024-07-25T09:34:06Z Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares. This assembly and annotation files corresponds to the version CIBIO-ISEM_LeTim1.0 reported in the article "An Annotated Draft Genome of the Mountain Hare ( Lepus timidus )" Funding provided by: Fundação para a Ciência e a Tecnologia Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871 Award Number: ... Other/Unknown Material Lepus timidus mountain hare Zenodo |
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ftzenodo |
language |
unknown |
topic |
whole-genome sequencing de novo Assembly annotation Hares Leporids Lagomorpha |
spellingShingle |
whole-genome sequencing de novo Assembly annotation Hares Leporids Lagomorpha Marques, João Pedro Seixas, Fernando A. Good, Jeffrey M. Farelo, Liliana Callahan, Colin M. Montgomery, W. Ian Reid, Neil Alves, Paulo C. Boursot, Pierre Melo-Ferreira, José Data from: An annotated draft genome of the mountain hare (Lepus timidus) |
topic_facet |
whole-genome sequencing de novo Assembly annotation Hares Leporids Lagomorpha |
description |
Hares (genus Lepus) provide clear examples of repeated and often massive introgressive hybridization and striking local adaptations. Genomic studies on this group have so far relied on comparisons to the European rabbit (Oryctolagus cuniculus) reference genome. Here, we report the first de novo draft reference genome for a hare species, the mountain hare (Lepus timidus), and evaluate the efficacy of whole-genome re-sequencing analyses using the new reference versus using the rabbit reference genome. The genome was assembled using the ALLPATHS-LG protocol with a combination of overlapping pair and mate-pair Illumina sequencing (77x coverage). The assembly contained 32,294 scaffolds with a total length of 2.7 Gb and a scaffold N50 of 3.4 Mb. Re-scaffolding based on the rabbit reference reduced the total number of scaffolds to 4,205 with a scaffold N50 of 194 Mb. A correspondence was found between 22 of these hare scaffolds and the rabbit chromosomes, based on gene content and direct alignment. We annotated 24,578 protein coding genes by combining ab-initio predictions, homology search, and transcriptome data, of which 683 were solely derived from hare-specific transcriptome data. The hare reference genome is therefore a new resource to discover and investigate hare-specific variation. Similar estimates of heterozygosity and inferred demographic history profiles were obtained when mapping hare whole-genome re-sequencing data to the new hare draft genome or to alternative references based on the rabbit genome. Our results validate previous reference-based strategies and suggest that the chromosome-scale hare draft genome should enable chromosome-wide analyses and genome scans on hares. This assembly and annotation files corresponds to the version CIBIO-ISEM_LeTim1.0 reported in the article "An Annotated Draft Genome of the Mountain Hare ( Lepus timidus )" Funding provided by: Fundação para a Ciência e a Tecnologia Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001871 Award Number: ... |
format |
Other/Unknown Material |
author |
Marques, João Pedro Seixas, Fernando A. Good, Jeffrey M. Farelo, Liliana Callahan, Colin M. Montgomery, W. Ian Reid, Neil Alves, Paulo C. Boursot, Pierre Melo-Ferreira, José |
author_facet |
Marques, João Pedro Seixas, Fernando A. Good, Jeffrey M. Farelo, Liliana Callahan, Colin M. Montgomery, W. Ian Reid, Neil Alves, Paulo C. Boursot, Pierre Melo-Ferreira, José |
author_sort |
Marques, João Pedro |
title |
Data from: An annotated draft genome of the mountain hare (Lepus timidus) |
title_short |
Data from: An annotated draft genome of the mountain hare (Lepus timidus) |
title_full |
Data from: An annotated draft genome of the mountain hare (Lepus timidus) |
title_fullStr |
Data from: An annotated draft genome of the mountain hare (Lepus timidus) |
title_full_unstemmed |
Data from: An annotated draft genome of the mountain hare (Lepus timidus) |
title_sort |
data from: an annotated draft genome of the mountain hare (lepus timidus) |
publisher |
Zenodo |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.j0zpc86bk |
genre |
Lepus timidus mountain hare |
genre_facet |
Lepus timidus mountain hare |
op_relation |
https://doi.org/10.1093/gbe/evz273 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.j0zpc86bk oai:zenodo.org:4147956 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.j0zpc86bk10.1093/gbe/evz273 |
_version_ |
1810455875573252096 |