An annotated draft genome of the mountain hare (Lepus timidus)
International audience 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...
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2019
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Online Access: | https://hal.umontpellier.fr/hal-02428653 https://hal.umontpellier.fr/hal-02428653/document https://hal.umontpellier.fr/hal-02428653/file/Marques-2020-An%20annotated%20draft%20genome%20of%20the.pdf https://doi.org/10.1093/gbe/evz273 |
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ftecolephe:oai:HAL:hal-02428653v1 2024-05-19T07:43:41+00:00 An annotated draft genome of the mountain hare (Lepus timidus) Marques, João Seixas, Fernando Farelo, Liliana Callahan, Colin Good, Jeffrey Montgomery, W Ian Reid, Neil Alves, Paulo, C. Boursot, Pierre Melo-Ferreira, José CIBIO/UP Universidade do Porto = University of Porto Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE) Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO) Division of Biological Sciences Missoula, MT University of Montana Institute of Global Food Security Queen's University Belfast (QUB) Centro de Investigacao em Biodiverdidade e Recursos Geneticos (CIBIO-UP) 2019-12-13 https://hal.umontpellier.fr/hal-02428653 https://hal.umontpellier.fr/hal-02428653/document https://hal.umontpellier.fr/hal-02428653/file/Marques-2020-An%20annotated%20draft%20genome%20of%20the.pdf https://doi.org/10.1093/gbe/evz273 en eng HAL CCSD Society for Molecular Biology and Evolution info:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evz273 hal-02428653 https://hal.umontpellier.fr/hal-02428653 https://hal.umontpellier.fr/hal-02428653/document https://hal.umontpellier.fr/hal-02428653/file/Marques-2020-An%20annotated%20draft%20genome%20of%20the.pdf doi:10.1093/gbe/evz273 info:eu-repo/semantics/OpenAccess ISSN: 1759-6653 EISSN: 1759-6653 Genome Biology and Evolution https://hal.umontpellier.fr/hal-02428653 Genome Biology and Evolution, 2019, ⟨10.1093/gbe/evz273⟩ whole-genome sequencing de novo assembly annotation hares Leporids Lagomorpha [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] info:eu-repo/semantics/article Journal articles 2019 ftecolephe https://doi.org/10.1093/gbe/evz273 2024-05-02T00:20:10Z International audience 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. Article in Journal/Newspaper Lepus timidus mountain hare EPHE (Ecole pratique des hautes études, Paris): HAL Genome Biology and Evolution 12 1 3656 3662 |
institution |
Open Polar |
collection |
EPHE (Ecole pratique des hautes études, Paris): HAL |
op_collection_id |
ftecolephe |
language |
English |
topic |
whole-genome sequencing de novo assembly annotation hares Leporids Lagomorpha [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
spellingShingle |
whole-genome sequencing de novo assembly annotation hares Leporids Lagomorpha [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] Marques, João Seixas, Fernando Farelo, Liliana Callahan, Colin Good, Jeffrey Montgomery, W Ian Reid, Neil Alves, Paulo, C. Boursot, Pierre Melo-Ferreira, José An annotated draft genome of the mountain hare (Lepus timidus) |
topic_facet |
whole-genome sequencing de novo assembly annotation hares Leporids Lagomorpha [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] |
description |
International audience 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. |
author2 |
CIBIO/UP Universidade do Porto = University of Porto Institut des Sciences de l'Evolution de Montpellier (UMR ISEM) Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE) Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement IRD : UR226-Centre National de la Recherche Scientifique (CNRS) Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO) Division of Biological Sciences Missoula, MT University of Montana Institute of Global Food Security Queen's University Belfast (QUB) Centro de Investigacao em Biodiverdidade e Recursos Geneticos (CIBIO-UP) |
format |
Article in Journal/Newspaper |
author |
Marques, João Seixas, Fernando Farelo, Liliana Callahan, Colin Good, Jeffrey Montgomery, W Ian Reid, Neil Alves, Paulo, C. Boursot, Pierre Melo-Ferreira, José |
author_facet |
Marques, João Seixas, Fernando Farelo, Liliana Callahan, Colin Good, Jeffrey Montgomery, W Ian Reid, Neil Alves, Paulo, C. Boursot, Pierre Melo-Ferreira, José |
author_sort |
Marques, João |
title |
An annotated draft genome of the mountain hare (Lepus timidus) |
title_short |
An annotated draft genome of the mountain hare (Lepus timidus) |
title_full |
An annotated draft genome of the mountain hare (Lepus timidus) |
title_fullStr |
An annotated draft genome of the mountain hare (Lepus timidus) |
title_full_unstemmed |
An annotated draft genome of the mountain hare (Lepus timidus) |
title_sort |
annotated draft genome of the mountain hare (lepus timidus) |
publisher |
HAL CCSD |
publishDate |
2019 |
url |
https://hal.umontpellier.fr/hal-02428653 https://hal.umontpellier.fr/hal-02428653/document https://hal.umontpellier.fr/hal-02428653/file/Marques-2020-An%20annotated%20draft%20genome%20of%20the.pdf https://doi.org/10.1093/gbe/evz273 |
genre |
Lepus timidus mountain hare |
genre_facet |
Lepus timidus mountain hare |
op_source |
ISSN: 1759-6653 EISSN: 1759-6653 Genome Biology and Evolution https://hal.umontpellier.fr/hal-02428653 Genome Biology and Evolution, 2019, ⟨10.1093/gbe/evz273⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1093/gbe/evz273 hal-02428653 https://hal.umontpellier.fr/hal-02428653 https://hal.umontpellier.fr/hal-02428653/document https://hal.umontpellier.fr/hal-02428653/file/Marques-2020-An%20annotated%20draft%20genome%20of%20the.pdf doi:10.1093/gbe/evz273 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1093/gbe/evz273 |
container_title |
Genome Biology and Evolution |
container_volume |
12 |
container_issue |
1 |
container_start_page |
3656 |
op_container_end_page |
3662 |
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1799483437936017408 |