An Annotated Draft Genome of the Mountain Hare (Lepus timidus)

João P. Marques; Fernando A. Seixas; Liliana Farelo; Colin M. Callahan; Jeffrey M. Good; W. Ian Montgomery; Neil Reid; Paulo C. Alves; Pierre Boursot; José Melo-Ferreira

doi:10.1093/gbe/evz273

An Annotated Draft Genome of the Mountain Hare (Lepus timidus)

João P. Marques
, Fernando A. Seixas
, Liliana Farelo
, Colin M. Callahan
, Jeffrey M. Good
, W. Ian Montgomery
, Neil Reid
, Paulo C. Alves
, Pierre Boursot
, José Melo-Ferreira

Division of Biological and Biomedical Sciences

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	3656-3662
Number of pages	7
Journal	Genome Biology and Evolution
Volume	12
Issue number	1
DOIs	https://doi.org/10.1093/gbe/evz273
State	Published - Dec 16 2019

Funding

In Ireland, a license (no. C 337/2012 dated October 31, 2012) to take animals for scientific purposes under the Wildlife Acts 1976–-2012 Sections 9, 23, and 34 was issued by Laura Claffey, Wildlife Licensing Unit, National Parks & Wildlife Service (NPWS), Department of Arts, Heritage & the Gaeltacht (DAHG). Thanks to Jimi Conroy, the local NPWS Conservation Officer, who consented to sampling within his jurisdiction. The Irish Coursing Club (ICC) captured animals from the wild and we thank D.J. Histon, Chief Executive and Secretary, who supported the research. William Fitzgerald, Department of Agriculture, Food and the Marine (DAFM) dispatched animals in a humane manner and provided dissection skills. This work was funded by the project HybridAdapt, supported by Portuguese National Funds through the Fundac¸ão para a Ciência e a Tecnologia (FCT) (reference FCT-ANR/BIA-EVF/0250/2012), and by French Agence Nationale de la Recherche (ANR) (reference ANR-12-ISV7–0002-01). Additional support was obtained from Programa Operacional Potencial Humano – Quadro de Referência Estratégica Nacional (POPH-QREN) funds from the European Social Fund (ESF) and FCT (IF/00033/2014/ CP1256/CT0005 FCT Investigator grant to J.M.-F., and SFRH/BD/115089/2016 and SFRH/BD/87126/2012 PhD grants to J.P.M. and F.A.S., respectively), and from a National Science Foundation (NSF) EPSCoR grant (OIA-1736249 to J.M.G.). Instrumentation, laboratory, and/or computational support were provided by CIBIO NEW-GEN sequencing platform, supported by the European Union under grant agreement no. 286431, by the Montpellier Bioinformatics Biodiversity platform supported by LabEx CeMEB, an ANR “Investissements d’avenir” program (ANR-10-LABX-04-01), and by the University of Montana Genomics Core. Additional support was obtained from the projects NORTE-01-0145-FEDER-000007 (NORTE2020 Programme, PORTUGAL 2020, through the European Regional Development Fund – ERDF), and POCI-01-0145-FEDER-022184 (COMPETE2020, PORTUGAL2020, and ERDF). It was also supported by Portugal–France bilateral cooperation programs PESSOA (FCT in Portugal; Ministère de l’Europe et des Affaires étrangères (MEAE) and Ministère de l’Education nationale, de l’Enseignement supérieur et de la Recherche (MESRI) in France) and Cotutelles/Cotutelas PESSOA (FCT through Conselho de Reitores das Universidades Portuguesas (CRUP) in Portugal; MEAE and MESRI through Conférence des Présidents d’Université (CPU) in France). This research was conducted in the frame of the Laboratoire International Associé (LIA) “Biodiversity and Evolution” supported by Institut écologie et environnement – InEE (Centre national de la recherche scientifique – CNRS, France) and FCT (Portugal).

Funders	Funder number
FCT-ANR/BIA-EVF/0250/2012
ANR-10-LABX-04-01
OIA-1736249
NORTE-01-0145-FEDER-000007
European Commission	286431
ANR-12-ISV7–0002-01
SFRH/BD/115089/2016, IF/00033/2014/ CP1256/CT0005, SFRH/BD/87126/2012
COMPETE2020, POCI-01-0145-FEDER-022184, PORTUGAL2020

Keywords

Lagomorpha
Leporids
annotation
de novo assembly
hares
whole-genome sequencing

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10.1093/gbe/evz273

Cite this

@article{29fd5ae2bf224821ab99dbc520eaea78,

title = "An Annotated Draft Genome of the Mountain Hare (Lepus timidus)",

abstract = "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.",

keywords = "Lagomorpha, Leporids, annotation, de novo assembly, hares, whole-genome sequencing",

author = "Marques, \{Jo{\~a}o P.\} and Seixas, \{Fernando A.\} and Liliana Farelo and Callahan, \{Colin M.\} and Good, \{Jeffrey M.\} and Montgomery, \{W. Ian\} and Neil Reid and Alves, \{Paulo C.\} and Pierre Boursot and Jos{\'e} Melo-Ferreira",

note = "Publisher Copyright: {\textcopyright} 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.",

year = "2019",

month = dec,

day = "16",

doi = "10.1093/gbe/evz273",

language = "English",

volume = "12",

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T1 - An Annotated Draft Genome of the Mountain Hare (Lepus timidus)

AU - Marques, João P.

AU - Seixas, Fernando A.

AU - Farelo, Liliana

AU - Callahan, Colin M.

AU - Good, Jeffrey M.

AU - Montgomery, W. Ian

AU - Reid, Neil

AU - Alves, Paulo C.

AU - Boursot, Pierre

AU - Melo-Ferreira, José

PY - 2019/12/16

Y1 - 2019/12/16

N2 - 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.

AB - 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.

KW - Lagomorpha

KW - Leporids

KW - annotation

KW - de novo assembly

KW - hares

KW - whole-genome sequencing

UR - https://www.scopus.com/pages/publications/85077760929

U2 - 10.1093/gbe/evz273

DO - 10.1093/gbe/evz273

M3 - Article

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AN - SCOPUS:85077760929

SN - 1759-6653

VL - 12

SP - 3656

EP - 3662

JO - Genome Biology and Evolution

JF - Genome Biology and Evolution

IS - 1

ER -

An Annotated Draft Genome of the Mountain Hare (Lepus timidus)

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Keywords

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