Author’s Accepted Manuscript
Draft genome sequence of Japanese wood mouse,
Apodemus speciosus
Masatoshi Matsunami, Daiji Endo, Naruya Saitou,Hitoshi Suzuki, Manabu Onuma
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https://doi.org/10.1016/j.dib.2017.10.063
DIB1887

To appear in: Data in Brief
Received date: 26 August 2017
Revised date: 7 October 2017
Accepted date: 26 October 2017
Cite this article as: Masatoshi Matsunami, Daiji Endo, Naruya Saitou, Hitoshi
Suzuki and Manabu Onuma, Draft genome sequence of Japanese wood mouse,Apodemus speciosus, Data in Brief, https://doi.org/10.1016/j.dib.2017.10.063
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Data in Brief

Draft genome sequence of Japanese wood mouse,
Apodemus speciosus
Masatoshi Matsunami1,4,5, Daiji Endo2, Naruya Saitou3, Hitoshi Suzuki1, and Manabu
Onuma4*

1

Laboratory of Ecology and Genetics, Graduate School of Environmental Science,

Hokkaido University, Kita-ku, Sapporo, 060-0810, Japan
2

School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, 069-8501, Japan3

Department of Genetics, School of Life Science, The Graduate University for Advanced

Studies (SOKENDAI), Moshima, 411-8540, Japan
4

Ecological Genetics Analysis Section, Center for Environmental Biology and Ecosystem

Studies, National Institute for Environmental Studies, Tsukuba, 305-8506, Japan
5

Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, 903-0215,

Japan*Corresponding author
Manabu Onuma, 16-2, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
Tel.: +81-29-850-2498; Email: monuma@nies.go.jp

1Abstract
The wood mouse (genus Apodemus ) is one of the most common rodents in broad-leaf
forests in the temperate zone of the Palaearctic region. Molecular studies of woodmice have critically enhanced the understanding of their evolution and ancestralbiogeographic events. However, their molecular data are currently only limited topartial mitochondrial sequences and a few genes. Therefore, we sequenced the woodmouse genome to facilitate the acquisition of useful resources for inferring theirmolecular evolution. We sampled a wild wood mouse at Tsukuba, Japan, andsequenced its whole-genome using the Illumina Hiseq 2000. To reduce the risk ofnon-randomness, three paired-end libraries (insert sizes: 150, 300, and 500 bp) and,two mate-pair reads (insert sizes: 8 and 20 kbp) were constructed. In total, wegenerated approximately 210 Gbp data. From these sequences, we reconstructed336,124 scaffolds. These data will enhance our understanding of the evolution andecological factors that affect their genetic constitution. The genome scaffolds
generated are available in the National Center Biotechnology Information (NCBI)
BioProject with accession number PRJDB5914.

Keywords: Rodent; mouse; Apodemus speciosus; phylogeography; mammal; evolution2

Specifications Table
Subject area
More specific subject area
Type of data
How data was acquired
Data format
Experimental factors
Experimental featuresData source location
Data accessibility

Related research article

biology
Genomics
Genome sequences
High throughput DNA sequencing using Hiseq2000
FASTA format
Total DNA extraction from liver samples
Freshly collected healthy liver was used for total DNA
extraction
Tsukuba, Ibaraki, JapanThe genome scaffolds generated are available in the
National Center Biotechnology Information (NCBI)
BioProject with accession number PRJDB5914.
Not applicable

Value of the Data

The Japanese wood mouse could be a model mammal for investigating the natural
histories of organisms inhabiting the Japanese Archipelago.

We sequenced the Japanese wood mouse genome to facilitate the acquisition of
useful resources for inferring the molecular evolution of this species.

This data allows other researchers focusing on this species to start genome-wideanalysis.

1. Data
The genus Apodemus, which is a member of the subfamily Murinae, is one of
the most species rich taxa of the murine rodents, next to Rattus and Mus, which are
the first and second speciose genera, respectively [1]. Species belonging to Apodemus,
known as field or wood mice, are distributed in the temperate region of the Eurasiancontinent including the Japanese Archipelago. According to previous molecularphylogenetic analyses, Apodemus diversified in Asia and Europe, around the early3

Pliocene and early Pleistocene eras, respectively [2]. Deciphering the genome
sequences of this genus would facilitate our understanding of the evolutionary trait of
the group adapted to the temperate environment, with the aid of those of Rattus andMus. The genome of a representative species of Apodemus from Europe, Apodemus
sylvaticus, was sequenced by a research group at the Liverpool University according to
the JGI GOLD database (https://gold.jgi.doe.gov/; project ID = Gp0143296), but its
project status is "permanent draft." In Asian species, no genome sequence data are
currently available.
The large Japanese wood mouse, Apodemus speciosus, is widely distributed inJapan from Hokkaido to Kyushu, including the remote peripheral islands. This species
inhabits forests and grasslands, eats insects and acorns, and shows seasonal breedingin the wild. A recent phylogeographic analysis revealed that this species experienced arapid population growth in response to the effect of the Quaternary ice ages [3]. Thus,
the species could be a model mammal for investigating the natural histories oforganisms inhabiting the Japanese Archipelago [4]. We sequenced the Japanese woodmouse genome to facilitate the acquisition of useful resources for inferring themolecular evolution of this species.
The genome was assembled using the ALLPATHS-LG program using two-stepprocesses of assembling and scaffolding. The paired-end reads were first assembled
into contigs, which were then joined to form concatenated scaffolds by using mate-pairreads. We reconstructed 647,983 contigs (N50 is 3.5 kbp). These contigs were joined in336,124 scaffolds (Table 2), and the N50 value of the scaffolds was 47 kbp. The woodmouse genome sequenced is a potentially useful resource for the future molecular
evolutionary analysis of rodents.

4

2. Experimental Design, Materials, and Methods
2.1. Sample preparation and sequencing
We sampled the A. speciosus at Tsukuba, Japan (NIES ID; IB14-021, male). All
rodent experiments were conducted in accordance with the guidelines for using wild
mammals of the Mammal Society of Japan [5] and the rules of the National Institutefor Environmental Studies for analysis and experimentation with environmental
samples contaminated with radioactive materials. Genomic DNA was extracted fromthe liver using proteinase K and phenol:chloroform:isoamyl alcohol [6]. The library
preparations and sequencings were conducted by the Eurofin Sequencing Service(Eurofin MWG Operon, Germany). Paired-end sequencing of each 100-bp end of theDNA fragments was performed using the Hiseq2000 sequencing system (Illumina, San
Diego, CA, USA). We sequenced libraries showing five different insert sizes: 150 bp, 300
bp, 500 bp, 8 kbp, and 20 kbp.

2.2. De novo genome assembly
We sequenced three paired-end libraries (insert sizes: 150, 300, and 500 bp) andtwo mate-pair reads (insert sizes: 8, and 20 kbp). In total, we generated approximately
210 Gbp data. We obtained 362107447, 336419570, 369663105, 22370797, and12377116 reads for each library showing 150-bp, 300-bp, 500-bp, 8-kbp, and 20-kbp
insert sizes, respectively (Table 1). The sequenced reads were used for de novo genome
assembly using the ALLPATHS-LG program ver. 51927 under default parameter settings[6].

Conflict of interest

5

The authors have no potential conflicts of interest to disclose.

Acknowledgements
We would like to appreciate Dr. Hiroko Ishiniwa for the helpful discussions.
This work was supported by an NIG Collaborative Research Program Grant to H. S. (No.
2015-A1-14) and a KAKENHI Grant-in-Aid for Young Scientists (B) to M.M. (No.
16K18613). The computational analysis utilized the supercomputer system of theNational Institute of Genetics, Research Organization of Information and Systems.

Reference[1]J.J. Schenk, K.C. Rowe, S.J. Steppan, Ecological opportunity and incumbency in thediversification of repeated continental colonizations by muroid rodents, Syst. Biol.
62 (2013) 837–864.

[2]

K. Serizawa, H. Suzuki, K. Tsuchiya, A phylogenetic view on species radiation in
Apodemus inferred from variation of nuclear and mitochondrial genes, Biochem.
Genet. 38 (2000) 27–40.

[3]

M. Tomozawa, H. Suzuki, A trend of central versus peripheral structuring inmitochondrial and nuclear gene sequences of the Japanese wood mouse,
Apodemus speciosus, Zool. Sci. 25 (2008):273–285.

[4]

Y. Suzuki, M. Tomozawa, Y. Koizumi, K. Tsuchiya, H. Suzuki, Estimating themolecular evolutionary rates of mitochondrial genes referring to Quaternary Ice
Age events with inferred population expansions and dispersals in Japanese
Apodemus, BMC Evol. Biol. 15 (2015) 187.

[5]

Committee of Reviewing Taxon Names and Specimen Collections. Guidelines forusing wild mammals, Mamm. Sci. 49 (2009) 303–309.

6

[6]

J. Sambrook, D.W. Russel, Preparation of genomic DNA from mouse tails andother small samples, in molecular cloning: a laboratory manual, third ed, Cold
Spring Harbor Laboratory, New York, 2001, 6.23–6.25.

[7]

S. Gnerre, I. Maccallum, D. Przybylski, F. J. Ribeiro, J.N. Burton, B.J. Walker, T.
Sharpe, G. Hall, T.P. Shea, S. Sykes, A.M. Berlin, D. Aird, M. Costello, R. Daza, L.
Williams, R. Nicol, A. Gnirke, C. Nusbaum, E.S. Lander, D.B. Jaffe, High-quality draft
assemblies of mammalian genomes from massively parallel sequence data, Proc.
Natl. Acad. Sci. U. S. A. 108 (2011) 1513–1518.

Table 1. Data amount
Insert size(bp)No. of read pairs

No. of reads

Read length (bp)

Total data (GB)150

362,107,447

724,214,894

100

72.4

300

336,419,570

892,839,140

100

89.3

500

369,663,105

739,326,210

100

73.9

8,000

22,370,797

44,741,594

100

4.5

20,00012,377,116

24,754,232

100

2.5

Table 2. General features of the Apodemus speciosus genome
Number of contigs
Number of contigs per megabase (Mb)
Number of scaffolds
Total contig length
Total scaffold length, with gaps
N50 contig size (kb)
N50 scaffold size (kb)N50 scaffold size (kb), with gaps
Number of scaffolds per megabase (Mb)
Median size of gaps in scaffolds
Median deviation of gaps in scaffolds

7647,983
189
336,124
2,009,551,775
3,428,181,270
3.5
25
47
98.05
2,846
852