Open Access Research article

A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)

Ryo Kakioka1*, Tomoyuki Kokita2*, Hiroki Kumada2, Katsutoshi Watanabe1 and Noboru Okuda3

Author Affiliations

1 Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, 606-8502, Kyoto, Japan

2 Department of Marine Bioscience, Fukui Prefectural University, 1-1 Gakuen-cho, 917-0003, Obama, Japan

3 Center for Ecological Research, Kyoto University, 509-3, Hirano 2-chome, 520-2113, Otsu, Japan

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BMC Genomics 2013, 14:32  doi:10.1186/1471-2164-14-32

Published: 16 January 2013

Additional files

Additional file 1:

List of RAD stack sequences, including consensus sequences of RAD loci.

Format: FASTA Size: 3.4MB Download file

Open Data

Additional file 2: Figure S1:

A detailed linkage map of the interspecific cross between Gnathopogon caerulescens and Gnathopogon elongatus. The lengths of the linkage groups are based on Kosambi cM.

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Additional file 3: Figure S2:

Linkage maps of LG3, LG3M, and LG3D, and extent of deviation from Mendelian segregation in LG3D. (A) Linkage maps of LG3, LG3M, and LG3D. The map distance estimates are in Kosambi cM. The homology of loci between linkage groups is indicated with a line. (B) Degree of deviation from the expected 1:2:1 segregation along LG3D. The x-axis represents the position on LG3D; y-axis represents χ2-test P-values for distorted segregation. The dotted line represent α = 0.001.

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Additional file 4: Figure S3:

Comparison of syntenic pairs of a linkage group of Gnathopogon and a chromosome of zebrafish. Each dot represents the position of a homologous locus. The x-axis is proportional to physical length; the y-axis is proportional to Kosambi cM.

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