A BAC-based integrated linkage map of the silkworm Bombyx mori

Kimiko Yamamoto^*¹ , Junko Nohata^*¹ , Keiko Kadono-Okuda^*¹ , Junko Narukawa¹ , Motoe Sasanuma¹ , Shun-ichi Sasanuma¹ , Hiroshi Minami² , Michihiko Shimomura² , Yoshitaka Suetsugu¹ , Yutaka Banno³ , Kazutoyo Osoegawa⁴ , Pieter J de Jong⁴ , Marian R Goldsmith⁵ and Kazuei Mita¹

¹Insect Genome Research Unit, National Institute of Agrobiological Sciences, Owashi, Tsukuba, Ibaraki 305-8634, Japan

²Genome Project Department, Tsukuba Bank, Mitsubishi Space Software Co., Ltd, Takezono, Tsukuba, Ibaraki 305-8602, Japan

³Laboratory of Insect Genetic Resources, Faculty of Agriculture, Kushu University, Fukuoka 812-8581, Japan

⁴Children's Hospital Oakland Research Institute, 52nd Street, Oakland, California 94609, USA

⁵Biological Sciences Department, University of Rhode Island, Kingston, Rhode Island 02881-0816, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R21doi:10.1186/gb-2008-9-1-r21


Published:	28 January 2008

Subject areas: Evolution, Genetics, Genome studies

Abstract

Background

In 2004, draft sequences of the model lepidopteran Bombyx mori were reported using whole-genome shotgun sequencing. Because of relatively shallow genome coverage, the silkworm genome remains fragmented, hampering annotation and comparative genome studies. For a more complete genome analysis, we developed extended scaffolds combining physical maps with improved genetic maps.

Results

We mapped 1,755 single nucleotide polymorphism (SNP) markers from bacterial artificial chromosome (BAC) end sequences onto 28 linkage groups using a recombining male backcross population, yielding an average inter-SNP distance of 0.81 cM (about 270 kilobases). We constructed 6,221 contigs by fingerprinting clones from three BAC libraries digested with different restriction enzymes, and assigned a total of 724 single copy genes to them by BLAST (basic local alignment search tool) search of the BAC end sequences and high-density BAC filter hybridization using expressed sequence tags as probes. We assigned 964 additional expressed sequence tags to linkage groups by restriction fragment length polymorphism analysis of a nonrecombining female backcross population. Altogether, 361.1 megabases of BAC contigs and singletons were integrated with a map containing 1,688 independent genes. A test of synteny using Oxford grid analysis with more than 500 silkworm genes revealed six versus 20 silkworm linkage groups containing eight or more orthologs of Apis versus Tribolium, respectively.

Conclusion

The integrated map contains approximately 10% of predicted silkworm genes and has an estimated 76% genome coverage by BACs. This provides a new resource for improved assembly of whole-genome shotgun data, gene annotation and positional cloning, and will serve as a platform for comparative genomics and gene discovery in Lepidoptera and other insects.