Retrotransposable Elements, Chromosomes and Chromatin Cytogenet Genome Res 110:144–151 DOI: 10.1159/000084946 Retrotransposable elements on the W chromosome of the silkworm, Bombyx mori H. Abe, a K. Mita, b Y. Yasukochi, b T. Oshiki, a T. Shimada c a Department of Biological Production, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo; b National Institute of Agrobiological Sciences, Ibaraki; c Graduate School of Agriculture and Life Science, The University of Tokyo, Tokyo (Japan) Manuscript received 1 December 2003; accepted in revised form for publication by J.-N. Volff 30 January 2004. Supported by grants from the Research for the Future Program, the Japan Society for the Promotion of Science (to T.S.), and from the Animal Genome Research Pro- gram, Ministry of Agriculture, Forestry and Fisheries, Japan (to K.M. and T.S.). Request reprints from Hiroaki Abe, Department of Biological Production Faculty of Agriculture, Tokyo University of Agriculture and Technology Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509 (Japan) telephone/fax: +81-42-367-5848; e-mail: wfem@cc.tuat.ac.jp ABC Fax + 41 61 306 12 34 E-mail karger@karger.ch www.karger.com © 2005 S. Karger AG, Basel 1424–8581/05/1104–0144$22.00/0 Accessible online at: www.karger.com/cgr Abstract. The sex chromosomes of the silkworm, Bombyx mori, are designated ZW(XY) for females and ZZ(XX) for males. The W chromosome of B. mori does not recombine with the Z chromosome and autosomes and no genes for morpholog- ical characters have been mapped to the W chromosome as yet. Furthermore, femaleness is determined by the presence of a single W chromosome, regardless of the number of autosomes or Z chromosomes. To understand these interesting features of the W chromosome, it is necessary to analyze the W chromo- some at the molecular biology level. Initially to isolate DNA sequences specific for the W chromosome as randomly ampli- fied polymorphic DNA (RAPD) markers, we compared the genomic DNAs between males and females by PCR with arbi- trary 10-mer primers. To the present, we have identified 12 W-specific RAPD markers, and with the exception of one RAPD marker, all of the deduced amino acid sequences of these W-specific RAPD markers show similarity to previously reported amino acid sequences of retrotransposable elements from various organisms. After constructing a genomic DNA lambda phage library of B. mori we obtained two lambda phage clones, one containing the W-Kabuki RAPD sequence and one containing the W-Samurai RAPD sequence and found that these DNA sequences comprised nested structures of many retrotransposable elements. To further analyze the W chromo- some, we obtained 14 W-specific bacterial artificial chromo- some (BAC) clones from three BAC libraries and subjected these clones to shotgun sequencing. The resulting assembly of sequences did not produce a single contiguous sequence due to the presence of many retrotransposable elements. Therefore, we coupled PCR with shotgun sequencing. Through these anal- yses, we found that many long terminal repeat (LTR) and non- LTR retrotransposons, retroposons, DNA transposons and their derivatives, have accumulated on the W chromosome as strata. These results strongly indicate that retrotransposable elements are the main structural component of the W chromo- some. Copyright © 2005 S. Karger AG, Basel The silkworm, Bombyx mori, belongs to the family Bomby- cidae in the order Lepidoptera. Sericulture and development of the silkworm for the production of silk dates back about 4,500 years. While silkworm B. mori is no longer found as a wild insect, it’s assumed ancestral species, Bombyx mandarina can still be found in nature. It is believed that the sericulture began in ancient times on the Chinese continent. The silkworm undergoes complete metamorphosis; that is, it passes through four stages in its life cycle: egg, larva, pupa, and moth. Eggs laid by the female moth develop into embryos and hatch out as larvae. The larvae are fed on the leaves of the mulberry tree, which belongs to the genus Morus. When the larvae reach their full growth, they emit silk thread and con- struct cocoons. In the cocoon, the larval tissues and organs degenerate, the larva transforms into the pupa, and adult organs are formed. If the cocoon is left undisturbed by man, the pupa transforms into the moth and escapes from the “prison” that it has built for itself. Both female and male moths live only to carry out reproduction, without feeding, and subsequently die.