Open Access Research article

Segmental duplications in the silkworm genome

Qian Zhao1, Zhenglin Zhu1, Masahiro Kasahara2, Shinichi Morishita2 and Ze Zhang1*

Author Affiliations

1 Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 400044, China

2 Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan

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BMC Genomics 2013, 14:521  doi:10.1186/1471-2164-14-521

Published: 31 July 2013



Segmental duplications (SDs) or low-copy repeats play important roles in both gene and genome evolution. SDs have been extensively investigated in many organisms, however, there is no information about SDs in the silkworm, Bombyx mori.


In this study, we identified and annotated the SDs in the silkworm genome. Our results suggested that SDs constitute ~1.4% of the silkworm genome sequence (≥1 kb in length and ≥90% in the identity of sequence); the number is similar to that in Drosophila melanogaster but smaller than mammalian organisms. Almost half (42%) of the SD sequences are not assigned to chromosomes, indicating that the SDs are challenges for the assembling of genome sequences. We also provided experimental validation of large duplications using qPCR. The analysis of SD content indicated that the genes related to immunity, detoxification, reproduction, and environmental signal recognition are significantly enriched in the silkworm SDs.


Our results suggested that segmental duplications have been problematic for sequencing and assembling of the silkworm genome. SDs may have important biological significances in immunity, detoxification, reproduction, and environmental signal recognition in the silkworm. This study provides insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research.