BMC Genomics. 2013 Jul 31;14:521. doi: 10.1186/1471-2164-14-521.
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.
片段重复（SDs）或低拷贝重复在基因和基因组进化中都起着重要作用。SD 在许多生物体中都得到了广泛的研究，然而，在蚕（Bombyx mori）中却没有关于 SD 的信息。
在这项研究中，我们鉴定并注释了家蚕基因组中的 SD。我们的结果表明，SD 构成了家蚕基因组序列的约 1.4%（长度≥1 kb，序列同一性≥90%）；数量与黑腹果蝇相似，但小于哺乳动物。几乎一半（42%）的 SD 序列未分配到染色体上，这表明 SD 是基因组序列组装的挑战。我们还使用 qPCR 对大的重复进行了实验验证。SD 含量的分析表明，与免疫、解毒、繁殖和环境信号识别相关的基因在家蚕 SD 中显著富集。
我们的结果表明，SD 给家蚕基因组的测序和组装带来了问题。SD 在免疫、解毒、繁殖和环境信号识别中可能对家蚕具有重要的生物学意义。本研究为家蚕基因组的进化提供了深入的了解，并为昆虫基因组学研究提供了宝贵的资源。
