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. 2014 Mar 31:15:251.
doi: 10.1186/1471-2164-15-251.

Copy number variations among silkworms

Qian Zhao, Min-Jin Han, Wei Sun, Ze Zhang  1
Affiliations

Copy number variations among silkworms

Qian Zhao et al. BMC Genomics. .

Abstract

Background: Copy number variations (CNVs), which are important source for genetic and phenotypic variation, have been shown to be associated with disease as well as important QTLs, especially in domesticated animals. However, little is known about the CNVs in silkworm.

Results: In this study, we have constructed the first CNVs map based on genome-wide analysis of CNVs in domesticated silkworm. Using next-generation sequencing as well as quantitative PCR (qPCR), we identified ~319 CNVs in total and almost half of them (~ 49%) were distributed on uncharacterized chromosome. The CNVs covered 10.8 Mb, which is about 2.3% of the entire silkworm genome. Furthermore, approximately 61% of CNVs directly overlapped with SDs in silkworm. The genes in CNVs are mainly related to reproduction, immunity, detoxification and signal recognition, which is consistent with the observations in mammals.

Conclusions: An initial CNVs map for silkworm has been described in this study. And this map provides new information for genetic variations in silkworm. Furthermore, the silkworm CNVs may play important roles in reproduction, immunity, detoxification and signal recognition. This study provided insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research.

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Figures

Figure 1
Figure 1
Cluster analysis of the 348 copy number variable regions in four silkworms.
Figure 2
Figure 2
Silkworm CNVs map. Only 30 scaffolds were shown and all scaffolds with CNVs information were listed in Additional file 4. The silkworm assembly scaffold is represented as black bars. Larger bars in colors which intersect the scaffold represent the segmental duplications and copy number variation.
Figure 3
Figure 3
GO terms associated with the CNV regions and comparison with the genes in SDs.
Figure 4
Figure 4
Depth comparisons of CNVs in four silkworms. The average read depth are listed in Table  1. The read depth are shown the RD for XiaF, N4, NanC and AK. (A) Depth comparison of CNVs in four silkworms for the region 1–12948 of scaffold 890 shows wild-specific region (loss). (B) Depth comparison of CNVs in four silkworms for the region 1–15850 of scaffold 880 shows domesticated-specific region (gain). (C) Depth comparison of CNVs in four silkworms for the region 1–26564 of nscaf 2457 shows all-possess region (gain).
Figure 5
Figure 5
qPCR confirmation. Different bars represent different genes. X-axis shows the different individuals while Y-axis is the value of 2-∆∆CT that is indicator of duplications (RQ). The domesticated silkworms include JianPZ, Ou, N4, XiaF, Yi, J115, wild silkworms include ZiY, YanT, Rong, Lu.
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