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Open Access Highly Accessed Research article

Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication

Hui Xiang1, Xin Li1, Fangyin Dai2, Xun Xu3, Anjiang Tan4, Lei Chen1, Guojie Zhang3, Yun Ding1, Qiye Li3, Jinmin Lian3, Andrew Willden1, Qiuhong Guo4, Qingyou Xia2, Jun Wang3* and Wen Wang1*

Author Affiliations

1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province 650223, China

2 State Key Laboratory of Silkworm Genome Biology, Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, No.2 Tiansheng Road, Chongqing, BeiBei District 400715, China

3 BGI-Shenzhen, Shenzhen, China, Beishan Industrial Zone, Shenzhen, Yantian District 518083, China

4 Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China

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BMC Genomics 2013, 14:646  doi:10.1186/1471-2164-14-646

Published: 23 September 2013

Abstract

Background

In contrast to wild species, which have typically evolved phenotypes over long periods of natural selection, domesticates rapidly gained human-preferred agronomic traits in a relatively short-time frame via artificial selection. Under domesticated conditions, many traits can be observed that cannot only be due to environmental alteration. In the case of silkworms, aside from genetic divergence, whether epigenetic divergence played a role in domestication is an unanswered question. The silkworm is still an enigma in that it has two DNA methyltransferases (DNMT1 and DNMT2) but their functionality is unknown. Even in particular the functionality of the widely distributed DNMT1 remains unknown in insects in general.

Results

By embryonic RNA interference, we reveal that knockdown of silkworm Dnmt1 caused decreased hatchability, providing the first direct experimental evidence of functional significance of insect Dnmt1. In the light of this fact and those that DNA methylation is correlated with gene expression in silkworms and some agronomic traits in domesticated organisms are not stable, we comprehensively compare silk gland methylomes of 3 domesticated (Bombyx mori) and 4 wild (Bombyx mandarina) silkworms to identify differentially methylated genes between the two. We observed 2-fold more differentiated methylated cytosinces (mCs) in domesticated silkworms as compared to their wild counterparts, suggesting a trend of increasing DNA methylation during domestication. Further study of more domesticated and wild silkworms narrowed down the domesticates’ epimutations, and we were able to identify a number of differential genes. One such gene showing demethyaltion in domesticates correspondently displays lower gene expression, and more interestingly, has experienced selective sweep. A methylation-increased gene seems to result in higher expression in domesticates and the function of its Drosophila homolog was previously found to be essential for cell volume regulation, indicating a possible correlation with the enlargement of silk glands in domesticated silkworms.

Conclusions

Our results imply epigenetic influences at work during domestication, which gives insight into long time historical controversies regarding acquired inheritance.

Keywords:
dnmt1; Comparative methylomics; Silkworm; Domestication