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

Hui Xiang,Anjiang Tan,Guojie Zhang,Yun Ding,Qiuhong Guo,Jun Wang,Qiye Li,Wen Wang,Jinmin Lian,Qingyou Xia,Fangyin Dai,Xun Xu,Lei Chen,Xin Li,Andrew Willden

doi:10.1186/1471-2164-14-646

Abstract

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

Highlights

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
To explore the possible evolution role of DNA methylation, we first test if the two silkworm DNA methyltransferase genes (Dnmt1, Dnmt2), have biological function
Injections of double strand RNA of Dnmt1 and Dnmt2, respectively to ~ 8 h eggs led to down regulation of their expression level (Figure 1A)

Summary

Introduction

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. It is often to see many obtained traits instable to environmental alteration The mechanisms underlying these distinct phenomena are not a new issue—as far back as the 1860s, with no knowledge of Mendelian genetics, Darwin speculated such mechanisms underlying the environmentinduced changes [1], and in the extreme, this conjecture fits Lamarck’s idea of acquired inheritance. While under many circumstances epigenetically influenced agronomic traits are not so stable as to genetically controlled ones [2,3], many case studies have shown that epigenetic alterations could promptly respond to environmental signals independent of genetic bases [4,5] and differentially methylated alleles could lead to heritable phenotypic changes across generations [2,6,7,8], including some agronomically important traits [2]. Functionality of the more widely distributed DNMT1 (Additional file 1: Figure S1), which is essential for developmental normality and critically required for transgenerational stability of mammals’ and plants’ epigenomes [16,17], remains unknown in insects

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