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

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.

SUBMITTER: Xiang H

PROVIDER: S-EPMC3852238 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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

Xiang Hui H Li Xin X Dai Fangyin F Xu Xun X Tan Anjiang A Chen Lei L Zhang Guojie G Ding Yun Y Li Qiye Q Lian Jinmin J Willden Andrew A Guo Qiuhong Q Xia Qingyou Q Wang Jun J Wang Wen W

BMC genomics 20130923

<h4>Background</h4>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 quest ...[more]

PMID: 24059350

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Project description:In this study, five wild edible herbs traditionally consumed in the Tuscany region (Italy) were evaluated for their potential in human nutrition. The nutraceutical characterization of Rumex acetosa, Cichorium intybus, Picris hieracioides, Sanguisorba minor, and Plantago coronopus, as well as their sensory profile were reported. Additionally, a preliminary assessment of completely different domestication of the wild species (named "soilless", pot, and open field) was conducted to verify the possibility of their marketability, which is impossible if the plants are only gathered as wild. The open field domestication allowed to obtain plants with nutraceutical and sensory profiles similar to those of the wild species, especially in C. intybus, P. hieracioides, and S. minor. The pot domestication allow to obtain plants with chlorophyll and carotenoid contents close to those of the wild species, as well as a lower total phenolic and flavonoid content and ascorbic acid content than wild species. In the "soilless" method, R. acetosa and P. coronopus exhibited a high quality in terms of phytochemicals and antioxidant activity. Afterward, the sensory profile was strongly affected by the domestication in terms of the palatability, except for R. acetosa and P. coronopus, which displayed Hedonic Index (HI) values close to the consumer acceptability limit (HI = 6). A sensory profile similar to that of wild species was reported in open field domestication, whereas a worse sensory profile was reported in P. hieracioides and C. intybus domesticated using the soilless method. Finally, according to the preliminary assessment carried out in this study through an analysis of the general nutraceutical properties, S. minor was shown to be the most promising species thanks to its intrinsically highest nutraceutical properties considering the marketability of wild edible herbs as "new" functional food. However, further research on the bioavailability and bioactivity tests of nutraceutical compounds present in this species are required to confirm the findings of this study.

Dataset Information

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

Publications

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

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