Dataset Information

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

ABSTRACT: A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.

SUBMITTER: Xia Q

PROVIDER: S-EPMC3951477 | biostudies-literature | 2009 Oct

REPOSITORIES: biostudies-literature

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Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

Xia Qingyou Q Guo Yiran Y Zhang Ze Z Li Dong D Xuan Zhaoling Z Li Zhuo Z Dai Fangyin F Li Yingrui Y Cheng Daojun D Li Ruiqiang R Cheng Tingcai T Jiang Tao T Becquet Celine C Xu Xun X Liu Chun C Zha Xingfu X Fan Wei W Lin Ying Y Shen Yihong Y Jiang Lan L Jensen Jeffrey J Hellmann Ines I Tang Si S Zhao Ping P Xu Hanfu H Yu Chang C Zhang Guojie G Li Jun J Cao Jianjun J Liu Shiping S He Ningjia N Zhou Yan Y Liu Hui H Zhao Jing J Ye Chen C Du Zhouhe Z Pan Guoqing G Zhao Aichun A Shao Haojing H Zeng Wei W Wu Ping P Li Chunfeng C Pan Minhui M Li Jingjing J Yin Xuyang X Li Dawei D Wang Juan J Zheng Huisong H Wang Wen W Zhang Xiuqing X Li Songgang S Yang Huanming H Lu Cheng C Nielsen Rasmus R Zhou Zeyang Z Wang Jian J Xiang Zhonghuai Z Wang Jun J

Science (New York, N.Y.) 20090827 5951

A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication ev ...[more]

PMID: 19713493

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Project description:BackgroundCarboxyl/cholinesterases (CCEs) have pivotal roles in dietary detoxification, pheromone or hormone degradation and neurodevelopment. The recent completion of genome projects in various insect species has led to the identification of multiple CCEs with unknown functions. Here, we analyzed the phylogeny, expression and genomic distribution of 69 putative CCEs in the silkworm, Bombyx mori (Lepidoptera: Bombycidae).ResultsA phylogenetic tree of CCEs in B. mori and other lepidopteran species was constructed. The expression pattern of each B. mori CCE was also investigated by a search of an expressed sequence tag (EST) database, and the relationship between phylogeny and expression was analyzed. A large number of B. mori CCEs were identified from a midgut EST library. CCEs expressed in the midgut formed a cluster in the phylogenetic tree that included not only B. mori genes but also those of other lepidopteran species. The silkworm, and possibly also other lepidopteran species, has a large number of CCEs, and this might be a consequence of the large cluster of midgut CCEs. Investigation of intron-exon organization in B. mori CCEs revealed that their positions and splicing site phases were strongly conserved. Several B. mori CCEs, including juvenile hormone esterase, not only showed clustering in the phylogenetic tree but were also closely located on silkworm chromosomes. We investigated the phylogeny and microsynteny of neuroligins in detail, among many CCEs. Interestingly, we found the evolution of this gene appeared not to be conserved between B. mori and other insect orders.ConclusionsWe analyzed 69 putative CCEs from B. mori. Comparison of these CCEs with other lepidopteran CCEs indicated that they had conserved expression and function in this insect order. The analyses showed that CCEs were unevenly distributed across the genome of B. mori and suggested that neuroligins may have a distinct evolutionary history from other insect order. It is possible that such an uneven genomic distribution and a unique neuroligin evolution are shared with other lepidopteran insects. Our genomic analysis has provided novel information on the CCEs of the silkworm, which will be of value to understanding the biology, physiology and evolution of insect CCEs.

Dataset Information

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

Publications

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).

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