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SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data.

Kunpeng Lu^1,2, Yifei Pan¹, Jianghong Shen¹

¹State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400715, China.

Nucleic Acids Research

|November 9, 2023

Summary

SilkMeta is a new database integrating silkworm pan-genome and multi-omics data. This resource aids research into genomic diversity and phenotype-genotype associations in Bombyx mori.

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Area of Science:

Genomics
Bioinformatics
Animal Models

Background:

The silkworm (Bombyx mori) is a vital animal model in research and agriculture.
Previous work established a silkworm super-pan-genome dataset for studying genomic diversity.

Purpose of the Study:

To present SilkMeta, a comprehensive database of silkworm pan-genome and multi-omics data.
To provide a platform for comparative and functional genomics research in silkworms and other insects.

Main Methods:

Integrated 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, and 294 phenome characterizations.
Included tens of millions of variations (variome), lncRNAs, full-length transcripts, and population statistics.
Developed an interactive bioinformatics platform with twelve functional modules and data visualization tools.

Main Results:

SilkMeta offers a rich repository of silkworm genomic and multi-omics data.
The database incorporates functional genomics research publications and a mutant map.
Provided bioinformatics tools facilitate data retrieval and analysis.

Conclusions:

SilkMeta serves as a valuable resource for understanding silkworm global genomic diversity and phenotype-genotype associations.
The platform supports comparative genomics and benefits the broader insect biology community.