# Chromosome-Level Genome and Variation Map of Eri Silkworm Samia cynthia ricini

## TL;DR

Researchers created a detailed genome map for the eri silkworm, revealing its genetic structure and variations to support breeding and research.

## Contribution

The first chromosome-level genome and comprehensive variation map for the eri silkworm, Samia cynthia ricini.

## Key findings

- The genome assembly spans 456.16 Mb with 15,729 protein-coding genes and 48.51% repetitive content.
- Over 4 million SNPs, 1 million InDels, and 53 thousand SVs were identified, forming the first variation map for this species.
- Comparative analysis with Bombyx mori revealed syntenic relationships and chromosomal fusion/fission events.

## Abstract

The eri silkworm (Samia cynthia ricini) is a resource insect valued for its silk production, nutrient-rich pupae used in food and animal feed, and unique biological traits that intrigue scientists. Despite its importance, genomic resources for this species have remained limited. In this study, we generated a chromosome-level genome (456.16 Mb) using advanced DNA sequencing technologies, revealing key genomic insights such as 15,729 protein-coding genes, a 48.51% repetitive content, and syntenic relationships (including chromosomal fusion/fission events) with the well-studied domestic silkworm (Bombyx mori). We further discovered millions of genetic variations, including SNPs, InDels, and SVs. All the data are freely available in the SilkMeta database, helping researchers and breeders improve silk production, explore sustainable food sources, and advance research on insect biology.

The eri silkworm Samia cynthia ricini (S. ricini) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for S. ricini generated through integrated long-read, short-read, and Hi-C sequencing data. The final 456.16 Mb assembly spans 14 chromosomes, exhibiting 98.5% BUSCO completeness and a 48.51% repetitive content. Functional annotation of the 15,729 protein-coding genes against five major databases (NR, SwissProt, Pfam, GO, and KEGG) revealed a maximum annotation rate of 92.71%, demonstrating high gene set quality. Comparative genomics with B. mori uncovered conserved syntenic blocks interspersed with chromosomal fusion/fission events and inversions. We further identified 4.27 million SNPs, 1.02 million InDels, and 53,367 SVs, establishing the first comprehensive variation map for this species. These genomic variations provide a foundation for marker-assisted breeding programs and trait association studies. All the genomic resources and interactive visualization tools were integrated into the SilkMeta database. This study establishes S. ricini as a pivotal resource for comparative lepidopteran genomics and accelerates molecular breeding programs for this agriculturally valuable insect.