# The Genome Survey Analysis of Female and Male Sepiella japonica

## TL;DR

This study provides a genome survey of female and male Sepiella japonica, offering insights into their genomic characteristics and laying the groundwork for future research.

## Contribution

The study presents the first genome survey of female and male S. japonica, including key genomic metrics and mitochondrial genome sequences.

## Key findings

- Estimated genome sizes were 4317 Mb (female) and 4222 Mb (male), with high repeat content (76%) and low heterozygosity.
- Mitochondrial genomes were 16,729 bp (female) and 16,725 bp (male), with mononucleotide repeats being the most abundant SSR motif.
- The study provides foundational data for future high-quality genome assembly and comparative analysis of S. japonica.

## Abstract

Background/Objectives: Sepiella japonica is a highly adaptable cephalopod with an advanced nervous system and complex reproductive behavior, capable of reproducing two to three generations annually depending on water temperature. However, the absence of a complete genome assembly has limited molecular investigations of its unique biological characteristics. This study aimed to perform a genome survey of female and male S. japonica, systematically characterize and compare key genomic characteristics. Methods: Quality-filtered short reads enabled K-mer-based estimation of genome size, heterozygosity, repeat content, and GC content; generation of draft genome assemblies, SSR identification from the draft assemblies, complete mitogenome assemblies and annotations with ML phylogeny based on 13 concatenated PCGs, and PSMC-based demographic inference. Results: The estimated genome sizes were 4317 Mb (female) and 4222 Mb (male), with revised estimates of 4310 Mb and 4215 Mb, respectively. K-mer analysis revealed heterozygosity rates of 0.85% (female) and 0.77% (male) and repeat content of 76.05% (female) and 75.91% (male). The assembled genome sizes were 4197 Mb for females (N50: 508 bp) and 4206 Mb for males (N50: 511 bp); the GC content was 34.15% for both genomes. Deduplicated data showed GC content of 35.16% (female) and 35.27% (male). Microsatellite analysis revealed that mononucleotide repeats were the most abundant simple sequence repeat motif. The mitochondrial genome sequences measured 16,729 bp for the female genome and 16,725 bp for the male genome. Conclusions: This study provides fundamental data for subsequent high-quality whole-genome assembly and comparative analysis of female and male genomes.