High-resolution chromosome-level genome of Scylla paramamosain provides molecular insights into adaptive evolution in crab

Crabs exhibit adaptability across diverse ecosystems, encompassing shallow coral reefs, hydrothermal vents, as well as freshwater, seawater, and terrestrial habitats. Our study presents a thorough genomic analysis of the mud crab leveraging ultralong sequencing technologies. We achieved a high-quality chromosome-level assembly, covering 1.21 Gb (scaffold N50 23.61 Mb) with 33,662 protein-coding genes. Anchoring contigs into 49 pseudochromosomes revealed Chromosome 06 as a significant sex chromosome. Notably, the Hox genes are implicated in abdomen limb morphology, with the Abd-A gene identified as a linchpin in pleopod development, shedding light on brachyurization. fru gene, negatively regulated by novel-miR35, plays critical role in ovarian maturation. Additionally, we elucidated neo-functionalization of the elovl6 gene and identified tissue-specific splice variants, suggesting a potential role for Elovl6 in long-chain polyunsaturated fatty acid biosynthesis. These findings contribute..., Sample preparation and genomic DNA isolation
Genomic DNA for sequencing was extracted from the testis of a wild adult male green mud crab S. paramamosain with stage III testis, which was caught off the coast of Shantou, China. A Grandomics Genomic BAC-long DNA Kit was used to isolate ONT ultralong DNA according to the manufacturer's guidelines. The total DNA quantity and quality were evaluated using a NanoDrop One UV-Vis Spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and a Qubit 3.0 Fluorometer (Invitrogen Life Technologies, Carlsbad, CA). Large DNA fragments were obtained through gel cutting with the Blue Pippin system (Sage Science, Beverly, MA). Qualification of DNA involved visual inspection for foreign matter, assessment of degradation and size via 0.75 % agarose gel electrophoresis, check on purity (OD260/280 between 1.8-2.0; OD260/230 between 2.0-2.2) using Nanodrop, and precise quantification with Qubit 3.0 Fluorometer (Invitrogen, USA).
Library construction and seque..., , # High-resolution chromosome-level genome provides molecular insights into adaptive evolution in crab

[https://doi.org/10.5061/dryad.kwh70rzc3](https://doi.org/10.5061/dryad.kwh70rzc3)

The sequences and the annotation files of the green mud crab genome. The dataset consists of SP2022.Chr.bed, SP2022.fasta, SP2022.genome.gff, and SP2022.genome.pep.fasta files.

## Description of the data and file structure

The sequences file was in fasta format and the annotation file was in gff including genome sequencing, assembly, and annotation of green mud crab.

## Sharing/Access information

Links to other publicly accessible locations of the data:

* [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1059155](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1059155)