Genomic features for adaptation and evolutionary dynamics of four Asian domestic carps

The four major Asian domestic carps, namely grass carp, black carp, bighead carp, and silver carp, belonging to Cypriniformes, and are among the most important aquaculture species and sources of animal protein in China. they have similar habitats, closely phylogenetic relationships, and large body sizes. However, they differ in their diet preferences, behavior, and physical traits. Here, to better understand their evolution, we generated the chromosome-level genomes of the four domestic carps. We uploaded the assembled genomes of four carps, the gene annotation files in gff format of four carps, the protein sequences files of four carps, and the analysis code or pipeline used in the article, and the readme file. This study shed light on the genomic bases driving species divergence and adaptation, providing valuable insights for future research in this field., The four major Asian domestic carps, Mylopharyngodon piceus, Ctenopharyngodon idella, Hypophtalmichthys molitrix, and Aristichthys nobilis, were obtained from the Hunan Fisheries Science Institute (Changsha City, Hunan Province, China) and fresh tissues were stored in liquid nitrogen for high-quality sample preparation and sequencing. HiFi and Hi-C sequencing were performed on genomic DNA extracted from fish muscle and liver, respectively.
To obtain high-quality reads for subsequent analyses, Illumina raw reads were filtered to remove unknown and low-quality bases, as well as adaptor and primer sequences, using Trimmomatic software (V0.39) with specific parameters, including LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, and MINLEN:50. HiFi raw reads were processed using SMRTLink to generate subread bam files, with the following criteria: --chunk 12/16 --min-passes 3 --min-snr 2.5 --min-length 50 --max-length 50000 --min-rq 0.99. The resulting bam files were converted to fasta files using t..., , # Genomic features for adaptation and evolutionary dynamics of four Asian domestic carps

[https://doi.org/10.5061/dryad.4qrfj6qgm](https://doi.org/10.5061/dryad.4qrfj6qgm)

## Description of the data and file structure

genomes:
silver_carp.genome.fasta
bighead_carp.genome.fasta
grass_carp.genome.fasta
black_carp.genome.fasta

proteins:
silver_carp.pep.fasta
bighead_carp.pep.fasta
grass_carp.pep.fasta
black_carp.pep.fasta

gffs:
silver_carp.gff
bighead_carp.gff
grass_carp.gff
black_carp.gff