DOI: 10.5061/dryad.4qrfj6qgm
title: Genomic features for adaptation and evolutionary dynamics of four Asian domestic carps

description: 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.
description: The four major Asian
 domestic carps, <em>Mylopharyngodon piceus</em>,
 <em>Ctenopharyngodon idella</em>, <em>Hypophtalmichthys
 molitrix</em>, and <em>Aristichthys nobilis</em>, were
 obtained from the Hunan Fisheries Science Institute (Changsha City, Hunan
 Province, China) and fresh tissues were stored in liquid
 nitrogen<strong> </strong>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 the bam2fasta
 program. The HiFi reads obtained had an average length ranging from 15 to
 17 Kbp and a maximum length ranging from 47 to 50
 Kbp. <strong>Genome size
 estimation</strong> All clean Illumina
 reads were used for k-mer analysis to estimate genome size using GCE
 (V1.0.2) software after filtering. The k-mer length was 17, and kmerfreq
 calculated the 17-mer depth frequency distribution, and gce calculated the
 genome size, repeat content, homozygosity, and heterozygosity using the
 following formula: genome size=Total kmer number / kmer coverage depth.
 For black carp, grass carp, silver carp, and bighead carp, the predicted
 genome sizes were 833, 840, 804, and 846 Mb,
 respectively. <strong>Genome
 <em>de-novo</em>
 assembly</strong> The contigs from HiFi
 reads were assembled using hifiasm software (V0.15.4-r343) to create a
 primary contig assembly in the GFA format, which included contigs of the
 two haplotypes. The GFA format files were then converted into fasta files
 using a custom Python script. Due to the advantages of HiFi reads, such as
 their length (10–20 kb) and high accuracy (&gt;99.9%), the contig
 assembly did not require polishing. The primary contig assembly was then
 used to create a chromosome-level assembly of the genome, which was
 anchored using Juicer (V1.9.9) and 3D-DNA (V180114) software. Manual
 adjustment was performed on assembled genomes with discrepant chromatin
 interaction patterns caused by placement and orientation issues using
 juicebox (V1.9.8) tools to improve assembly
 quality.
description: # 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