DOI: 10.5061/dryad.bk3j9kdgh
title: Chromosome-level genome assembly and annotation of Pterygoplichthys pardalis

description: Suckermouth catfishes, with their evolved powerful features, have become
 notorious invasive species, causing significant damage to aquatic
 ecosystems. However, the lack of high-quality genomes severely restricts
 research on this group within the field. In this study, we de
 novo  assembled the chromosome-level genome assembly of
 Pterygoplichthys pardalis using multiple platforms of sequencing data,
 including Illumina short reads, Nanopore long reads, and Hi-C sequencing
 reads, resulting in a 1.51 Gb genome assembly. Multiple evaluations,
 including read mapping ratio (98.52%), transcript mapping ratio (99.61%),
 conserved BUSCO gene set (98.8%), and N50 score (49.47 Mb), indicated the
 high continuity and accuracy of the genome assembly we generated. Genome
 annotation found that 0.97 Gb of genome sequences are repetitive
 sequences, accounting for 64.47% of the genome assembly. Further, 23,859
 protein-coding genes were successfully predicted, 92.92% of which could be
 annotated in functional databases. This high-quality genome assembly
 of P. pardalis provides a valuable resource for understanding the
 genetic underpinnings of P. pardalis's invasive success and offers
 critical data for future fisheries research and management.
description: # Chromosome-level genome assembly and annotation of Pterygoplichthys
 pardalis Dataset DOI: [10.5061/dryad.bk3j9kdgh](10.5061/dryad.bk3j9kdgh)
 ## Description of the data and file structure Dataset DOI:
 [10.5061/dryad.bk3j9kdgh](10.5061/dryad.bk3j9kdgh) The catfish samples
 used in this study were purchased from an ornamental fish wholesale market
 in Xi'an, China. The remaining samples of this specimen (Catfish_01)
 have been cryopreserved at -80°C in the Biodiversity Repository of the
 Institute of Basic and Translational Medicine at Xi'an Medical
 University. All animal specimens were collected legally in accordance with
 the policy of the Animal Care and Use Ethics of the institution. Genomic
 DNA was extracted from the muscle tissue of one suckermouth catfish (*P.
 pardalis*) using the Blood & Cell Culture DNA Mini Kit (Qiagen). ###
 Files and variables #### File: Pterygoplichthys\\\_pardalis.cds
 **Description:**  Gene coding sequence #### File:
 Pterygoplichthys\\\_pardalis.pep **Description:** Gene Protein Sequence
 #### File: Pterygoplichthys\\\_pardalis.gff3 **Description:** Final gene
 annotation results based on three methods #### File:
 Pterygoplichthys\\\_pardalis\\\_genome.fasta **Description:** Genome
 assembly file We add these files in the new version: #### File:
 Pterygoplichthys\\\_pardalis\\\_denovo.gff3 **Description:** The *de
 novo*-based prediction of protein-coding genes #### File:
 Pterygoplichthys\\\_pardalis\\\_transcripts.gff3 **Description:**  The 
 transcript-based prediction of protein-coding genes #### File:
 Pterygoplichthys\\\_pardalis\\\_homology.gff3 **Description:** The
 homology-based annotation of protein-coding genes ## Code/software
 **Genome assembly** The genome assembly was performed with the following
 steps: 1) Long reads from the Nanopore platform were used for the
 contig-level assembly using NextDenovo (v2.2). Key parameters were
 carefully set to ensure optimal assembly, including a read cutoff of 1k, a
 seed cutoff of 59754, and a blocksize of 5g. 2) Cleaned short reads
 generated from the Illumina short-insert library were mapped onto the
 assembled contigs using BWA (v0.7.17) . To further enhance the accuracy of
 the assembly at the single-base level, we performed two iterations of
 correction using Pilon (v1.22) . 3) We mapped the Hi-C sequencing reads to
 the corrected contigs, and subsequently utilized Juicer (v1.5.7) and 3D
 *de novo* assembly (v180922) to perform chromosome-level genome assembly.
 **Genome annotation** Tandem repetitive sequences within the genome were
 identified using Tandem Repeat Finder (v4.07) .Non-interspersed repeats in
 the genome were annotated using RepeatMasker (v4.1.0).Transposable
 elements (TEs) in the genome were annotated at both the DNA and protein
 levels. A *de novo *repeat library at the DNA level was constructed using
 RepeatModeler (v1.0.4)  enabling the identification of potential novel
 repetitive sequences. The genome assembly was searched against Repbase
 (v23.06 ) using RepeatMasker to detect homologous repetitive sequences,
 providing a more comprehensive picture of the repetitive sequence content.
 RM-BLASTX within RepeatProteinMask (v4.1.0)  was employed to query the TE
 protein database at the protein level. ## Access information Other
 publicly accessible locations of the data: * Not applicable Data was
 derived from the following sources: * Not applicable ## Version changes
 **29-April-2025:**  * Added Pterygoplichthys_pardalis_denovo.gff3 file
 which contains the *de novo*-based prediction of protein-coding genes; *
 Added Pterygoplichthys_pardalis_transcripts.gff3 file which contains the 
 transcript-based prediction of protein-coding genes; *
 Added Pterygoplichthys_pardalis_homology.gff3 file which contains the 
 homology-based annotation of protein-coding genes.