Chromosome-level genome assembly of largemouth bass (Micropterus salmoides) using PacBio and Hi-C technologies

Abstract

The largemouth bass (Micropterus salmoides) has become a cosmopolitan species due to its widespread introduction as game or domesticated fish. Here a high-quality chromosome-level reference genome of M. salmoides was produced by combining Illumina paired-end sequencing, PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. Ultimately, the genome was assembled into 844.88 Mb with a contig N50 of 15.68 Mb and scaffold N50 length of 35.77 Mb. About 99.9% assembly genome sequences (844.00 Mb) could be anchored to 23 chromosomes, and 98.03% assembly genome sequences could be ordered and directed. The genome contained 38.19% repeat sequences and 2693 noncoding RNAs. A total of 26,370 protein-coding genes from 3415 gene families were predicted, of which 97.69% were functionally annotated. The high-quality genome assembly will be a fundamental resource to study and understand how M. salmoides adapt to novel and changing environments around the world, and also be expected to contribute to the genetic breeding and other research.

Chromosome-level assembly of Dictyophora rubrovolvata genome using third-generation DNA sequencing and Hi-C analysis

“…Library concentration and insert size were determined using the Qubit 2.0 and Agilent 2100, respectively, and Q-PCR was used to estimate the effective concentration of the library. High-quality Hi-C libraries were sequenced on the Illumina NovaSeq PE150 sequencing platform, and the sequencing data were used for chromosome-level assembly ( He et al 2022 ). Hi-C data were filtered and evaluated using HiC-Pro software ( Servant et al 2015 ), it could identify the valid interaction pairs and invalid interaction pairs in the Hi-C sequencing results by analyzing the comparison results, and realize the quality assessment of the Hi-C libraries.…”

Comparative Transcriptomic Analysis of Largemouth Bass (Micropterus salmoides) Livers Reveals Response Mechanisms to High Temperatures

“…Raw sequencing reads were quality-trimmed using Fastp (v.0.19.5) [33] to get rid of low-quality reads, as described by Zhang et al [32]. The clean reads were aligned to the reference genome of largemouth bass (NCBI accession number: GCF_014851395.1) [34] using HISAT2 (v.2.1.0) [35] in the orientation mode. Then, the mapped reads were assembled using StringTie [36] with the largemouth bass genome.…”