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.

Fig. 1

The pipelines overview of the largemouth bass chromosome-level genome assembly. Chrs: chromosomes.

Fig. 2

K‐mer distribution of M. salmoides genome sequencing reads. The K-mers distribution (K = 19) was constructed using 350 bp library data. A total of 49,157,214,151 K-mers were used for genomic length estimation after the removal of the K-mers with abnormal depth. The peak 19‐mer depth was 56, and the genome size was calculated as 49,157,214,151/56 = 874.14 Mb.

Fig. 3

Hi-C assembly of chromosome interactive heat map. Chr01 - Chr23 are the abbreviations of 23 Chromosome. The abscissa and ordinate represent the order of each bin on the corresponding chromosome group. The colour block illuminates the intensity of interaction from yellow (low) to red (high).