Chromosome-scale assembly and high-density genetic map of the yellow drum, Nibea albiflora

Dongdong Xu,Bao Lou,Lu Tian,Juhong Zhou,Ruiyi Chen,Qihui Zhu,Ligai Wang,Wanchang Zhang,Jiumeng Min,Hongbin Song,Bin Wu,Peng Tan

doi:10.1038/s41597-021-01045-z

Dongdong Xu, Bao Lou + Show 10 more

Open Access

https://doi.org/10.1038/s41597-021-01045-z

Copy DOI

Abstract

The yellow drum (Nibea albiflora) is an economically important sciaenid fish in East Asian countries. In this study, we sequenced and assembled a near-complete gynogenetic yellow drum genome. We generated 45.63 Gb of Illumina short-reads and 80.27 Gb of PacBio long-reads and assembled them into a 628.01-Mb genome with a contig N50 of 4.42 Mb. Twenty-four chromosomes with a scaffold N50 of 26.73 Mb were obtained using the Hi-C analysis. We predicted a set of 27,069 protein-coding genes, of which 1,581 and 2,583 were expanded and contracted gene families, respectively. The most expanded genes were categorised into the protein binding, zinc-ion binding and ATP binding functional pathways. We built a high-density genetic linkage map that spanned 4,300.2 cM with 24 linkage groups and a resolution of 0.69 cM. The high-quality reference genome and annotated profiles that we produced will not only increase our understanding of the genetic architecture of economic traits in the yellow drum, but also help us explore the evolution and unique biological characteristics of sciaenid fishes.

Highlights

Background & SummarySciaenidae is one of the largest families within Perciformes; it consists of 66 genera and approximately 294 species[1]
The yellow drum (Nibea albiflora) is a sciaenid found from the South China Sea to the coastal waters of Japan and Korea and is one of the most economically important marine fish in China and other East Asian countries (FishBase: www.fishbase.org)
Sea cage farming of this fish has rapidly spread throughout the coastal regions of Southeast China; the annual production of the yellow drum in China currently exceeds 60,000 tons[3] and has the potential to become a large-scale industry, akin to the farming of the large yellow croaker, which is the most heavily farmed species among all net-cage-farmed marine fish[4]

Summary

Introduction

Background & SummarySciaenidae is one of the largest families within Perciformes; it consists of 66 genera and approximately 294 species[1]. We constructed a high-quality chromosome-level reference genome using long-reads generated by the PacBio platform, short reads generated by the Illumina platform, and the Hi-C analysis.

Results

Conclusion