A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon.

Meiqi Lv,Guangyi Fan,Huanming Yang,Xin Liu,Kaiqiang Liu,Shahid Mahboob,Changlin Liu,Jiahao Wang,Chang Li,Changwei Shao,Yaolei Zhang,Junnian Liu

doi:10.3389/fgene.2020.581161

Abstract

Anglerfishes are a highly diverse group of species with unique characteristics. Here, we report the first chromosome-level genome of a species in the order Lophiiformes, the yellow goosefish (Lophius litulon), obtained by whole genome shotgun sequencing and high-throughput chromatin conformation capture. Approximately 97.20% of the assembly spanning 709.23 Mb could be anchored to 23 chromosomes with a contig N50 of 164.91 kb. The BUSCO value was 95.4%, suggesting that the quality of the assembly was high. A comparative gene family analysis identified expanded and contracted gene families, and these may be associated with adaptation to the benthic environment and the lack of scales in the species. A majority of positively selected genes were related to metabolic processes, suggesting that digestive and metabolic system evolution expanded the diversity of yellow goosefish prey. Our study provides a valuable genetic resource for understanding the mechanisms underlying the unique features of the yellow goosefish and for investigating anglerfish evolution.

Highlights

Lophiiformes is a teleost order containing 68 genera and more than ∼300 species found in benthic, shallow-water, and deep sea habitats (Miya et al, 2010)
By performing quality control of Hi-C sequencing data and implementing the 3DDNA pipeline, we obtained 166,195,977 valid Hi-C read pairs and anchored 689.34 Mb (∼97.20%) of the assembled scaffolds to 23 clear linkage groups based on chromatin interactions (Supplementary Table 3 and Figure 1B), indicating that the karyotype number for Lophius litulon is 2n = 46, which is different from that of Lophiomus setigerus (2n = 48)
We investigated the evolutionary relationships between yellow goosefish and nine representative fish taxa (Gasterosteus aculeatus, Oryzias latipes, Oreochromis niloticus, Takifugu rubripes, Tetraodon nigroviridis, Cynoglossus semilaevis, Danio rerio, and Larimichthys crocea) using Lepisosteus oculatus as an outgroup based on gene families, defining 19,487 gene families in these 10 species

Summary

Introduction

Lophiiformes (commonly known as anglerfishes) is a teleost order containing 68 genera and more than ∼300 species found in benthic, shallow-water, and deep sea habitats (Miya et al, 2010). Yellow goosefish (Lophius litulon) belonging to Lophiiformes is mainly distributed in seas of Korea, Japan, and China. It is an important commercial fish and is widely consumed. Phylogenetic relationships in Lophiiformes have been studied by using mitochondrial genomes of 39 species from 33 genera (Miya et al, 2010). High-quality whole genome sequences for species in this order are not available, limiting our understanding of the molecular basis of the unique characteristics of this group, such as the lack of scales on the body surface, diverse feeding habits, and large liver

Methods

Results

Conclusion