Whole-genome sequencing of leopard coral grouper ( Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution.

Xiao-Chun Liu,Hao-Ran Lin,Zi-Ning Meng,Yang Yang,Jun-Hong Xia,Jing-Fang Chen,Xi Wu,Li-Na Wu

doi:10.24272/j.issn.2095-8137.2020.038

Abstract

Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.

Highlights

Groupers (Epinephelidae, Perciformes) are predators found in coral reef ecosystems, and include more than 160 species in 16 genera (Zhuang et al, 2013)
Benchmarking Universal Single-Copy Orthologs (BUSCO) was used to verify the integrality of the assembled genome
BUSCO alignment showed that our final assembly contained 4 149 complete BUSCOs (90.5%), including 4 034 single-copy and 115 duplicated BUSCOs (Supplementary Table S2)

Summary

Introduction

Groupers (Epinephelidae, Perciformes) are predators found in coral reef ecosystems, and include more than 160 species in 16 genera (Zhuang et al, 2013). They are commercially important in aquaculture, with approximately 47 grouper species cultured in East and Southeast Asia Whereby they firstly differentiate as females, with some later changing to males (Adams, 2003). They have a complicated social system and the occurrence of sex reversal can be triggered by a change in social status (Chen et al, 2019). Groupers are a good model for studies on sex inversion, speciation, and social systems

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Discussion

Conclusion