Chromosome-level genome assembly of the endangered humphead wrasse
Cheilinus undulates insight into unexpected expansion of opsin genes in
fishes
Abstract
Wrasses are distributed worldwide in coral reef environments, and
display a specialized feature of paired pharyngeal bones united into a
single jawbone. Among wrasses, Cheilinus undulatus is an endangered
species with high economic and ecological values. Here, we present
genome assembly of C. undulatus, using Illumina, Nanopore, and Hi-C
sequencing. The 1.17 Gb genome was generated from 328 contigs with an
N50 length of 16.5 Mb, and anchored to 24 chromosomes. A total of 22,218
genes were functionally annotated, and 96.36% of BUSCO genes were
completely represented. Transcriptomic analyses showed to express
96.79% of the predicted gene. Transposons were most abundant,
accounting for 39.88% of genome, with low divergence, owing to evolve
with close species approximately 58.37 million years ago, and 560/1,848
gene families were expanded and contracted in the reconstructed
phylogeny, respectively. Additionally, 46 genes underwent positive
selection. Comparative genomic analyses with other fishes revealed
unexpected expansion of opsins SWS2, LWS1, and Rh2, showing single-gene
expansion up to five copies in tandem arrays. Gene conversion was
responsible for abundance of opsin specific for C. undulatus, and the
uneven distribution of transposons in opsin windows and adjacent windows
probably contributed to gene conversion, providing gene function
fluidity. Divergence of opsin expression in tissues indicated
alternative adaptations of the increased opsin copies for the visual
foraging and sexual behavior. Genome sequencing of the humphead wrasse
provides valuable resources for future investigation of conservation,
evolution, and functional morphology of fishes.