Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus

Abstract

Background The shuttles hoppfish (mudskipper), Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods. Results A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus. Conclusions We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception.

Genomics comparisons of three chromosome-level mudskipper genome assemblies reveal molecular clues for water-to-land evolution and adaptation

“…Their terrestrial adaptation abilities are largely diverse. For instance, BP takes less time out of water, whereas PM and PMO have more residential time on their terrestrial habitats [8] , [9] .…”

“…These genome assemblies contained long scaffolds but relatively low contigs, without chromosomal details [8] . Yang’s team recently assembled a chromosome-level genome for PMO with 23 chromosomes, which was sequenced by Illumina, PacBio, 10X and Hi-C (high-through-put chromosome conformation capture) methods [9] . However, this PMO annotation has too much redundancy, leading to over 30,000 genes with 10% BUSCO duplicates.…”

“…Here, we provided two improved chromosome-level genome assemblies for BP and PM by integrating PacBio, Nanopore, Hi-C sequencing and our previous Illumina [8] data. We also reannotated the PMO genome data [9] to obtain a redundancy-reduced annotation set. This PMO genome resource will be valuable for us to reveal genomic divergence among Periophthalmus species .…”

Chromosome-level genome assembly of the primitive loach goby,Rhyacichthys aspro, reveals mechanisms underlying Gobioidei diversification

“…Hu et al, 2021;Q. Liu et al, 2021;Y. Yang et al, 2022;You et al, 2014), a reference genome for the earliest divergent family of Gobioidei, the Rhyacichthyidae, is yet to be assembled.…”

“…Liu et al, 2021; Y. Yang et al, 2022; You et al, 2014), a reference genome for the earliest divergent family of Gobioidei, the Rhyacichthyidae, is yet to be assembled. Analysis and annotation of a representative Rhyacichthyidae genome will enable comparison to other recently diverged Gobioidei species and should offer invaluable perspectives on the evolution and diversification of this suborder.…”