Chromosome‐level assembly of southern catfish (silurus meridionalis) provides insights into visual adaptation to nocturnal and benthic lifestyles

Abstract

The Southern catfish (Silurus meridionalis) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome-level draft genome of S. meridionalis using 69.7-Gb Nanopore long reads and 49.5-Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9-Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod-dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S. meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

“…Nevertheless, the heterozygosity estimated for TARdn1 is one of the highest reported for a fish species. To our knowledge, this is the highest heterozygosity estimated for a fish through k -mer analysis, with other reported values ranging from 0.1% (Tibetan loach Triplophysa tibetana and Murray cod Maccullochella peelii ) to 0.9% (Java medaka Oryzias javanicus ) (Austin et al, 2017; Ge et al, 2019; Gong et al, 2018; Lu et al, 2020; Nguinkal et al, 2019; Takehana et al, 2020; Vij et al, 2016; Yang et al, 2019; H. H. Zhang et al, 2020; Zheng et al, 2021). Even the heterozygosity estimated through SNPs (0.64%) is high compared to estimations from other fish using the same method (e.g.…”

“…Triplophysa tibetana and Murray cod Maccullochella peelii) to 0.9% (Java medaka Oryzias javanicus) (Austin et al, 2017;Ge et al, 2019;Gong et al, 2018;Lu et al, 2020;Nguinkal et al, 2019;Takehana et al, 2020;Vij et al, 2016;Yang et al, 2019;Zheng et al, 2021). Even the heterozygosity estimated through SNPs (0.64%) is high compared to estimations from other fish using the same method (e.g.…”

Identification of sex chromosome and sex-determining gene of southern catfish ( Silurus meridionalis ) based on XX, XY and YY genome sequencing

“…Our previous study identified sex-linked DNA markers and demonstrated an XX/XY sex-determination system in this species [12]. We also generated a whole-genome assembly anchored on chromosomes for an XX female individual [13]. Yet, little is known about genetic sex determination in southern catfish beyond males being the heterogametic sex, and its sex locus and SD gene remain elusive.…”

Insights into chromosomal evolution and sex determination of Pseudobagrus ussuriensis (Bagridae, Siluriformes) based on a chromosome-level genome

“…Through combining the third-generation sequencing method (Oxford Nanopore or PacBio) and the high-through chromosome conformation capture (Hi-C) technology, genomes can be assembled into the chromosome level, which have been successfully used in many fish species. 29–31 Chromosome-level genomes have also been reported in catfishes, such as channel catfish ( Ictalurus punctatus ), 32 yellow catfish ( Pelteobagrus fulvidraco ), 33 giant devil catfish ( Bagarius yarrelli ), 34 Southern catfish ( Silurus meridionalis ), 35 Chinese longsnout catfish ( Leiocassis longirostris ), 36 striped catfish ( Pangasianodon hypophthalmus ), 37 and redtail catfish ( Hemibagrus wyckioides ). 38 These chromosome-level assemblies have been widely used as reliable reference genomes for studies of many fields, including ecological adaptation, 35 , 39 , 40 genome evolution, 41–43 gene evolution, 44 , 45 immunology, 46–48 and identification of target-trait-related genes, 49 , 50 in aquatic animals.…”