Data from: Chromosome-level assembly of Southern catfish (Silurus meridionalis) provides insights into visual adaptation to the nocturnal and benthic lifestyles

Southern catfish (Silurus meridionalis) is a nocturnal and benthic
freshwater fish endemic to the Yangtze River and its
tributaries with an important economic value but a drastically
declining wild population. 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 that
catfish possess a rod-dominated visual
system which is responsible for scotopic
vision. The absence of cone opsins SWS1 and
SWS2 resulted in the lack of UV and 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 color vision. A higher expression
level of rod phototransduction genes than that of cone genes and
higher rod-to-cone ratio leaded to higher optical sensitivity
under dim light conditions. In addition, analysis of
the genes involved in eye morphogenesis and
development revealed the loss of conserved
noncoding elements (CNEs), which might be associated
with the small eyes in catfish. Taken together, our
study provided important clues for the adaptation of the
catfish visual system to a benthic lifestyle. The draft genome of
S. meridionalis represents a valuable resource for
elucidation of molecular mechanism of ecological adaptation, as
well as genetic breeding in aquaculture.