3.6 Expansion of opsin genes in ray-finned fishes
To test whether the diversity of opsin genes is useful for behavioral
functions, we investigated copy number of opsin genes in 13
well-assembled genomes of ray-finned fishes, representing several visual
types, and C. milli as an outgroup (Fig. 6B). For example,L. maculates usually rely on eye development and the visual
system for prey capture (Shao et al. 2018). B.
pectinirostris , an amphibious fish adapted to terrestrial environments,
is adapted for aerial vision in order to avoid terrestrial predators
(You et al. 2014). In contrast, S. anshuiensis is a
cavefish, and its eyes are completely lost (Yang et al. 2016).
Opsin genes in the zebrafish genome were used as a sequence reference.
We finally identified 122 opsin genes (Table S11), including 117
complete genes, 5 incomplete genes (missing DNA segments less than 100
bp in four, and inserting DNA fragments of 480 bps in one), and sorted
into five subfamilies. The LWS2 and Rh2-1 genes were lost
in these fishes. Genes in the Rh1 subfamily were lost in G.
aculeatus ; the Rh1-2 gene was only found in S.
anshuiensis . Rh2-2 and three genes were found only in three
species. The SWS1 gene was lost in S. melops , T.
rubripes , C. semilaevis , and B. pectinirostris . Species
lost opsin genes that were not related to that species’ visual
sensitivity variation.
Synteny analyses of opsin genes, together with evolutionary trees,
showed LWS1 as a single ancient opsin, and duplicated an
immediately adjacent component of SWS2 in evolutionary origins
(Fig. 7A), which was a result of the second run of whole-genome
duplication events (2R) (Lin et al. 2017). A duplicate of the
SWS2- LWS1 complexity in different chromosomes of S. anshuiensiswas believed to be a result of the 4R that occurred in the common
ancestor of Cypriniformes (Lin et al. 2017). The SWS2 gene
has two duplicated copies in B. pectinirostris , L.
maculates , and O. niloticus, and up to four adjacent copies inC. undulatus , which could improve visual acuity of these species
by gene duplications to adapt to dim-light environments (Yokoyama & Jia
2020). SWS2 is a single-gene duplication that often acts as a
springboard for adaptive diversification in a genomic region
(~ 30 kb), where two additional duplication events
occurred to produce up to three SWS2 genes in some percomorph
fish lineages (Cortesi et al. 2015). Interestingly, we observed
the retention of up to four SWS2 genes in C. undulatus ,
suggesting an unexpected expansion of the SWS2 gene in the
percomorph group. However, the SWS2 gene in L. maculatesshowed divergence due to an inserted fragment, and a gene that was
located between SWS2 and LWS1 could be diversified from
the SWS2 gene in O. latipes (Fig. 7A). Our results provide
evidence that SWS2 could diversify after gene duplication,
subsequently causing gene functional changes (Porath-Krause et
al. 2016).
Surprisingly, the LWS1 gene has displayed single-gene
duplications to produce four copies, and a retrotransposed duplicate inC. undulatus , whereas other species showed either one LWS1gene, or one LWS1 gene plus a retrotransposed duplicate, such asB. pectinirostris and L. bergylta (Fig. 7A).
Traditionally, expansion events of the LWS1 gene have not been
observed in approximately 100 ray-finned fish genomes (Cortesi et
al. 2015; Lin et al. 2017; Phillips et al. 2016; Rennisonet al. 2012). However, an insect species, Xenos vesparum ,
with compound eyes possessed five unique LWS opsin genes, and
these LWS duplications were used to restore the longer-wavelength
sensitivity due to SWS gene loss (Sharkey et al. 2017).LWS1 expansions were notably important in C. undulatus ,
with behaviors often guided by visual cues. C. undulatusjuveniles inhabit sandy inshore regions, shallow reefs, and murky outer
river areas to capture zooplankton (Sadovy et al. 2003), and theLWS1 gene is required for the prevalent wavelengths under shallow
water conditions, such as depths less than 30 m (Lin et al.2017). Therefore, duplication of the LWS1 gene could increase the
ability of juveniles to detect prey against a light background.LWS1 gene duplications indicated an independent opsin expansion
event, rather than whole-genome duplication. C. undulatus has 48
chromosomes (Huo et al. 2009), suggesting that this species
underwent the 3R, a fish-specific genome duplication, similar to that of
most percomorph fishes (Cortesi et al. 2015). We inferred thatLWS1 expansion occurred in C. undulatus after 3R with very
few changes in copy number, except for one copy translocated to another
chromosome (Fig. 7A).
Synteny analyses of Rh2 showed that gene expansions have occurred
to produce three to five tandem copies in the branches composed of
Labridae fishes, including C. undulatus , S. melops , andL. bergylta (Fig. 7B). One copy was translocated to another
chromosome in L. bergylta , and one copy was diversified to
acquire a novel function different from the opsin gene in S.
melops . In contrast, other species displayed no more than threeRh2 copies in tandem arrays, except zebrafish. C.
undulatus has five Rh2 copies, the most reported of any fish
(Phillips et al. 2016). Rh2 duplications may coincide with
eye evolution in which they have played an important role in expanding
the photoreceptive capabilities of organisms by opsin copies (Davieset al. 2007). Labridae fish are more commonly observed inhabiting
offshore habitats along steep outer reef slopes, reef flats, and lagoon
reefs to depths of up to 60 m (Sadovy et al. 2003). It is
reported that marine fish below 50 m possess more Rh2 genes than
those living above 30 m (Lin et al. 2017). Green-sensitive Rh2
helps vertebrate species to better discriminate wavelengths in this
environment (Yokoyama & Jia 2020). Multiple Rh2 genes imply good visual
adaptation in predating sea hares, boxfish, and starfish, which employ
color disguises, similar to reef environments. In contrast, the Rh2 gene
was reduced to one in C. semilaevis and A. percula (Fig.
7B), suggesting that these species likely adapted alternative mechanisms
instead of gene copy to contribute to visual sensitivity, such as the
known opsin sequence tuning sites (Phillips et al. 2016).
To detect duplication events in the SWS2 , LWS1 , andRh2 genes, we constructed phylogenetic trees of these genes. Four
duplications of the SWS1 gene were present in C. undulatus , and
one duplication in L. maculates (Fig. S3). As divergence after
gene duplication, B. pectinirostris and O. niloticus did
not show SWS1 gene duplication, although synteny analyses
revealed two adjacent genes in one chromosome (Fig. 7A). In theLWS1 gene tree, gene duplications were observed in two species
(Fig. S4). Due to 4R, the S. anshuiensis genome showedLWS1 gene duplications, whereas four gene duplications plus a
retrotransposed duplicate was found in C. undulatus (Fig. 7A,
Fig. S4). Phylogenetic analysis was applied to infer Rh2 gene
duplication, and many species showed duplication events (Fig. S5). In
the C. undulatus genome, the Rh2 gene showed one
duplication and two copies were separated into different closed clades,
which was regarded as diversification after gene duplication. To our
knowledge, it is not known whether opsin genes, such as SWS1 ,LWS1 , and Rh2 , expanded their copy numbers in one species.
Opsin genes can change copies by genome duplication, gene duplication,
and gene conversion (Sawyer 1989). Interestingly, C. undulatusshowed unexpected opsin copies, revealing multiple genetic mechanisms of
opsin expansion.