Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris

The Chinese longsnout catfish(Leiocassis longirostris Günther)is one of the most economically important freshwater fish in China.As wild populations have declined sharply in recent years,it is also a valuable model for research on sexual dimorphism,comparative biology,and conservation.However,the current lack of high-quality chromosome-level genome information for the species hinders the advancement of comparative genomic analysis and evolutionary studies.Therefore,we constructed the first high-quality chromosomelevel reference genome for L.longirostris.The total genome was 703.19 Mb,with 389 contigs and contig N50 length of 4.29 Mb.Using high-throughput chromosome conformation capture(Hi-C)data,the genome sequences(685.53 Mb)were scaffolded into 26 chromosomes ranging from 17.36 to 43.97 Mb,resulting in a chromosomal anchoring rate for the genome of 97.44%.In total,23708 protein-coding genes were identified in the genome.Phylogenetic analysis indicated that L.longirostris and its closest related species P.fulvidraco diverged approximately 26.6 million years ago.This highquality reference genome of L.longirostris should pave the way for future genomic comparisons and evolutionary research.

Phylogenetic relationships of Cypriniformes and plasticity of pharyngeal teeth in the adaptive radiation of cyprinids

The Cypriniformes comprise approximately 4,200 species accounting for 25% of the diversity of all freshwater fish, which is widely distributed across the world's continents except Antarctica, South America, and Australia. The highest species diversity is found in Southeastern Asia. Despite its remarkable species diversity and broad-scale geographic patterns of distribution, the evolutionary history of this major freshwater fish group remains largely unresolved. To gain insight of the evolutionary history of Cypriniformes, we present a phylogeny of this group using 1 mitochondrial gene and 15 nuclear genes comprising a total of14,061 bp. Bayesian inference using all gene fragments yielded a well resolved phylogeny, which is mostly consistent with topologies obtained from Maximum Likelihood analyses. Our results further confirmed the monophyly of Cypriniformes and seven constituent subclades including Cyprinidae, Catostomidae, Gyrinocheilidae, Balitoridae, Cobitidae, Nemacheilidae, and Botiidae. Bayesian divergence time analysis indicated that the origin of the Cypriniformes was about 193 Mya during the early Jurassic, coinciding with the onset of the Pangaea breakup. The basal divergence of Cypriniformes is 154 Mya during the late Jurassic. Our findings from molecular divergence and biogeographical analysis indicate the most likely initial geographical range of the ancient Cypriniformes was both East and South Asia(Southeastern area of Mesozoic Laurasia). Moreover, the burst in species diversity in Cyprinidae afforded by the nearly worldwide colonization is possibly in response to the plasticity of pharyngeal dentition. The present study demonstrates that the Cypriniformes was about 193 Mya during the early Jurassic,coinciding with the onset of the Pangaea breakup. The plasticity of pharyngeal dentition of cyprinids might contribute to the burst and radiation of this lineage. The phylogenetic and biogeographic analyses in this study help to improve our understanding of the evolutionary history of this diverse and important freshwater fish group.

Sex chromosome turnover and biodiversity in fishes

The impact of sex chromosomes and their turnover in speciation remains a subject of ongoing debate in the field of evolutionary biology.Fishes are the largest group of vertebrates,and they exhibit unparalleled sexual plasticity,as well as diverse sex-determining(SD)genes,sex chromosomes,and sex-determination mechanisms.This diversity is hypothesized to be associated with the frequent turnover of sex chromosomes in fishes.Although it is evident that amh and amhr2 are repeatedly and independently recruited as SD genes,their relationship with the rapid turnover of sex chromosomes and the biodiversity of fishes remains unknown.We summarize the canonical models of sex chromosome turnover and highlight the vital roles of gene mutation and hybridization with empirical evidence.We revisit Haldane’s rule and the large Xeffect and propose the hypothesis that sex chromosomes accelerate speciation by multiplying genotypes via hybridization.By integrating recent findings on the turnover of SD genes,sex chromosomes,and sexdetermination systems in fish species,this review provides insights into the relationship between sex chromosome evolution and biodiversity in fishes.

Cortisol safeguards oogenesis by promoting follicular cell survival

The role of glucocorticoids in oogenesis remains to be elucidated. cyp11c1 encodes the key enzyme involved in the synthesis of cortisol, the major glucocorticoid in teleosts. In our previous study, we mutated cyp11c1 in tilapia and analyzed its role in spermatogenesis. In this study, we analyzed its role in oogenesis. cyp11c1^(+/-)XX tilapia showed normal ovarian morphology but poor egg quality, as indicated by the mortality of embryos before 3 d post fertilization, which could be partially rescued by the supplement of exogenous cortisol to the mother fish. Transcriptome analyses revealed reduced expression of maternal genes in the eggs of the cyp11c1^(+/-)XX fish. The cyp11c1^(-/-)females showed impaired vitellogenesis and arrested oogenesis due to significantly decreased serum cortisol. Further analyses revealed decreased serum E2 level and expression of amh, an important regulator of follicular cell development, and increased follicular cell apoptosis in the ovaries of cyp11c1^(-/-)XX fish, which could be rescued by supplement of either exogenous cortisol or E2. Luciferase assays revealed a direct regulation of cortisol and E2 on amh transcription via GRs or ESRs. Taken together, our results demonstrate that cortisol safeguards oogenesis by promoting follicular cell survival probably via Amh signaling.

The transcription factor Sox30 is involved in Nile tilapia spermatogenesis

Spermatogenesis is a complex process in which spermatogonial stem cells differentiate and develop into mature spermatozoa.The transcriptional regulatory network involved in fish spermatogenesis remains poorly understood.Here,we demonstrate in Nile tilapia that the Sox transcription factor family member Sox30 is specifically expressed in the testes and mainly localizes to spermatocytes and spermatids.CRISPR/Cas9-mediated sox30 mutation results in abnormal spermiogenesis,reduction of sperm motility,and male subfertility.Comparative transcriptome analysis shows that sox30 mutation alters the expression of genes involved in spermatogenesis.Further chromatin immunoprecipitation followed by high-throughput sequencing(Ch IP-seq),Ch IP-PCR,and luciferase reporter assays revealed that Sox30 positively regulates the transcription of ift140 and ptprb,two genes involved in spermiogenesis,by directly binding to their promoters.Our data,taken together,indicate that Sox30 plays an essential role in Nile tilapia spermatogenesis by directly regulating the transcription of the spermiogenesis-related genes ift140 and ptprb.

Gene editing nuclease and its application in tilapia

Gene editing nucleases including zinc-finger nucleases(ZFNs), transcription activator like effector nucleases(TALENs) and clustered regularly interspaced short palindromic repeats(CRISPR)–CRISPR-associated(Cas) system(CRISPR/Cas9) provide powerful tools that improve our ability to understand the physiological processes and their underlying mechanisms. To date, these approaches have already been widely used to generate knockout and knockin models in a large number of species. Fishes comprise nearly half of extant vertebrate species and provide excellent models for studying many aspects of biology. In this review, we present an overview of recent advances in the use of gene editing nucleases for studies of fish species. We focus particularly on the use of TALENs and CRISPR/Cas9 genome editing for studying sex determination in tilapia.

Interspecific differences and ecological correlations between scale number and skin structure in freshwater fishes

Fish skin is mainly composed of the epidermis,dermis,and its derivative scales.There is a wide diversity in scale number in fishes,but the diversity of skin structure lacks systematic histological comparison.This research aimed to improve our understanding of the functional relationship between the scale number and the skin structure in freshwater fishes and to determine which ecological factors affect the scale number and skin structure.First,we presented a method to quantify skin structure in fish and histologically quantified the skin structure of 54 freshwater fishes.Second,we collected the scale number and habitat information of 509 Cyprinidae fishes in China and explored which ecological factors were related to their scale number.Third,common carp and scaleless carp were used as models to study the effects of scale loss on swimming.We found a strong negative correlation between scale thickness and scale number.The main factor affecting the skin structure of fishes was the species’water column position,and the skin of benthic fishes was the most well-developed(thicker skin layers(dermis,epidermis)or more/larger goblet cells and club cells).The scale number was related to two factors,namely,temperature and water column position,and cold,benthic and pelagic adaptation may have contributed to increased scale numbers.Only in benthic fishes,the more well-developed their skin,the more scales.In common carp,scale loss did not affect its swimming performance.In summary,we suggest that there is a rich diversity of skin structure in freshwater fishes,and the scales of fish with well-developed skin tend to degenerate(greater number/smaller size/thinner,or even disappear),but the skin of fish with degenerated scales is not necessarily well developed.