Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi-C technology.

Onychostoma macrolepis is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the O.macrolepis genome obtained from the integration of nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that O. macrolepis diverged from common carp approximately 24.25 million years ago. The chromosomes of O. macrolepis showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of O. macrolepis.

Establishment of three estrogen receptors (esr1, esr2a, esr2b) knockout lines for functional study in Nile tilapia.

Estrogens play fundamental roles in regulating reproductive activities and they act through estrogen receptors (ESRs) in all vertebrates. To date, distinct roles of estrogen receptors have been characterized only in human and model organisms, including mouse, rat, zebrafish and medaka. Physiological role of estrogen/receptor signaling in reproduction remains poorly defined in non-model organisms. In the present study, we successfully generated esr1, esr2a and esr2b mutant lines in tilapia by CRISPR/Cas9 and examined their phenotypes. Surprisingly, the esr1 mutants showed no phenotypes of reproductive development and function in both females and males. The esr2a mutant females showed significantly delayed ovarian development and follicle growth at 90 and 180 dah, and the development caught up later at 360 dah. The esr2a mutant males showed no phenotypes at 90 dah, and displayed smaller gonads and efferent ducts, less spermatogonia and more abnormal sperms at 180 dah. In contrast, the esr2b mutants displayed abnormal development of ovarian ducts and efferent ducts which failed to connect to the genital orifice, and which in turn, resulted in infertility in female and male, respectively, although they produced gametes in their gonads. Taken together, our study provides evidence for differential functions of esr1, esr2a and esr2b in fish reproduction.

Genome-wide identification, evolution of DNA methyltransferases and their expression during gonadal development in Nile tilapia.

DNA methyltransferases (dnmts) are responsible for DNA methylation and play important roles in organism development. In this study, seven dnmts genes (dnmt1, dnmt2, dnmt3aa, dnmt3ab, dnmt3ba, dnmt3bb.1, dnmt3bb.2) were identified in Nile tilapia. Comprehensive analyses of dnmts were performed using available genome databases from representative animal species. Phylogenetic analysis revealed that the dnmts family were highly conserved in teleosts. Based on transcriptome data from eight adult tilapia tissues, the dnmts were found to be dominantly expressed in the head kidney, testis and ovary. Analyses of the gonadal transcriptome data in different developmental stages revealed that all dnmts were expressed in both ovary and testis, and four de novo dnmts (dnmt3aa, dnmt3ab, dnmt3bb.1, dnmt3bb.2) showed higher expression in the testis than in the ovary. Furthermore, during sex reversal induced by Fadrozole, the expression of these four de novo dnmts increased significantly in treated group compared to female control group. By in situ hybridization, the seven dnmts were found to be expressed mainly in phase I and II oocytes of the ovary and spermatocytes of the testis. When gonads were incubated with a methyltransferase inhibitor (5-AzaCdR) in vitro, the expression of dnmts genes were down-regulated significantly, while the expression of cyp19a1a (a key gene in female pathway) and dmrt1 (a key gene in male pathway) increased significantly. Our results revealed the conservation of dnmts during evolution and indicated a potential role of dnmts in epigenetic regulation of gonadal development.