Chromosome-level genome assembly of Acrossocheilus fasciatus using PacBio sequencing and Hi-C technology.

Acrossocheilus fasciatus (Cypriniformes, Cyprinidae) is emerged as a newly commercial stream fish in the south of China with high economic and ornamental value. In this study, a chromosome-level reference genome of A. fasciatus was assembled using PacBio, Illumina and Hi-C sequencing technologies. As a result, a high-quality genome was generated with a size of 879.52 Mb (accession number: JAVLVS000000000), scaffold N50 of 32.7 Mb, and contig N50 of 32.7 Mb. The largest and smallest scafford was 60.57 Mb and 16 kb, respectively. BUSCO analysis showed a completeness score of 98.3%. Meanwhile, the assembled sequences were anchored to 25 pseudo-chromosomes with an integration efficiency of 96.95%. Additionally, we found approximately 390.91 Mb of repetitive sequences that accounting for 44.45% of the assembled genome, and predicted 24,900 protein-coding genes. The available genome reported in the present study provided a crucial resource to further investigate the regulation mechanism of genetic diversity, sexual dimorphism and evolutionary histories.

Zheng J ，Jiang J ，Rui Q ，Li F ，Liu S ，Cheng S ，Chi M ，Jiang W ... -  《Scientific Data》

Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae.

The barred knifejaw (Oplegnathus fasciatus), a member of the Oplegnathidae family of the Centrarchiformes, is a commercially important rocky reef fish native to East Asia. Oplegnathus fasciatus has become an important fishery resource for offshore cage aquaculture and fish stocking of marine ranching in China, Japan, and Korea. Recently, sexual dimorphism in growth with neo-sex chromosome and widespread biotic diseases in O. fasciatus have been increasing concern in the industry. However, adequate genome resources for gaining insight into sex-determining mechanisms and establishing genetically resistant breeding systems for O. fasciatus are lacking. Here, we analyzed the entire genome of a female O. fasciatus fish using long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly. We assembled the O. fasciatus genome with a total of 245.0 Gb of raw reads that were generated using both Pacific Bioscience (PacBio) Sequel and Illumina HiSeq 2000 platforms. The final draft genome assembly was approximately 778.7 Mb, which reached a high level of continuity with a contig N50 of 2.1 Mb. The genome size was consistent with the estimated genome size (777.5 Mb) based on k-mer analysis. We combined Hi-C data with a draft genome assembly to generate chromosome-length scaffolds. Twenty-four scaffolds corresponding to the 24 chromosomes were assembled to a final size of 768.8 Mb with a contig N50 of 2.1 Mb and a scaffold N50 of 33.5 Mb using 1,372 contigs. The identified repeat sequences accounted for 33.9% of the entire genome, and 24 003 protein-coding genes with an average of 10.1 exons per gene were annotated using de novo methods, with RNA sequencing data and homologies to other teleosts. According to phylogenetic analysis using protein-coding genes, O. fasciatus is closely related to Larimichthys crocea, with O. fasciatus diverging from their common ancestor approximately 70.5-88.5 million years ago. We generated a high-quality draft genome for O. fasciatus using long-read PacBio sequencing technology, which represents the first chromosome-level reference genome for Oplegnathidae species. Assembly of this genome assists research into fish sex-determining mechanisms and can serve as a resource for accelerating genome-assisted improvements in resistant breeding systems.

Xiao Y ，Xiao Z ，Ma D ，Liu J ，Li J ... -  《GigaScience》

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.

Sun L ，Gao T ，Wang F ，Qin Z ，Yan L ，Tao W ，Li M ，Jin C ，Ma L ，Kocher TD ，Wang D ... -  《-》

Chromosome-scale genome assemblies of sexually dimorphic male and female Acrossocheilus fasciatus.

Acrossocheilus fasciatus is a stream-dwelling fish species of the Barbinae subfamily. It is valued for its colorfully striped appearance and delicious meat. This species is also characterized by apparent sexual dimorphism and toxic ovum. Biology and aquaculture researches of A. fasciatus are hindered by the lack of a high-quality reference genome. Here, we report chromosome-level genome assemblies of the male and female A. fasciatus. The HiFi-only genome assemblies for both female and male individuals were 899.13 Mb (N50 length of 32.58 Mb) and 885.68 Mb (N50 length of 33.06 Mb), respectively. Notably, a substantial proportion of the assembled sequences, accounting for 96.15% and 98.35% for female and male genomes, respectively, were successfully anchored onto 25 chromosomes utilizing Hi-C data. We annotated the female assembly as a reference genome and identified a total of 400.62 Mb (44.56%) repetitive sequences, 27,392 protein-coding genes, and 35,869 ncRNAs. The high-quality male and female reference genomes will provide genomic resources for developing sex-specific molecular markers, inform single-sex breeding, and elucidate genetic mechanisms of sexual dimorphism.

Yuan Y ，Zhong T ，Wang Y ，Yang J ，Gui L ，Shen Y ，Zhou J ，Chung-Davidson YW ，Li W ，Xu J ，Li J ，Li M ，Ren J ... -  《Scientific Data》

Chromosome-level genome assembly and annotation of the yellow grouper, Epinephelus awoara.

Epinephelus awoara, as known as yellow grouper, is a significant economic marine fish that has been bred artificially in China. However, the genetic structure and evolutionary history of yellow grouper remains largely unknown. Here, this work presents the high-quality chromosome-level genome assembly of yellow grouper using PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The 984.48 Mb chromosome-level genome of yellow grouper was assembled, with a contig N50 length of 39.77 Mb and scaffold N50 length of 41.39 Mb. Approximately 99.76% of assembled sequences were anchored into 24 pseudo-chromosomes with the assistance of Hi-C reads. Furthermore, approximately 41.17% of the genome was composed of repetitive elements. In total, 24,541 protein-coding genes were predicted, of which 22,509 (91.72%) genes were functionally annotated. The highly accurate, chromosome-level reference genome assembly and annotation are crucial to the understanding of population genetic structure, adaptive evolution and speciation of the yellow grouper.

Zhang W ，Yang Y ，Hua S ，Ruan Q ，Li D ，Wang L ，Wang X ，Wen X ，Liu X ，Meng Z ... -  《Scientific Data》