Chromosome-level genome assembly of the spotted sea bass, <i>Lateolabrax maculatus</i>

Shao, Changwei; Li, Chang; Wang, Na; Qin, Yating; Xu, Wenteng; Li, Qun; Zhou, Qian; Zhao, Yong; Li, Xihong; Liu, Shanshan; Chen, Xiaowu; Mahboob, Shahid; Liu, Xin; Chen, Songlin

doi:10.1093/gigascience/giy114

Cited by 43 publications

(40 citation statements)

References 42 publications

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“…The larger genome size estimated by the fluorometric assay could be due to the non-specific nature of the fluorescent dye used, possibly detecting binding to non-genomic nucleotides. The size of the genome of S. argus estimated in this study was larger than that of Sillago sinica (534 MB) [42], but smaller than that of Lateolabrax maculatus (670 MB) [43], Dicentrarchus labrax (675 MB) [44] and Larimichthys crocea (679 MB) [45].…”

Section: Discussionmentioning

confidence: 51%

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Huang

Jiang

et al. 2019

Animals

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Simple Summary: The spotted scat, Scatophagus argus, is a marine aquaculture fish species that is economically important in Asia. As the spotted scat exhibits notable sexual dimorphism with respect to growth, aquaculture efficiency can be increased through the practice of sex control breeding. However, genomic data from S. argus is lacking. In the present study, a genomic survey was conducted using next-generation sequencing technologies. Data, including the size of the genome, sequence repeat ratio, heterozygosity ratio, whole genome sequence and gene annotation were obtained. This information will serve to support the breeding and aquaculture of S. argus. Abstract:The spotted scat, Scatophagus argus, is a species of fish that is widely propagated within the Chinese aquaculture industry and therefore has significant economic value. Despite this, studies of its genome are severely lacking. In the present study, a genomic survey of S. argus was conducted using next-generation sequencing (NGS). In total, 55.699 GB (female) and 51.047 GB (male) of high-quality sequence data were obtained. Genome sizes were estimated to be 598.73 (female) and 597.60 (male) Mbp. The sequence repeat ratios were calculated to be 27.06% (female) and 26.99% (male). Heterozygosity ratios were 0.37% for females and 0.38% for males. Reads were assembled into 444,961 (female) and 453,459 (male) contigs with N50 lengths of 5,747 and 5,745 bp for females and males, respectively. The average guanine-cytosine (GC) content of the female genome was 41.78%, and 41.82% for the male. A total of 42,869 (female) and 43,283 (male) genes were annotated to the non-redundant (NR) and SwissProt databases. The female and male genomes contained 66.6% and 67.8% BUSCO core genes, respectively. Dinucleotide repeats were the dominant form of simple sequence repeats (SSR) observed in females (68.69%) and males (68.56%). Additionally, gene fragments of Dmrt1 were only observed in the male genome. This is the first report of a genome-wide characterization of S. argus.

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Section: Discussionmentioning

confidence: 51%

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Huang

Jiang

et al. 2019

Animals

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“…The blood sample was fixed by formaldehyde and a restriction enzyme (MboI) was added to digest the DNA, followed by repairing the 5′ overhang using a biotinylated residue. A PE library with ~300-bp insert size was constructed following the Hi-C library protocol (Shao et al, 2018). Sequencing of the Hi-C library was performed using the BGISEQ-500 platform (Goodwin, Mcpherson, & Mccombie, 2016) with a read length of 100 bp for each end.…”

Section: Sample Collection and Sequencingmentioning

confidence: 99%

A chromosome‐level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth

Zhou

Gao²,

Zhang

et al. 2019

Molecular Ecology Resources

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The giant grouper (Epinephelus lanceolatus) is the largest coral reef teleost, with a native range that spans temperate and tropical waters in the Pacific and the Indian Oceans. It is cultured artificially and used as a breeding species in aquaculture due to its rapid growth rate. Here we report a giant grouper genome assembled at the chromosome scale from sequences generated using Illumina and high‐throughput chromatin conformation capture (Hi‐C) technology. The assembly comprised 1.086 Gb, with 98.4% of the scaffold sequences anchored into 24 chromosomes. The contig and scaffold N50 values were 119.9 kb and 46.2 Mb, respectively. The assembly is of high integrity, including 96.4% universal single‐copy orthologues based on BUSCO analysis. Through chromosome‐scale evolution analysis, we identified alignments of six giant grouper chromosomes to three stickleback chromosomes and some of the genes located within the breakpoints of reshuffling events may related to development and growth. From the 24,718 protein‐coding genes, we found that several gene families related to innate immunity and glycan biosynthesis were significantly expanded in the giant grouper genome compared to other teleost genomes. In addition, we identified several genes related to the hormone signalling pathway and innate immunity that have experienced positive selection or accelerated evolution, implicating their roles in immune defence and fast growth of the species. The high‐quality genome assembly will provide a valuable genomic resource for further biological and evolutionary studies, and useful genomic tools for breeding of the giant grouper.

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“…In this way, up to 21.47 % of the assembled sequences were found to be repeat sequences (Figure 3). Protein-coding gene were then predicted by a combination of two ways: (1) the ab initio gene prediction and (2) the homology-based annotation 22-24 . For ab initio gene prediction approaches, Augustus 25 and GlimmerHMM 26 were used with Danio rerio as the species of HMM model to predict gene models; For homology-based annotation, four homolog species including Pundamilia nyererei, Maylandia zebra, Astatotilapia calliptera and Perca_flavescens were aligned against the genome assembly using BLAT software (version 0.36) 27 and GeneWise software (version 2.4.1) 28 .…”

Section: Methodsmentioning

confidence: 99%

Chromosome-level genome assembly of a butterflyfish,Chelmon rostratus

Huang

Song

Zhang

et al. 2019

Preprint

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1 6Chelmon rostratus (Teleostei, Perciformes, Chaetodontidae) is a copperband 1 7 butterflyfish, living in tropical areas. Just as other coral reef fish, it can be cultivated 1 8as an ornamental fish, thus providing genome information for this species might help 1 9understanding the genome evolution of Chaetodontidae (without previous genomes 2 0 available) and adaptation/evolution of coral reef fish. 2 1In this study, we sequenced and assembled a draft genome of Chelmon rostratus. 2 2Using the stLFR linked-read data, we assembled a genome of 638.88 Mb in size with 2 3 contig and scaffold N50 sizes of 294.41 kb and 2,62 Mb, respectively. Up to 21.47 % 2 4 of the genome was found to be repetitive sequences and 21,375 protein-coding genes 2 5 were annotated. Among these annotated protein-coding genes, 20,163 (94.33%) 2 6 proteins were assigned with possible functions. 2 7As the first genome for Chaetodontidae family, the information of these data helpfully 2 8 to improve the essential to the further understanding and exploration of marine 2 9 ecological environment symbiosis with coral and the genomic innovations and 3 0 molecular mechanisms contributing to its unique morphology and physiological 1 features. 2

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Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus

Cited by 43 publications

References 42 publications

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

Genome Survey of Male and Female Spotted Scat (Scatophagus argus)

A chromosome‐level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth

Chromosome-level genome assembly of a butterflyfish,Chelmon rostratus

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