Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili

Sarropoulou, Elena; Sundaram, Arvind; Kaitetzidou, Elisavet; Kotoulas, Georgios; Gilfillan, Gregor D.; Papandroulakis, Nikos; Mylonas, Constantinos C.; Magoulas, Antoniοs

doi:10.1093/gigascience/gix108

Cited by 21 publications

(16 citation statements)

References 60 publications

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“…Because lower rates of heterozygosity tend to simplify genome assembly, the data presented here suggest that female S. argus would be preferable to males for the development of a draft genome in future studies [28]. The heterozygosity rate observed here was higher than that of Oplegnathus fasciatus (0.29%) [48], but smaller than that of Pelteobagrus fulvidraco (0.45%) [49], Seriola dumerili (0.65%) [50] and Sillago sinica (0.66-0.76%) [42]. The lower heterozygosity rate of S. argus suggests that wild-caught fish are close to being over-fished.…”

Section: Discussionmentioning

confidence: 59%

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: 59%

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

Huang

Jiang

et al. 2019

Animals

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“…Zorba has been used for building and annotating numerous de novo genome and transcriptome assemblies of marine species, such as the gilthead sea bream Sparus aurata [ 50 ] or the greater amberjack Seriola dumerili [ 51 ]. Both genome and transcriptome assemblies of species with large genomes often exceed the maximum available memory limit, eventually affecting the strategic choices for Zorba future upgrades (see Section Future Directions).…”

Section: Scientific Impact Storiesmentioning

confidence: 99%

0s and 1s in marine molecular research: a regional HPC perspective

et al. 2021

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High-performance computing (HPC) systems have become indispensable for modern marine research, providing support to an increasing number and diversity of users. Pairing with the impetus offered by high-throughput methods to key areas such as non-model organism studies, their operation continuously evolves to meet the corresponding computational challenges. Here, we present a Tier 2 (regional) HPC facility, operating for over a decade at the Institute of Marine Biology, Biotechnology, and Aquaculture of the Hellenic Centre for Marine Research in Greece. Strategic choices made in design and upgrades aimed to strike a balance between depth (the need for a few high-memory nodes) and breadth (a number of slimmer nodes), as dictated by the idiosyncrasy of the supported research. Qualitative computational requirement analysis of the latter revealed the diversity of marine fields, methods, and approaches adopted to translate data into knowledge. In addition, hardware and software architectures, usage statistics, policy, and user management aspects of the facility are presented. Drawing upon the last decade’s experience from the different levels of operation of the Institute of Marine Biology, Biotechnology, and Aquaculture HPC facility, a number of lessons are presented; these have contributed to the facility’s future directions in light of emerging distribution technologies (e.g., containers) and Research Infrastructure evolution. In combination with detailed knowledge of the facility usage and its upcoming upgrade, future collaborations in marine research and beyond are envisioned.

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“…Draft genomes for greater amberjack ( S. dumerili ) 51 and California yellowtail ( S. dorsalis ) 52 have recently been published. We compared the predicted-protein sequences of yellowtail with those of these two Seriola species.…”

Section: Resultsmentioning

confidence: 99%

The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract

et al. 2018

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Seriola quinqueradiata (yellowtail) is the most widely farmed and economically important fish in aquaculture in Japan. In this study, we used the genome of haploid yellowtail fish larvae for de novo assembly of whole-genome sequences, and built a high-quality draft genome for the yellowtail. The total length of the assembled sequences was 627.3 Mb, consisting of 1,394 scaffold sequences (>2 kb) with an N50 length of 1.43 Mb. A total of 27,693 protein-coding genes were predicted for the draft genome, and among these, 25,832 predicted genes (93.3%) were functionally annotated. Given our lack of knowledge of the yellowtail digestive system, and using the annotated draft genome as a reference, we conducted an RNA-Seq analysis of its three digestive organs (stomach, intestine and rectum). The RNA-Seq results highlighted the importance of certain genes in encoding proteolytic enzymes necessary for digestion and absorption in the yellowtail gastrointestinal tract, and this finding will accelerate development of formulated feeds for this species. Since this study offers comprehensive annotation of predicted protein-coding genes, it has potential broad application to our understanding of yellowtail biology and aquaculture.

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Full genome survey and dynamics of gene expression in the greater amberjack Seriola dumerili

Cited by 21 publications

References 60 publications

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

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

0s and 1s in marine molecular research: a regional HPC perspective

The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract

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