Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer)

Thevasagayam, Natascha May; Sridatta, Prakki Sai Rama; Jiang, Junhui; Tong, Amy; Saju, Jolly M.; Purushothaman, K.; Kwan, Hsiao Yuen; Ngoh, Si Yan; Liew, Woei Chang; Kuznetsova, Irina M.; Shen, Xueyan; Lok, Si; Vij, Shubha; Orbán, László

doi:10.3390/jmse3020382

Cited by 12 publications

(13 citation statements)

References 39 publications

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“…Earlier, transcriptome sequence data was obtained from multiple platforms and assembled into 267,616 contigs [ 16 ]. The scaffolded genome assembly (v2) was obtained using the transcriptome [ 17 ] and yielded 3,807 genomic contigs resulting in a ~10% improvement in N50 metrics.…”

Section: Resultsmentioning

confidence: 99%

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Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

et al. 2016

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We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species’ native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics.

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Section: Resultsmentioning

confidence: 99%

“…The assembled seabass transcriptome [ 16 ] was used for scaffolding the 90X PacBio genome assembly using the L_RNA_scaffolder tool [ 17 ] ( S1 Table ) resulting in the scaffolded genome assembly (v2).…”

Section: Methodsmentioning

confidence: 99%

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

et al. 2016

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“…Whether promoter methylation of dmrt1 (and nr5a2 ) and demethylation of cyp19a1 (and amh ) during barramundi sex inversion is a progressive phenomenon like it has previously been reported for the protogynous ricefield eel [ 16 ] and for the protandrous black porgy [ 17 ], still remains to be elucidated. Nevertheless, this report contributes to the recent body of work aiming to elucidate the genetic mechanisms regulating key reproductive genes involved within the gonads of the large protandrous hermaphrodite barramundi [ 23 , 33 ] and for the first time provides evidence for epigenetics and alternative splicing affecting genes central to sex differentiation pathways in this important aquaculture species.…”

Section: Discussionmentioning

confidence: 91%

“…Results from RT-qPCR revealed that dmrt1 expression was on average 1.9 times higher in the testis than in ovaries, whereas no sex-specific differences were found for cyp19a1 ( Fig 3 ). Further investigation using a publicly available [ 33 ] L . calcarifer RNASeq library of one testes and one ovary (NCBI SRA accessions SRX867251 and SRX867252), whereby raw reads were mapped back to L .…”

Section: Resultsmentioning

confidence: 99%

Sex-specific dmrt1 and cyp19a1 methylation and alternative splicing in gonads of the protandrous hermaphrodite barramundi

et al. 2018

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Epigenetics is involved in sex differentiation of gonochoristic and hermaphroditic fish species, whereby two genes dmrt1 (pro-male) and cyp19a1 (pro-female) are known to play major roles. Barramundi, Lates calcarifer, is an important tropical aquaculture species that undergo natural and permanent male to female sex change, a process for which the exact underlying molecular mechanisms are still unknown. To elucidate whether DNA methylation is involved in sex control of barramundi, a next-generation bisulfite amplicon sequencing approach was used to target 146 CpG sites within proximal promoters and first exons of seven sex-related genes (dmrt1, cyp19a1, amh, foxl2, nr5a2, sox8 and sox9) of 24 testis and 18 ovaries of captive and wild adult barramundi. Moreover, comparative expression profiles of the key dmrt1 and cyp19a1 genes were further investigated using RT-qPCR and Sanger sequencing approaches, whereas expression levels of remaining targeted genes were based on available literature for the species. Results showed that cyp19a1 and amh were more methylated in males, whereas dmrt1 and nr5a2 were more methylated in females (P < 0.001), with no gender differences found for foxl2, sox8 or sox9 genes (P > 0.05). Sex-biased promoter DNA methylation was inversely related to gene expression only for dmrt1 and nr5a2, and directly related to amh expression, whereas no differences in cyp19a1 expression were found between testes and ovaries. Notably, unique sex-specific alternative splicing of dmrt1 and cyp19a1 were discovered, whereby males lacked the full-length aromatase coding cyp19a1 mRNA due to partial or total exon splicing, and females lacked the dmrt1 exon containing the DM-domain sequence. This study advances the current knowledge aiming to elucidate the genetic mechanisms within male and female gonads of this large protandrous hermaphrodite by providing the first evidence of epigenetics and alternative splicing simultaneously affecting key genes (cyp19a1 and dmrt1) central to sex differentiation pathways.

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“…Therefore, in our present study, three commercially available pelleted grow-out feeds (Feed B-D) and frozen baitfish (Feed A as control) were evaluated based on the overall growth performance, nutritional quality of fillets and histological changes of the mid-gut and liver in juvenile Asian seabass. These data allow us to glimpse into the effects of different feeds onto the gene expression profile of the liver and with the recent availability of the Asian seabass transcriptome [ 29 ], its draft genome [ 30 ] and a comprehensive Asian seabass genome assembly [ 31 ] more detailed analysis of such datasets will be possible in the near future.…”

Section: Introductionmentioning

confidence: 99%

Nutrigenomic and Nutritional Analyses Reveal the Effects of Pelleted Feeds on Asian Seabass (Lates calcarifer)

et al. 2015

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As nutrition-related expenses constitute the majority of the costs for aquaculture farms, it is essential for them to use feeds that provide an ideal combination of nutrients for the species of choice. In this study, the relative effect of consuming three different pelleted feeds (B, C and D) in comparison to frozen baitfish (A; control) were compared on juvenile Asian seabass (77.3 ± 22.4g) that were selected for increased growth rate over two generations. Our objectives were: 1) to evaluate the effects of different pelleted feeds based on overall physiological changes and nutritional quality of fillets; 2) improve our understanding of the underlying mechanisms with transcriptomic analysis; 3) if possible, identify the feed type that supports the growth of these fishes without substantially reducing the nutritional quality of fillet. The growth performance, fatty acid composition of fillet, hepatic histology and transcriptome of the fishes (Groups A-D) were analyzed. The majority of fatty acids of the fillets, except γ-linolenic acid (GLA, C18:3n6), correlated significantly with the respective diets. Asian seabass fed Feed C showed highest specific growth rate (SGR) and feed conversion efficiency (FCE) with closest histology and transcriptomic profile to control, but their fillet contained the highest n6/n3 ratio. When the liver-based transcriptomes were analyzed, a complex set of differentially expressed genes were detected between groups fed pelleted feeds and controls as well as among the pellet-fed groups themselves. Significant enrichment of genes with growth-related function tallied with the morphological data measured. When compared with control (Group A), ‘Biosynthesis of unsaturated fatty acids’ and ‘Steroid biosynthesis’ pathways were significantly enriched in pellet-fed groups. Reduced goblet cell numbers were observed in the gut of pellet-fed fish compared to controls and fads6 was found to be a suitable candidate gene to separate wild-caught Asian seabass, from pellet-fed ones. These results provide insights for researchers on the various effects of feeds on the biochemistry and global gene expression of the fish and potentially for seabass farms to make more informed feed choices.

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Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer)

Cited by 12 publications

References 39 publications

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding

Sex-specific dmrt1 and cyp19a1 methylation and alternative splicing in gonads of the protandrous hermaphrodite barramundi

Nutrigenomic and Nutritional Analyses Reveal the Effects of Pelleted Feeds on Asian Seabass (Lates calcarifer)

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