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Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper.

ABSTRACT: Plectropomus leopardus, as known as leopard coral grouper, is a valuable marine fish that has gradually been bred artificially. To promote future conservation, molecular breeding, and comparative studies, we generated an improved high-quality chromosomal-level genome assembly of leopard coral grouper using Nanopore long-reads, Illumina short reads, and the Hi-C sequencing data. The draft genome is 849.74 Mb with 45 contigs and N50 of 35.59 Mb. Finally, a total of 846.49 Mb corresponding to 99.6% of the contig sequences was anchored to 24 pseudo-chromosomes using Hi-C technology. A final set of 25,965 genes is annotated after manual curation of the predicted gene models, and BUSCO analysis yielded a completeness score of 99.5%. This study significantly improves the utility of the grouper genome and provided a reference for the study of molecular breeding, genomics and biology in this species.

SUBMITTER: Han W

PROVIDER: S-EPMC10033899 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper.

Han Wentao W Wu Shaoxuan S Ding Hui H Wang Mingyi M Wang Mengya M Bao Zhenmin Z Wang Bo B Hu Jingjie J

Scientific data 20230322 1

Plectropomus leopardus, as known as leopard coral grouper, is a valuable marine fish that has gradually been bred artificially. To promote future conservation, molecular breeding, and comparative studies, we generated an improved high-quality chromosomal-level genome assembly of leopard coral grouper using Nanopore long-reads, Illumina short reads, and the Hi-C sequencing data. The draft genome is 849.74 Mb with 45 contigs and N50 of 35.59 Mb. Finally, a total of 846.49 Mb corresponding to 99.6% ...[more]

PMID: 36949049

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Project description:An 8-week feeding trial was conducted to evaluate the effects of dietary lysine level on growth performance and protein metabolism of juvenile leopard coral grouper (Plectropomus leopardus) and thereby obtained the optimal dietary lysine requirement of P. leopardus. Six isoproteic and isolipidic experimental diets were formulated to contain 1.10%, 1.69%, 2.30%, 3.08%, 3.56%, and 4.36% lysine of diets, respectively. Each diet was assigned at random to triplicate groups of 25 juveniles (initial mean weight is 10.57 g) per tank in a flow-through mariculture system maintained at 27-30°C. Dietary inclusion of 2.30-3.08% lysine improved the weight gain rate (WGR) and specific growth rate and decreased the feed conversion ratio (FCR) of juveniles (P < 0.05). The intestinal digestive enzyme (trypsin, amylase, and lipase) activities were overall enhanced by dietary inclusion of 3.08-3.56% lysine (P < 0.05). The mammalian target of rapamycin (mTOR) signaling pathway was activated in fish fed diets with 1.69-2.30% lysine by upregulating the relative expression levels of hepatic TOR and S6K1 (p70 ribosomal protein S6 kinase 1) but downregulating the relative expression level of hepatic 4E-BP2 (eIF4E-binding protein 2). Conversely, the amino acid response signaling pathway was inhibited in fish fed diet with 2.30% lysine by downregulating the relative expression levels of hepatic GCN2 (general control nondepressible 2), ATF3 (activating transcription factor 3), ATF4a (activating transcription factor 4a), and ATF4b (activating transcription factor 4b). Additionally, dietary 1.69-3.08% lysine enhanced the plasma total protein level and hepatic lysine α-ketoglutarate reductase activity but depressed the blood urea nitrogen level and hepatic adenosine monophosphate deaminase activity (P < 0.05). Moreover, dietary 3.08% lysine increased the contents of whole-body crude protein and total amino acids, while 1.69%-4.36% lysine depressed the whole-body lipid content (P < 0.05). These results indicated that optimal dietary lysine increased the digestive enzyme activities, promoted protein synthesis but depressed protein degradation, and thereby improved the growth performance of P. leopardus. Based on the second-order polynomial model, the optimal lysine requirement of juvenile P. leopardus for WGR, FCR, and lysine deposition was 2.60%-2.97% of diets (4.91%-5.60% of dietary protein).

Project description:Background: Seagrasses (Alismatales) are the only fully marine angiosperms. Zostera marina (eelgrass) plays a crucial role in the functioning of coastal marine ecosystems and global carbon sequestration. It is the most widely studied seagrass and has become a marine model system for exploring adaptation under rapid climate change. The original draft genome (v.1.0) of the seagrass Z. marina (L.) was based on a combination of Illumina mate-pair libraries and fosmid-ends. A total of 25.55 Gb of Illumina and 0.14 Gb of Sanger sequence was obtained representing 47.7× genomic coverage. The assembly resulted in ~2000 unordered scaffolds (L50 of 486 Kb), a final genome assembly size of 203MB, 20,450 protein coding genes and 63% TE content. Here, we present an upgraded chromosome-scale genome assembly and compare v.1.0 and the new v.3.1, reconfirming previous results from Olsen et al. (2016), as well as pointing out new findings. Methods: The same high molecular weight DNA used in the original sequencing of the Finnish clone was used. A high-quality reference genome was assembled with the MECAT assembly pipeline combining PacBio long-read sequencing and Hi-C scaffolding. Results: In total, 75.97 Gb PacBio data was produced. The final assembly comprises six pseudo-chromosomes and 304 unanchored scaffolds with a total length of 260.5Mb and an N50 of 34.6 MB, showing high contiguity and few gaps (~0.5%). 21,483 protein-encoding genes are annotated in this assembly, of which 20,665 (96.2%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: As an important marine angiosperm, the improved Z. marina genome assembly will further assist evolutionary, ecological, and comparative genomics at the chromosome level. The new genome assembly will further our understanding into the structural and physiological adaptations from land to marine life.

Dataset Information

Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper.

Publications

Improved chromosomal-level genome assembly and re-annotation of leopard coral grouper.

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