Martín-Hernández R et al. (2021), Comparative Transcriptomes of the Body Wall of ...

ECB-ART-49211

Int J Mol Sci 2021 Apr 09;228:. doi: 10.3390/ijms22083882.

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Comparative Transcriptomes of the Body Wall of Wild and Farmed Sea Cucumber Isostichopus badionotus.

Martín-Hernández R , Rodríguez-Canul R , Kantún-Moreno N , Olvera-Novoa MA , Medina-Contreras O , Garikoitz-Legarda C , Triviño JC , Zamora-Briseño JA , May-Solis V , Poot-Salazar A , Pérez-Vega JA , Gil-Zamorano J , Grant G , Dávalos A , Olivera-Castillo L .

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Overfishing of sea cucumber Isostichopus badionotus from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed I. badionotus has now been studied for the first time by an RNA-Seq approach. The functional profile of wild I. badionotus was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed I. badionotus was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild I. badionotus is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed I. badionotus is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.

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References [+] :

Boyko, The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation. 2020, Pubmed, Echinobase

	Figure 1. Bioinformatics pipeline used for transcriptome de novo assembly.
	Figure 2. Comparison of BUSCO results among three assemblies. Quantitative assessment of transcriptome completeness for the newly assembled wild cucumber transcriptome, and comparison with related publicly available transcriptome assemblies.
	Figure 3. Distribution of annotated unigenes across databases. Venn diagram for common annotated unigenes in NT, UniProt and Gene Ontology databases.
	Figure 4. Gene Ontology (GO) classification of wild sea cucumber body wall assembled transcripts.
	Figure 5. Transcriptomic comparisons between wild and farmed sea cucumbers. (a) MA plots of differentially expressed genes (DEGs) between wild and farmed sea cucumbers. Red dots show transcripts with a false discovery rate (FDR) < 0.05. (b) PCA and variable contribution to the transcriptomic data. (c) Differentially altered transcripts. (d) Percentage of altered transcripts.
	Figure 6. Gene Ontology (GO) analysis of sea cucumber differentially expressed genes modulated in farmed animals.
	Figure 7. Reverse-transcription real-time PCR validation of eleven genes differentially modulated by captivity. COX1, cytochrome c oxidase subunit 1; TBA2, tubulin α chain 2; TBB, Tubulin β chain; ZN709, zinc finger protein 709; ATPA, ATP synthase subunit α; OST48, dolichyl-diphosphooligosaccharide-protein glycosyltransferase non-catalytic subunit; TBA, tubulin alpha chain; DMBT1, deleted in malignant brain tumors 1; RL39, ribosomal protein L39; RS5, ribosomal protein S5; RL18A, ribosomal protein L18a. Data is expressed as relative expression compared to that of wild sea cucumbers (n = 5).