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Biology (Basel)
2021 Oct 02;1010:. doi: 10.3390/biology10100995.
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De novo Assembly and Analysis of Tissue-Specific Transcriptomes of the Edible Red Sea Urchin Loxechinus albus Using RNA-Seq.
Antiqueo P
,
Zuloaga R
,
Bastias-Molina M
,
Meneses C
,
Estrada JM
,
Molina A
,
Valdés JA
.
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Edible red sea urchin (Loxechinus albus) is an endemic echinoderm species of the Chilean coasts. The worldwide demand for high-quality gonads of this species has addressed the depletion of its natural populations. Studies on this sea urchin are limited, and genomic information is almost nonexistent. Hence, generate a transcriptome is crucial information that will considerably enrich molecular data and promote future findings for the L. albus aquaculture. Here, we obtained transcriptomic data of the edible red sea urchin by Illumina platform. Total RNA was extracted from gonads, intestines, and coelomocytes of juvenile urchins, and samples were sequenced using MiSeq Illumina technology. A total of 91,119,300 paired-end reads were de novo assembled, 185,239 transcripts produced, and a reference transcriptome created with 38.8% GC content and an N50 of 1769 bp. Gene ontology analysis revealed notable differences in the expression profiles between gonads, intestines, and coelomocytes, allowing the detection of transcripts associated with specific biological processes and KEGG pathways. These data were validated using 12 candidate transcripts by real-time qPCR. This dataset will provide a valuable molecular resource for L. albus and other species of sea urchins.
1201498 Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT), 15110027 Fondo de Financiamiento de Centros de Investigación en Áreas Prioritarias (FONDAP), BIP 30480912-0 Fondo de Innovación para la Competitividad Regional (FIC)
Figure 1. Juvenile edible red sea urchins (Loxechinus albus).
Figure 2. A species-based BlastX comparative analysis revealed the major match with Strongylocentrotus purpuratus.
Figure 3. GO functional classification assigned the most percentage of the annotated transcripts to cellular component biogenesis term for biological process; cytosol term for cellular component; and small molecule binding term for molecular function, respectively. Analysis was carried out with the WEGO program for the edible sea urchin (L. albus) reference transcriptome.
Figure 4. The General Functional Prediction only was the most represented category for the 25 cluster of orthologous groups (COG) functional classification in the L. albus reference transcriptome.
Figure 5. The heat map showed differentiated clustering of expressed transcripts according to respective expression values across tissues. Parameters: fold change (absolute values > 4.0) and FDR corrected p value (p < 0.001). Abbreviations: CL: coelomocyte, INT: intestine, GN: gonad. R1: Replicate 1, R2: Replicate 2.
Figure 6. Paired comparisons of differentially expressed transcripts between tissues of L. albus. Upregulated and downregulated transcripts measured are indicated by black and gray columns, respectively. Parameters: fold change (absolute values > 4.0) and FDR corrected p value (p < 0.001). Abbreviations: CL: coelomocyte, INT: intestine, GN: gonad.
Figure 7. Differentially expressed transcripts between gonads, intestines, and coelomocytes of the edible sea urchin. Venn diagram of the total differentially expressed transcripts in L. albus. Each color indicates the comparison between tissue and the numbers of genes that were differentially expressed. Parameters: fold change (absolute values > 4.0) and FDR corrected p value (p < 0.001). Abbreviations: CL: coelomocyte, INT: intestine, GN: gonad.
Figure 8. The Top-16 Gene Ontology biological process (BP) enrichment of up-regulated transcripts from L. albus tissues. (a) In coelomocytes compared to intestine (CL vs. INT), the most enriched term was positive regulation of apoptotic process, and compared to the gonad (CL vs. GN) was intracellular signal transduction; (b) in the gonad compared to intestine (GN vs. INT), the most enriched term was DNA repair, and compared to coelomocytes (GN vs. CL) was microtubule-based process; (c) in intestine compared to coelomocytes (INT vs. CL) the most enriched term was transmembrane transport, and compared to the gonad (INT vs. GN) was microtubule-based process.
Figure 9. The quantitative real-time PCR validation of differentially expressed transcripts was highly correlated to RNA-seq. (a) coelomocyte; (b) gonad; (c) intestine; and (d) statistical correlation analysis. Expression fold changes measured by RT-qPCR and RNA-seq are indicated by black and gray columns, respectively. Abbreviations: heat shock protein 70 kDa 1 A (HSP70), lysosomal trafficking regulator (LYST), B-cell lymphoma 2 (BCL2), ubiquitin A-52 residue ribosomal protein fusion product 1 (UBA52), testis-specific serine/threonine-protein kinase 3 (TSSK3), centrin 2 (CETN2), cation channel sperm associated 3 (CATSPER3), sperm surface protein 17 (SPA17), notch homolog 1 (NOTCH1), toll-like receptor 3 (TLR3), glutathione s-transferase theta 1 (GSTT1), and caspase 3 (CASP3). * p < 0.05, ** p < 0.01.
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