Transcriptomic responses in ice ice diseased red algae Kappaphycus alvarezii

• Published in: Aquaculture Vol. 547; p. 737520
• Main Authors: Mohammed Riyaz, S.U., Inbakandan, D., Bhavadharani, P., Gopika, R., Elson, J., Bavani-Latha, M., Manikandan, D., Stalin-Dhas, T., Nalini, S., Simal-Gandara, J.
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 30-01-2022
• Subjects: FPKM; Functional annotation; Ice-ice disease; Kappaphycus alvarezii; KEGG; Transcriptome; Uni-genes; Transcriptome; Kappaphycus alvarezii; Functional annotation; GO; KEGG; Uni-genes; FPKM; Ice-ice disease
• ISSN: 0044-8486; 1873-5622
• DOI: 10.1016/j.aquaculture.2021.737520

This transcriptomic study for ice-ice diseased Kappaphycus alvarezii was done using Illumina sequencing technology. As many as 46 million raw reads were generated and after filtering the data, a clean read of 44 million was obtained. Further 59,942 uni-genes were obtained through De novo assembly with a mean length of 304 bp. Gene functional annotations were generated in respect to the non-redundant database (Nr), nucleotide sequence (Nt), Protein family (Pfam), Kyoto Encyclopedia of Genes and Genomes database (KEGG), SwissProt, Eukaryotic Orthologous Groups (KOG) database and the Gene Ontology database (GO). With respect to uni-genes, 47,725 (79.61%) unigenes were described in the minimum one database and 3351 uni-genes were described in entire databases. Functional annotation with GO extracted 24,903 uni-genes under three main domains. Gene interaction was scored using the KEGG pathway database with 125 pathways in which 8394 uni-genes were recognized. The study of enrichment of functional gene expression with a value greater than the FPKM average can reveal several essential pathways. Ice-ice diseased K. alvarezii mRNA transcripts were studied by Illumina sequencing technologyfor the potential changes in the level of genes and gene expressions.
[Display omitted]
•Ice-ice disease led to a significant disease in seaweed production and carrageenan yield.•Bacteria that hydrolyze carrageenan was identified and transcriptome investigated.•It also provided the insight into cell pathology and host response for causation.•Healthy and ice-ice disease in K. alvarezii and their molecular mechanisms were compared.•Transcript sequences of K. alvarezii is a valuable resource for potential gene identification.