Transcriptomic responses in ice ice diseased red algae Kappaphycus alvarezii

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 wi...

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Published inAquaculture 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
LanguageEnglish
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
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Abstract 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.
AbstractList 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.
ArticleNumber 737520
Author Manikandan, D.
Mohammed Riyaz, S.U.
Simal-Gandara, J.
Stalin-Dhas, T.
Inbakandan, D.
Bavani-Latha, M.
Nalini, S.
Gopika, R.
Bhavadharani, P.
Elson, J.
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  email: jsimal@uvigo.es
  organization: Universidade de Vigo, Nutrition and Bromatology Group, Analytical Chemistry and Food Science Department, Faculty of Science, E32004 Ourense, Spain
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Keywords Transcriptome
Kappaphycus alvarezii
Functional annotation
GO
KEGG
Uni-genes
FPKM
Ice-ice disease
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Snippet This transcriptomic study for ice-ice diseased Kappaphycus alvarezii was done using Illumina sequencing technology. As many as 46 million raw reads were...
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SubjectTerms FPKM
Functional annotation
Ice-ice disease
Kappaphycus alvarezii
KEGG
Transcriptome
Uni-genes
Title Transcriptomic responses in ice ice diseased red algae Kappaphycus alvarezii
URI https://dx.doi.org/10.1016/j.aquaculture.2021.737520
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