De Novo assembly and annotation of Perna indica transcriptome using next generation sequencing technology

Mary, Sujitha and Sukumaran, Sandhya and Sebastian, Wilson and Gopalakrishnan, A (2021) De Novo assembly and annotation of Perna indica transcriptome using next generation sequencing technology. Multilogic in Science, 12 (40). pp. 186-190. ISSN 2277-7601

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Abstract

Indian coastline is bestowed with a rich diversity of molluscan species of which mussels belonging to the genus Perna (Family; Mytilidae) occupy a major position. Aquaculture importance of these species is globally recognized. They are extensively used as pollution indicators as they can accumulate contaminants at levels higher than that present in water. This property has made them valuable biomarkers of environmental pollution. The scarcity in the genetic resources of this species is one of the major hindrances in its wide usage as a biomonitor. Here we sequenced the first transcriptome of Perna indica, collected from the southernmost part of Kerala coast, using NGS illumina HiSeq 2500 technology. The de novo assembly of Perna indica transcriptome generated 157203 contigs and 132641 non-redundant genes with a minimum length of 201bp. The blast search and InterPro database scan resulted in assigning domains, ontology and pathway mapping to these genes which helped in identifying genes involved in metabolism, immune related genes, proteins and domains associated with these genes. 84% of the transcripts which had atleast one blast-hit showed similarity to species from bivalves. 12420 transcripts with GO terms and 17835 transcripts with 395 KEGG pathways were identified in the assembled transcriptome of Perna indica.

Item Type:	Article
Uncontrolled Keywords:	NGS; transcriptome; mussel; ontology; pathway mapping
Subjects:	Molluscan Fisheries > Bivalves Molluscan Fisheries
Divisions:	CMFRI-Kochi > Marine Biotechnology, Fish Nutrition and Health Division Subject Area > CMFRI > CMFRI-Kochi > Marine Biotechnology, Fish Nutrition and Health Division CMFRI-Kochi > Marine Biotechnology, Fish Nutrition and Health Division Subject Area > CMFRI-Kochi > Marine Biotechnology, Fish Nutrition and Health Division
Depositing User:	Arun Surendran
Date Deposited:	04 Dec 2021 06:48
Last Modified:	04 Dec 2021 06:48
URI:	http://eprints.cmfri.org.in/id/eprint/15560

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