RNA-seq as an emerging tool for marine dinoflagellate transcriptome analysis

Process and challenges

Muhamad Afiq Akbar, Asmat Ahmad, Gires Usup, Bunawan Hamidun

Research output: Contribution to journalReview article

2 Citations (Scopus)

Abstract

Dinoflagellates are the large group of marine phytoplankton with primary studies interest regarding their symbiosis with coral reef and the abilities to form harmful algae blooms (HABs). Toxin produced by dinoflagellates during events of HABs cause severe negative impact both in the economy and health sector. However, attempts to understand the dinoflagellates genomic features are hindered by their complex genome organization. Transcriptomics have been employed to understand dinoflagellates genome structure, profile genes and gene expression. RNA-seq is one of the latest methods for transcriptomics study. This method is capable of profiling the dinoflagellates transcriptomes and has several advantages, including highly sensitive, cost effective and deeper sequence coverage. Thus, in this review paper, the current workflow of dinoflagellates RNA-seq starts with the extraction of high quality RNA and is followed by cDNA sequencing using the next-generation sequencing platform, dinoflagellates transcriptome assembly and computational analysis will be discussed. Certain consideration needs will be highlighted such as difficulty in dinoflagellates sequence annotation, post-transcriptional activity and the effect of RNA pooling when using RNA-seq.

Original languageEnglish
Article number5
JournalProcesses
Volume6
Issue number1
DOIs
Publication statusPublished - 1 Jan 2018

Fingerprint

RNA
Genes
Algae
Reefs
Phytoplankton
Gene expression
Complementary DNA
Health
Costs

Keywords

  • Dinoflagellates
  • Next-generation sequencing
  • RNA-seq
  • Transcriptome analysis
  • Transcriptomics

ASJC Scopus subject areas

  • Chemical Engineering (miscellaneous)
  • Bioengineering
  • Process Chemistry and Technology

Cite this

RNA-seq as an emerging tool for marine dinoflagellate transcriptome analysis : Process and challenges. / Akbar, Muhamad Afiq; Ahmad, Asmat; Usup, Gires; Hamidun, Bunawan.

In: Processes, Vol. 6, No. 1, 5, 01.01.2018.

Research output: Contribution to journalReview article

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