Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly

Nobuaki Kono, Hiroyuki Nakamura, Yusuke Ito, Masaru Tomita, Kazuharu Arakawa

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

With advances in high-throughput sequencing technologies, de novo transcriptome sequencing and assembly has become a cost-effective method to obtain comprehensive genetic information of a species of interest, especially in nonmodel species with large genomes such as spiders. However, high-quality RNA is essential for successful sequencing, and sample preservation conditions require careful consideration for the effective storage of field-collected samples. To this end, we report a streamlined feasibility study of various storage conditions and their effects on de novo transcriptome assembly results. The storage parameters considered include temperatures ranging from room temperature to -80°C; preservatives, including ethanol, RNAlater, TRIzol and RNAlater-ICE; and sample submersion states. As a result, intact RNA was extracted and assembly was successful when samples were preserved at low temperatures regardless of the type of preservative used. The assemblies as well as the gene expression profiles were shown to be robust to RNA degradation, when 30 million 150-bp paired-end reads are obtained. The parameters for sample storage, RNA extraction, library preparation, sequencing and in silico assembly considered in this work provide a guideline for the study of field-collected samples of spiders.

Original languageEnglish
JournalMolecular Ecology Resources
DOIs
Publication statusAccepted/In press - 2015

Fingerprint

Spiders
Transcriptome
transcriptome
spider
Araneae
RNA
Temperature
preservative
RNA Stability
Feasibility Studies
Immersion
preservatives
sampling
Computer Simulation
Libraries
Ethanol
feasibility study
methodology
Genome
Guidelines

Keywords

  • de novo transcriptome assembly
  • High-throughput sequencing
  • RNA preservation
  • Spiders

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Biotechnology
  • Genetics

Cite this

Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. / Kono, Nobuaki; Nakamura, Hiroyuki; Ito, Yusuke; Tomita, Masaru; Arakawa, Kazuharu.

In: Molecular Ecology Resources, 2015.

Research output: Contribution to journalArticle

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