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Hydrobiologia

, Volume 825, Issue 1, pp 5–27 | Cite as

Guidelines for RNA-seq projects: applications and opportunities in non-model decapod crustacean species

  • Tuan Viet NguyenEmail author
  • Hyungtaek Jung
  • Guiomar Rotllant
  • David Hurwood
  • Peter Mather
  • Tomer VenturaEmail author
CRUSTACEAN GENOMICS Review Paper

Abstract

Next-generation sequencing (NGS) has dramatically changed the way biological research is being conducted in the post-genomic era, and they have only been utilized widely over the recent decade for studies of non-model decapod crustacean species, predominantly by sequencing the transcriptome of various tissues across different life stages. Next-generation sequencing can now provide a rapid, cost-effective solution for discovery of genetic markers crucial in many applications that would previously have otherwise taken years to develop. Sequencing of the entire transcriptome (referred to as RNA sequencing; RNA-seq) is one of the most popular NGS tools. RNA-seq studies of non-model species in crustacean taxa, however, have faced some problems, including a lack of “good” experimental study design, a relative paucity of gene annotations, combined with limited knowledge of genomic technologies and analyses. The aim of the current review is to assist crustacean biologists to develop a better appreciation for the applications and scope of RNA-seq analysis, understand the basic requirements for optimal RNA-seq studies and provide an overview of each step, from RNA-seq experimental design to bioinformatics approaches to data analysis. Insights that have resulted from RNA-seq studies across a wide range of non-model decapod species are also summarized.

Keywords

RNA-sequencing Next-generation sequencing Differential gene expression Shrimp Prawn Crab Lobster Crayfish In silico 

Abbreviations

P. trituberculatus

Portunus trituberculatus

S. henanense

Sinopotamon henanense

P. vannamei

Penaeus vannamei

P. monodon

Penaeus monodon

M. japonicus

Marsupenaeus japonicus

P. virginalis

Procambarus virginalis or Procambarus fallax forma virginalis

S. olivacea

Scylla olivacea

S. paramamosain

Scylla paramamosain

E. sinensis

Eriocheir sinensis

N. norvegicus

Nephrops norvegicus

F. merguiensis

Fenneropenaeus merguiensis

P. clarkii

Procambrarus clarkii

M. rosenbergii

Macrobrachium rosenbergii

S. verreauxi

Sagmariasus verreauxi

N. denticulata

Neocaridina denticulata

P. hawaiensis

Parhyale hawaiensis

E. carinicauda

Exopalaemon carinicauda

M. olfersi

Macrobrachium olfersi

P. elegans

Palaemon elegans

P. australiensis

Paratya australiensis

H. rubra

Halocaridina rubra

Notes

Acknowledgements

The current study was supported through a Marie Curie International Research Staff Exchange Scheme Fellowship within the 7th European Community Framework Programme (612296-DeNuGReC). Tuan Viet Nguyen was supported through the Australian Research Council Discovery Project grant awarded to Dr Tomer Ventura (No. DP160103320) and a USC International PhD scholarship. The authors would like to acknowledge the precious help of Professor Abigail Elizur (University of the Sunshine Coast, Australia) and four anonymous reviewers for numerous feedbacks that helped improve the quality of this manuscript.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.GeneCology Research Centre, Faculty of Science, Health, Education and EngineeringUniversity of the Sunshine CoastMaroochydoreAustralia
  2. 2.Centre for Tropical Crops and Biocommodities, Institute for Future EnvironmentQueensland University of TechnologyBrisbaneAustralia
  3. 3.Institut de Ciències del Mar (CSIC)BarcelonaSpain
  4. 4.School of Earth, Environment and Biological Sciences, Science and Engineering FacultyQueensland University of TechnologyBrisbaneAustralia

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