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The next generation Is here: a review of transcriptomic approaches in marine ecology

The next generation Is here: a review of transcriptomic approaches in marine ecology
The next generation Is here: a review of transcriptomic approaches in marine ecology

As we enter the United Nations Decade of Ocean Science for Sustainable Development, extensive efforts to reverse the decline of ocean health are taking place. Moreover, the need to utilize innovative and integrative approaches to aid in these efforts and address marine ecological questions are urgent. Transcriptomic technologies provide tools to further our understanding of an organism’s biology by allowing researchers to rapidly gain information on the genetic variation of populations and the regulation of cellular processes and pathways through gene presence, absence, and expression. Here, we review the application of transcriptomics in the field of marine ecology over the last decade, following a systematic literature review approach. We found 478 articles that fit our search criteria of using transcriptomic approaches to address ecological hypotheses, with 70% of these studies occurring within the last 5 years. Among the analysed articles, 51.7% involved a type of stressor, 16.6% used transcriptomics to study adaptation, and another 15.9% researched ecological interactions. Most articles investigated species from kingdom Animalia, with a high representation from both molluscs (19.5%) and chordates (13.3%), and only 22% of studies had a fieldwork component. Our review demonstrates how the use of transcriptomic techniques in the field of marine ecology is increasing and how they are being applied. Although there are still challenges researchers experience using such techniques, particularly when annotating genes in non-model species and those with no prior genomic resources, these innovative technologies are extremely valuable in investigating differential gene expression, molecular pathways, and generating genomic resources.

RNA-Seq, gene expression, marine ecology, marine molecular ecology, microarrays, next generation sequencing, transcriptomics
2296-7745
Page, Tessa M.
d650dc79-64eb-4f14-b16c-86266cdeefc8
Lawley, Jonathan W.
3e43db06-e06a-4160-8caf-23f9209139bc
Page, Tessa M.
d650dc79-64eb-4f14-b16c-86266cdeefc8
Lawley, Jonathan W.
3e43db06-e06a-4160-8caf-23f9209139bc

Page, Tessa M. and Lawley, Jonathan W. (2022) The next generation Is here: a review of transcriptomic approaches in marine ecology. Frontiers in Marine Science, 9, [757921]. (doi:10.3389/fmars.2022.757921).

Record type: Review

Abstract

As we enter the United Nations Decade of Ocean Science for Sustainable Development, extensive efforts to reverse the decline of ocean health are taking place. Moreover, the need to utilize innovative and integrative approaches to aid in these efforts and address marine ecological questions are urgent. Transcriptomic technologies provide tools to further our understanding of an organism’s biology by allowing researchers to rapidly gain information on the genetic variation of populations and the regulation of cellular processes and pathways through gene presence, absence, and expression. Here, we review the application of transcriptomics in the field of marine ecology over the last decade, following a systematic literature review approach. We found 478 articles that fit our search criteria of using transcriptomic approaches to address ecological hypotheses, with 70% of these studies occurring within the last 5 years. Among the analysed articles, 51.7% involved a type of stressor, 16.6% used transcriptomics to study adaptation, and another 15.9% researched ecological interactions. Most articles investigated species from kingdom Animalia, with a high representation from both molluscs (19.5%) and chordates (13.3%), and only 22% of studies had a fieldwork component. Our review demonstrates how the use of transcriptomic techniques in the field of marine ecology is increasing and how they are being applied. Although there are still challenges researchers experience using such techniques, particularly when annotating genes in non-model species and those with no prior genomic resources, these innovative technologies are extremely valuable in investigating differential gene expression, molecular pathways, and generating genomic resources.

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Accepted/In Press date: 14 April 2022
Published date: 10 May 2022
Additional Information: Funding Information: We would like to thank Dr. Carmel McDougall for reviewing this manuscript and for her helpful comments and edits. This study was conceptualised after we hosted the session “The next generation is here – genomic approaches in marine science” in the International Conference for Young Marine Researchers (ICYMARE) 2020. Therefore, we would like to thank all participants who collaborated in that session, as well as conference organisers Dr. Simon Jungblut, Dr. Viola Liebich, and Jan Boelmann for their support. Publisher Copyright: Copyright © 2022 Page and Lawley.
Keywords: RNA-Seq, gene expression, marine ecology, marine molecular ecology, microarrays, next generation sequencing, transcriptomics

Identifiers

Local EPrints ID: 458100
URI: http://eprints.soton.ac.uk/id/eprint/458100
ISSN: 2296-7745
PURE UUID: 3dc8ffdc-05ba-43e1-849b-ff4abd8f32bd
ORCID for Tessa M. Page: ORCID iD orcid.org/0000-0002-5575-7049

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Date deposited: 28 Jun 2022 16:59
Last modified: 17 Mar 2024 04:12

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Contributors

Author: Tessa M. Page ORCID iD
Author: Jonathan W. Lawley

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