Molecular physiology of copepods

from biomarker to transcriptomes and back again

Ann M. Tarrant, Birgitte Nilsson, Benni Winding Hansen

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Planktonic copepods are a diverse and abundant group of small (~mm sized) aquatic animals that play a critical role in linking the base of the food chain with higher trophic levels. These invertebrates are a primary food source for marine fish larvae. Their ubiquitous presence is thus of vital importance for recruitment of fish stocks and also as promising live feed for finfish production in aquaculture. This paper reviews the application of molecular approaches to understanding copepod physiology, particularly in non-parasitic species. The review includes both targeted gene approaches and untargeted transcriptomic approaches, with suggestions for best practices in each case. Issues particularly relevant to studies of copepods include heterogeneity within species, morphologically cryptic species, experimental artifacts associated with sample handling, and limited annotation of copepod genes and transcripts. The emergence of high-throughput sequencing and associated increased availability of genomic and transcriptomic databases have presented a huge opportunity to advance knowledge of copepod physiology. The research community can leverage this opportunity through efforts to maintain or improve data accessibility, database annotation, and documentation of analytical pipelines.
OriginalsprogEngelsk
TidsskriftComparative Biochemistry and Physiology - Part D: Genomics and Proteomics
Vol/bind2019
Udgave nummer30
Sider (fra-til)230-247
Antal sider18
ISSN1744-117X
DOI
StatusUdgivet - 2019

Citer dette

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Molecular physiology of copepods : from biomarker to transcriptomes and back again. / Tarrant, Ann M.; Nilsson, Birgitte; Hansen, Benni Winding.

I: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, Bind 2019, Nr. 30, 2019, s. 230-247.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Molecular physiology of copepods

T2 - from biomarker to transcriptomes and back again

AU - Tarrant, Ann M.

AU - Nilsson, Birgitte

AU - Hansen, Benni Winding

PY - 2019

Y1 - 2019

N2 - Planktonic copepods are a diverse and abundant group of small (~mm sized) aquatic animals that play a critical role in linking the base of the food chain with higher trophic levels. These invertebrates are a primary food source for marine fish larvae. Their ubiquitous presence is thus of vital importance for recruitment of fish stocks and also as promising live feed for finfish production in aquaculture. This paper reviews the application of molecular approaches to understanding copepod physiology, particularly in non-parasitic species. The review includes both targeted gene approaches and untargeted transcriptomic approaches, with suggestions for best practices in each case. Issues particularly relevant to studies of copepods include heterogeneity within species, morphologically cryptic species, experimental artifacts associated with sample handling, and limited annotation of copepod genes and transcripts. The emergence of high-throughput sequencing and associated increased availability of genomic and transcriptomic databases have presented a huge opportunity to advance knowledge of copepod physiology. The research community can leverage this opportunity through efforts to maintain or improve data accessibility, database annotation, and documentation of analytical pipelines.

AB - Planktonic copepods are a diverse and abundant group of small (~mm sized) aquatic animals that play a critical role in linking the base of the food chain with higher trophic levels. These invertebrates are a primary food source for marine fish larvae. Their ubiquitous presence is thus of vital importance for recruitment of fish stocks and also as promising live feed for finfish production in aquaculture. This paper reviews the application of molecular approaches to understanding copepod physiology, particularly in non-parasitic species. The review includes both targeted gene approaches and untargeted transcriptomic approaches, with suggestions for best practices in each case. Issues particularly relevant to studies of copepods include heterogeneity within species, morphologically cryptic species, experimental artifacts associated with sample handling, and limited annotation of copepod genes and transcripts. The emergence of high-throughput sequencing and associated increased availability of genomic and transcriptomic databases have presented a huge opportunity to advance knowledge of copepod physiology. The research community can leverage this opportunity through efforts to maintain or improve data accessibility, database annotation, and documentation of analytical pipelines.

U2 - 10.1016/j.cbd.2019.03.005

DO - 10.1016/j.cbd.2019.03.005

M3 - Journal article

VL - 2019

SP - 230

EP - 247

JO - Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

JF - Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics

SN - 1744-117X

IS - 30

ER -