Comparative transcriptome analysis of four prymnesiophyte algae.
Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic...
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ftdoajarticles:oai:doaj.org/article:60b999c532724cf9adbabb89691666d8 2023-05-15T13:57:13+02:00 Comparative transcriptome analysis of four prymnesiophyte algae. Amy E Koid Zhenfeng Liu Ramon Terrado Adriane C Jones David A Caron Karla B Heidelberg 2014-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0097801 https://doaj.org/article/60b999c532724cf9adbabb89691666d8 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC4057078?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0097801 https://doaj.org/article/60b999c532724cf9adbabb89691666d8 PLoS ONE, Vol 9, Iss 6, p e97801 (2014) Medicine R Science Q article 2014 ftdoajarticles https://doi.org/10.1371/journal.pone.0097801 2022-12-31T13:09:49Z Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists. Article in Journal/Newspaper Antarc* Antarctica Directory of Open Access Journals: DOAJ Articles PLoS ONE 9 6 e97801 |
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Medicine R Science Q |
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Medicine R Science Q Amy E Koid Zhenfeng Liu Ramon Terrado Adriane C Jones David A Caron Karla B Heidelberg Comparative transcriptome analysis of four prymnesiophyte algae. |
topic_facet |
Medicine R Science Q |
description |
Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists. |
format |
Article in Journal/Newspaper |
author |
Amy E Koid Zhenfeng Liu Ramon Terrado Adriane C Jones David A Caron Karla B Heidelberg |
author_facet |
Amy E Koid Zhenfeng Liu Ramon Terrado Adriane C Jones David A Caron Karla B Heidelberg |
author_sort |
Amy E Koid |
title |
Comparative transcriptome analysis of four prymnesiophyte algae. |
title_short |
Comparative transcriptome analysis of four prymnesiophyte algae. |
title_full |
Comparative transcriptome analysis of four prymnesiophyte algae. |
title_fullStr |
Comparative transcriptome analysis of four prymnesiophyte algae. |
title_full_unstemmed |
Comparative transcriptome analysis of four prymnesiophyte algae. |
title_sort |
comparative transcriptome analysis of four prymnesiophyte algae. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2014 |
url |
https://doi.org/10.1371/journal.pone.0097801 https://doaj.org/article/60b999c532724cf9adbabb89691666d8 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_source |
PLoS ONE, Vol 9, Iss 6, p e97801 (2014) |
op_relation |
http://europepmc.org/articles/PMC4057078?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0097801 https://doaj.org/article/60b999c532724cf9adbabb89691666d8 |
op_doi |
https://doi.org/10.1371/journal.pone.0097801 |
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PLoS ONE |
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9 |
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6 |
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e97801 |
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1766264812588761088 |