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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ftpubmed:oai:pubmedcentral.nih.gov:4057078 2023-05-15T13:59:29+02:00 Comparative Transcriptome Analysis of Four Prymnesiophyte Algae Koid, Amy E. Liu, Zhenfeng Terrado, Ramon Jones, Adriane C. Caron, David A. Heidelberg, Karla B. 2014-06-13 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057078 http://www.ncbi.nlm.nih.gov/pubmed/24926657 https://doi.org/10.1371/journal.pone.0097801 en eng Public Library of Science http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/24926657 http://dx.doi.org/10.1371/journal.pone.0097801 This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. CC-BY Research Article Text 2014 ftpubmed https://doi.org/10.1371/journal.pone.0097801 2014-06-22T00:59:07Z 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. Text Antarc* Antarctica PubMed Central (PMC) PLoS ONE 9 6 e97801 |
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Research Article Koid, Amy E. Liu, Zhenfeng Terrado, Ramon Jones, Adriane C. Caron, David A. Heidelberg, Karla B. Comparative Transcriptome Analysis of Four Prymnesiophyte Algae |
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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 |
Text |
author |
Koid, Amy E. Liu, Zhenfeng Terrado, Ramon Jones, Adriane C. Caron, David A. Heidelberg, Karla B. |
author_facet |
Koid, Amy E. Liu, Zhenfeng Terrado, Ramon Jones, Adriane C. Caron, David A. Heidelberg, Karla B. |
author_sort |
Koid, Amy E. |
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 |
publishDate |
2014 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4057078 http://www.ncbi.nlm.nih.gov/pubmed/24926657 https://doi.org/10.1371/journal.pone.0097801 |
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Antarc* Antarctica |
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Antarc* Antarctica |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC http://www.ncbi.nlm.nih.gov/pubmed/24926657 http://dx.doi.org/10.1371/journal.pone.0097801 |
op_rights |
This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
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CC-BY |
op_doi |
https://doi.org/10.1371/journal.pone.0097801 |
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9 |
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6 |
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1766268055906680832 |