Functional and phylogenetic analysis of the core transcriptome of Ochromonadales
Background Most protist lineages consist of members with diverging features e.g. different modes of nutrition and adaptations for life in different habitat types and climatic zones. The nutritional mode is particularly variable in chrysophytes and they are therefore an excellent model g...
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doaj-e04d2a59c92c44b18698dd7e6a79bee02020-11-24T23:33:14ZengPensoft PublishersMetabarcoding and Metagenomics 2534-97082017-09-01112010.3897/mbmg.1.1986219862Functional and phylogenetic analysis of the core transcriptome of Ochromonadales Nadine Graupner0Jens Boenigk1Christina Bock2Manfred Jensen3Sabina Marks4Sven Rahmann5Daniela Beisser6Biodiversity, University of Duisburg-EssenCentre for Water and Environmental Research (ZWU), University of Duisburg-EssenBiodiversity, University of Duisburg-EssenBiodiversity, University of Duisburg-EssenBiodiversity, University of Duisburg-EssenGenome Informatics, University of Duisburg Essen, University Hospital EssenBiodiversity, University of Duisburg-Essen Background Most protist lineages consist of members with diverging features e.g. different modes of nutrition and adaptations for life in different habitat types and climatic zones. The nutritional mode is particularly variable in chrysophytes and they are therefore an excellent model group to study the core genes and metabolic pathways of a functionally diverse lineage. The objective of our study is the identification of the joint genetic repertoire expressed in closely related chrysophytes as well as the extent of variation on species and strain level. Therefore, we investigated the transcriptomes of six strains belonging to four species of Ochromonadales. We performed analyses on metabolic pathway level as well as on sequence level. Results We could identify 1,574 core genes shared between all six investigated strains of Ochromonadales. Most of these core genes were affiliated with the primary metabolism. Phylogenetic analysis of 166 protein-coding core genes supported a close relation of Poteriospumella lacustris and Poterioochromonas malhamensis and resolved for more than 50% of investigated genes the relationship of strains affiliated with the species P. lacustris. Further, we found diverging phylogenetic patterns for genes interacting with the environment. Conclusions In Ochromonadales, a functionally diverse lineage, the core transcriptome represents only a minor part of the individual transcriptomes. But this small fraction of genes comprises the basal metabolism essential for life in several protist lineages. Phylogenetic analyses of these genes indicate a similar degree of conservation as observed for genes coding for ribosomal proteins. https://mbmg.pensoft.net/article/19862/Chrysophyceaeprotistexpressed sequence tags |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Nadine Graupner Jens Boenigk Christina Bock Manfred Jensen Sabina Marks Sven Rahmann Daniela Beisser |
spellingShingle |
Nadine Graupner Jens Boenigk Christina Bock Manfred Jensen Sabina Marks Sven Rahmann Daniela Beisser Functional and phylogenetic analysis of the core transcriptome of Ochromonadales Metabarcoding and Metagenomics Chrysophyceae protist expressed sequence tags |
author_facet |
Nadine Graupner Jens Boenigk Christina Bock Manfred Jensen Sabina Marks Sven Rahmann Daniela Beisser |
author_sort |
Nadine Graupner |
title |
Functional and phylogenetic analysis of the core transcriptome of Ochromonadales |
title_short |
Functional and phylogenetic analysis of the core transcriptome of Ochromonadales |
title_full |
Functional and phylogenetic analysis of the core transcriptome of Ochromonadales |
title_fullStr |
Functional and phylogenetic analysis of the core transcriptome of Ochromonadales |
title_full_unstemmed |
Functional and phylogenetic analysis of the core transcriptome of Ochromonadales |
title_sort |
functional and phylogenetic analysis of the core transcriptome of ochromonadales |
publisher |
Pensoft Publishers |
series |
Metabarcoding and Metagenomics |
issn |
2534-9708 |
publishDate |
2017-09-01 |
description |
Background
Most protist lineages consist of members with diverging features e.g. different modes of nutrition and adaptations for life in different habitat types and climatic zones. The nutritional mode is particularly variable in chrysophytes and they are therefore an excellent model group to study the core genes and metabolic pathways of a functionally diverse lineage. The objective of our study is the identification of the joint genetic repertoire expressed in closely related chrysophytes as well as the extent of variation on species and strain level. Therefore, we investigated the transcriptomes of six strains belonging to four species of Ochromonadales. We performed analyses on metabolic pathway level as well as on sequence level.
Results
We could identify 1,574 core genes shared between all six investigated strains of Ochromonadales. Most of these core genes were affiliated with the primary metabolism. Phylogenetic analysis of 166 protein-coding core genes supported a close relation of Poteriospumella lacustris and Poterioochromonas malhamensis and resolved for more than 50% of investigated genes the relationship of strains affiliated with the species P. lacustris. Further, we found diverging phylogenetic patterns for genes interacting with the environment.
Conclusions
In Ochromonadales, a functionally diverse lineage, the core transcriptome represents only a minor part of the individual transcriptomes. But this small fraction of genes comprises the basal metabolism essential for life in several protist lineages. Phylogenetic analyses of these genes indicate a similar degree of conservation as observed for genes coding for ribosomal proteins.
|
topic |
Chrysophyceae protist expressed sequence tags |
url |
https://mbmg.pensoft.net/article/19862/ |
work_keys_str_mv |
AT nadinegraupner functionalandphylogeneticanalysisofthecoretranscriptomeofochromonadales AT jensboenigk functionalandphylogeneticanalysisofthecoretranscriptomeofochromonadales AT christinabock functionalandphylogeneticanalysisofthecoretranscriptomeofochromonadales AT manfredjensen functionalandphylogeneticanalysisofthecoretranscriptomeofochromonadales AT sabinamarks functionalandphylogeneticanalysisofthecoretranscriptomeofochromonadales AT svenrahmann functionalandphylogeneticanalysisofthecoretranscriptomeofochromonadales AT danielabeisser functionalandphylogeneticanalysisofthecoretranscriptomeofochromonadales |
_version_ |
1716301245907468288 |