Functional and phylogenetic analysis of the core transcriptome of Ochromonadales

Graupner, Nadine; Boenigk, Jens; Böck, Christina; Jensen, Manfred; Marks, Sabina; Rahmann, Sven; Beißer, Daniela

doi:10.3897/mbmg.1.19862

Cited by 1 publication

(4 citation statements)

References 44 publications

(64 reference statements)

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“…However, the overlap of shared genes could rise when the genome sequences are completed. On the other hand, Graupner et al. (2017) determined around 92% annotated shared genes ( n = 2,000) and 50% sequences variations in general ( n = 20,000), which confirms our results.…”

Section: Discussionsupporting

confidence: 90%

“…2008). The gene level is slightly lower than the estimated ∼20,000 genes found in the transcriptome study of P. lacustris (Graupner et al. 2017).…”

Section: Discussioncontrasting

confidence: 56%

“…(2017) and Stoeck et al. (2008), but contradicts the findings of Graupner et al. (2017) based on orthologous genes.…”

Section: Discussionmentioning

confidence: 71%

“…2017). However, the gene number in the study of Graupner et al. (2017) was based on gene components generated by the Trinity software, which could therefore be higher because of isoforms and variants of genes.…”

Section: Discussionmentioning

confidence: 99%

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Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)

Majda

Boenigk

Beißer

2019

Genome Biology and Evolution

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Species delimitation in protists is still a challenge, attributable to the fact that protists are small, difficult to observe and many taxa are poor in morphological characters, whereas most current phylogenetic approaches only use few marker genes to measure genetic diversity. To address this problem, we assess genome-level divergence and microevolution in strains of the protist Poteriospumella lacustris, one of the first free-living, nonmodel organisms to study genome-wide intraspecific variation. Poteriospumella lacustris is a freshwater protist belonging to the Chrysophyceae with an assumed worldwide distribution. We examined three strains from different geographic regions (New Zealand, China, and Austria) by sequencing their genomes with the Illumina and PacBio platforms. The assembled genomes were small with 49–55 Mb but gene-rich with 16,000–19,000 genes, of which ∼8,000 genes could be assigned to functional categories. At least 68% of these genes were shared by all three species. Genetic variation occurred predominantly in genes presumably involved in ecological niche adaptation. Most surprisingly, we detected differences in genome ploidy between the strains (diploidy, triploidy, and tetraploidy). In analyzing intraspecific variation, several mechanisms of diversification were identified including SNPs, change of ploidy and genome size reduction.

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Section: Discussionsupporting

confidence: 90%

“…2008). The gene level is slightly lower than the estimated ∼20,000 genes found in the transcriptome study of P. lacustris (Graupner et al. 2017).…”

Section: Discussioncontrasting

confidence: 56%

“…(2017) and Stoeck et al. (2008), but contradicts the findings of Graupner et al. (2017) based on orthologous genes.…”

Section: Discussionmentioning

confidence: 71%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)

Majda

Boenigk

Beißer

2019

Genome Biology and Evolution

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Functional and phylogenetic analysis of the core transcriptome of Ochromonadales

Abstract: Background

Cited by 1 publication

References 44 publications

Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)

Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)

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