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The holozoan Capsaspora owczarzaki possesses a diverse complement of active transposable element families.

Carr M, Suga H - Genome Biol Evol (2014)

Bottom Line: The families present in the genome show contrasting population histories and appear to be in different stages of their life cycles.Transcriptome data have been analyzed from multiple stages in the C. owczarzaki life cycle.Expression levels vary greatly both between families and between different stages of the life cycle, suggesting an unexpectedly complex level of transposable element regulation in a single celled organism.

View Article: PubMed Central - PubMed

Affiliation: School of Applied Sciences, University of Huddersfield, West Yorkshire, United Kingdom.

ABSTRACT
Capsaspora owczarzaki, a protistan symbiont of the pulmonate snail Biomphalaria glabrata, is the centre of much interest in evolutionary biology due to its close relationship to Metazoa. The whole genome sequence of this protist has revealed new insights into the ancestral genome composition of Metazoa, in particular with regard to gene families involved in the evolution of multicellularity. The draft genome revealed the presence of 23 families of transposable element, made up from DNA transposon as well as long terminal repeat (LTR) and non-LTR retrotransposon families. The phylogenetic analyses presented here show that all of the transposable elements identified in the C. owczarzaki genome have orthologous families in Metazoa, indicating that the ancestral metazoan also had a rich diversity of elements. Molecular evolutionary analyses also show that the majority of families has recently been active within the Capsaspora genome. One family now appears to be inactive and a further five families show no evidence of current transposition. Most individual element copies are evolutionarily young; however, a small proportion of inserts appear to have persisted for longer in the genome. The families present in the genome show contrasting population histories and appear to be in different stages of their life cycles. Transcriptome data have been analyzed from multiple stages in the C. owczarzaki life cycle. Expression levels vary greatly both between families and between different stages of the life cycle, suggesting an unexpectedly complex level of transposable element regulation in a single celled organism.

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Related in: MedlinePlus

Maximum likelihood phylogeny of chromoviral Pol amino acid sequences. The phylogeny was constructed from 630 aligned amino acid positions using the PROTCAT model with the LG substitution matrix. Values for mlBPs and biPPs are shown above and below the branches, respectively. 100% mlBP and 1.00 biPP are both denoted by ‘*’. Values <50% mlBP or <0.70 biPP are denoted by “-.” Capsaspora owczarzaki proteins are written in red bold font, metazoan proteins are written in dark blue, choanoflagellate proteins in light blue, fungal proteins in brown, plant proteins are in dark green, and amoebozoan proteins are written in purple. The scale bar represents the number of amino acid substitutions per site.
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evu068-F1: Maximum likelihood phylogeny of chromoviral Pol amino acid sequences. The phylogeny was constructed from 630 aligned amino acid positions using the PROTCAT model with the LG substitution matrix. Values for mlBPs and biPPs are shown above and below the branches, respectively. 100% mlBP and 1.00 biPP are both denoted by ‘*’. Values <50% mlBP or <0.70 biPP are denoted by “-.” Capsaspora owczarzaki proteins are written in red bold font, metazoan proteins are written in dark blue, choanoflagellate proteins in light blue, fungal proteins in brown, plant proteins are in dark green, and amoebozoan proteins are written in purple. The scale bar represents the number of amino acid substitutions per site.

Mentions: Maximum likelihood phylogeny of L1 Pol amino acid sequences. The phylogeny was constructed from 393 aligned amino acid positions using the PROTCAT model with the LG substitution matrix. Excavate proteins are in pink font, the formatting of the tree and labels is otherwise the same as in figure 1.


The holozoan Capsaspora owczarzaki possesses a diverse complement of active transposable element families.

Carr M, Suga H - Genome Biol Evol (2014)

Maximum likelihood phylogeny of chromoviral Pol amino acid sequences. The phylogeny was constructed from 630 aligned amino acid positions using the PROTCAT model with the LG substitution matrix. Values for mlBPs and biPPs are shown above and below the branches, respectively. 100% mlBP and 1.00 biPP are both denoted by ‘*’. Values <50% mlBP or <0.70 biPP are denoted by “-.” Capsaspora owczarzaki proteins are written in red bold font, metazoan proteins are written in dark blue, choanoflagellate proteins in light blue, fungal proteins in brown, plant proteins are in dark green, and amoebozoan proteins are written in purple. The scale bar represents the number of amino acid substitutions per site.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4007536&req=5

evu068-F1: Maximum likelihood phylogeny of chromoviral Pol amino acid sequences. The phylogeny was constructed from 630 aligned amino acid positions using the PROTCAT model with the LG substitution matrix. Values for mlBPs and biPPs are shown above and below the branches, respectively. 100% mlBP and 1.00 biPP are both denoted by ‘*’. Values <50% mlBP or <0.70 biPP are denoted by “-.” Capsaspora owczarzaki proteins are written in red bold font, metazoan proteins are written in dark blue, choanoflagellate proteins in light blue, fungal proteins in brown, plant proteins are in dark green, and amoebozoan proteins are written in purple. The scale bar represents the number of amino acid substitutions per site.
Mentions: Maximum likelihood phylogeny of L1 Pol amino acid sequences. The phylogeny was constructed from 393 aligned amino acid positions using the PROTCAT model with the LG substitution matrix. Excavate proteins are in pink font, the formatting of the tree and labels is otherwise the same as in figure 1.

Bottom Line: The families present in the genome show contrasting population histories and appear to be in different stages of their life cycles.Transcriptome data have been analyzed from multiple stages in the C. owczarzaki life cycle.Expression levels vary greatly both between families and between different stages of the life cycle, suggesting an unexpectedly complex level of transposable element regulation in a single celled organism.

View Article: PubMed Central - PubMed

Affiliation: School of Applied Sciences, University of Huddersfield, West Yorkshire, United Kingdom.

ABSTRACT
Capsaspora owczarzaki, a protistan symbiont of the pulmonate snail Biomphalaria glabrata, is the centre of much interest in evolutionary biology due to its close relationship to Metazoa. The whole genome sequence of this protist has revealed new insights into the ancestral genome composition of Metazoa, in particular with regard to gene families involved in the evolution of multicellularity. The draft genome revealed the presence of 23 families of transposable element, made up from DNA transposon as well as long terminal repeat (LTR) and non-LTR retrotransposon families. The phylogenetic analyses presented here show that all of the transposable elements identified in the C. owczarzaki genome have orthologous families in Metazoa, indicating that the ancestral metazoan also had a rich diversity of elements. Molecular evolutionary analyses also show that the majority of families has recently been active within the Capsaspora genome. One family now appears to be inactive and a further five families show no evidence of current transposition. Most individual element copies are evolutionarily young; however, a small proportion of inserts appear to have persisted for longer in the genome. The families present in the genome show contrasting population histories and appear to be in different stages of their life cycles. Transcriptome data have been analyzed from multiple stages in the C. owczarzaki life cycle. Expression levels vary greatly both between families and between different stages of the life cycle, suggesting an unexpectedly complex level of transposable element regulation in a single celled organism.

Show MeSH
Related in: MedlinePlus