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      Functional and phylogenetic analysis of the core transcriptome of Ochromonadales

      , , , , , ,

      Metabarcoding and Metagenomics

      Pensoft Publishers

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          Abstract

          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.

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          Most cited references 28

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          We present eXpress, a software package for highly efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time, and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. We demonstrate its use on RNA-seq data, showing greater efficiency than other quantification methods.
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            Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.

            We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.
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              Comparative genomics, minimal gene-sets and the last universal common ancestor.

              Comparative genomics, using computational and experimental methods, enables the identification of a minimal set of genes that is necessary and sufficient for sustaining a functional cell. For most essential cellular functions, two or more unrelated or distantly related proteins have evolved; only about 60 proteins, primarily those involved in translation, are common to all cellular life. The reconstruction of ancestral life-forms is based on the principle of evolutionary parsimony, but the size and composition of the reconstructed ancestral gene-repertoires depend on relative rates of gene loss and horizontal gene-transfer. The present estimate suggests a simple last universal common ancestor with only 500-600 genes.
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                Author and article information

                Journal
                Metabarcoding and Metagenomics
                Metabarcoding and Metagenomics
                Pensoft Publishers
                2534-9708
                September 20 2017
                September 20 2017
                : 1
                : e19862
                Article
                10.3897/mbmg.1.19862
                © 2017

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