Horizontal transfer of bacterial gene regions to chloroplast genomes of green algae

Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. In a paper we recently published in BMC Genomics, we report on the complete cpDNAs of Bryopsis plumosa and Tydemania expeditionis, as well as a re-annotated cpDNA of B. hypnoides (which was shown to contain a higher number of genes than originally published).

Gene maps of the chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones. The red arcs indicate gene regions of putative bacterial origin.
Gene maps of the chloroplast genomes of Bryopsis plumosa and Tydemania expeditionis. The red arcs indicate gene regions of bacterial origin.

The cpDNAs of B. plumosa and T. expeditionis are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta, and both lack a large inverted repeat.

Both chloroplast genomes contain DNA regions with genes of bacterial origin, including rhs-family genes, and several genes involved in mobile functions, such as transposases, integrases, DNA polymerases, and phage/plasmid DNA primases. Another unexpected finding was the presence of two genes in T. expeditionis showing close similarity to bacterial DNA methyltransferases, a family of genes that have up till now not been found in any plastid genome.

The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae. Our data adds to the scarce knowledge of horizontal transfer of bacterial DNA to plastid genomes.

In addition, chloroplast genomic data were used to evaluate phylogenetic hypotheses in the Chlorophyta. These analyses, however, were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta.

Phylogenetic trees of Chlorophyta inferred from a 50-gene dataset.  (A) Bayesian majority rule tree showing all compatible partitions, inference from the protein alignment of 51 concatenated chloroplast genes (9,300 amino acid positions and 44 terminal taxa). Node support is given as Bayesian posterior probabilities and maximum-likelihood (ML) bootstrap values of the protein analyses (above branches), and the nucleotide analyses (below branches); values <0.9 and 50, respectively, are not shown; asterisks indicated full support in both the Bayesian and ML analyses. (B) Bayesian tree inference from the nucleotide alignment (first two codon positions) of 51 concatenated chloroplast genes (18,600 nucleotide positions and 44 terminal taxa). Prasinophytes are not shown. Node support is given as Bayesian posterior probabilities and maximum-likelihood (ML) bootstrap values, and asterisks indicate full support in both analyses.
Phylogenetic trees of Chlorophyta inferred from a 50-gene dataset (A: protein dataset, B: nucleotide dataset).

Read more: www.biomedcentral.com/1471-2164/16/204 (i)

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