Cremen M.C.M., Leliaert F., Marcelino V.R. & Verbruggen H.
Large diversity of foreign genes and dynamic evolution of chloroplast genomes in siphonous green algae (Bryopsidales, Chlorophyta)
Genome Biology and Evolution: submitted


Green algal chloroplast genomes have undergone tremendous alterations across the main lineages of green algae (Chlorophyta). This study focuses on the underlying chloroplast genome dynamics of the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yields a dataset representing all but one family across the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genome features in the Bryopsidales. Our results showed the extensive variation in chloroplast genome architecture and intron content in the order. Variability in genome size is strongly correlated with the occurrence of intergenic space and free-standing open reading frames (fsORFs) involved in mobile functions. We show the diversity of these foreign fsORFs based on their conserved protein domains (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases), and show putative cases of horizontal gene transfers and intragenomic proliferation of these foreign genes. Investigation of the introns showed proliferation of group II introns in the early part of the evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss. In spite of the extensive rearrangement exhibited by the Bryopsidineae and core Halimedineae lineages, they still retain a few gene clusters similar to other ulvophycean lineages.

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