Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta)

Abstract

Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.

Dual influence of terrestrial and marine historical processes on the phylogeography of the Brazilian intertidal red alga Gracilaria caudata

“…, Iha et al. ). Gracilaria caudata is a haploid‐diploid intertidal rocky shore species characterized by forming dense beds.…”

“…Recent molecular-based analyses revealed the occurrence of numerous cryptic species in this group (Cohen et al 2004, Guillemin et al 2008, Destombe et al 2010, Lyra et al 2016. The difficulty in distinguishing species also explains the current debate about the classification of the PHYLOGEOGRAPHY OF GRACILARIA CAUDATA Gracilariales (see Gurgel et al 2018, Iha et al 2018 Santos et al (2006), Arruda et al (2013), Mill et al (2015 and Peluso et al (2018). Dotted and shaded areas indicate terrestrial coastal refugia and their boundaries, redrawn from the most historically stable Atlantic forest areas proposed in Carnaval and Moritz (2008).…”

Plasmid‐Associated Organelle Genome Evolution In Red Algae

“…2016b, Ng et al. , the Iha et al ). Originally, plasmids were defined as extrachromosomal genetic elements containing backbone (i.e., plasmid function) and accessory (i.e., beneficial to the host) genes.…”

“…Interestingly, the PDS regions are present in all reported organellar genomes in the Gracilariaceae. Iha et al (2018) summarized these organellar PDS in the Gracilariaceae with the addition of nine plastid and 10 mitochondrial genomes from 10 species (Gracilaria caudata, G. ferox, G. gracilis, G. rangiferina, G. tenuistipitata, G. vermiculophylla, Gracilariopsis longissima, Gp. mclachlanii, Gp.…”

“…What is the role of PDS insertions? The possible role of plasmids as mediators of HGTs is intriguing because the plasmid sequences frequently deliver foreign genetic material to their host genome (Janou skovec et al 2013, Ruck et al 2014, Lee et al 2016b, Ng et al 2017, the Iha et al 2018. Originally, plasmids were defined as extrachromosomal genetic elements containing backbone (i.e., plasmid function) and accessory (i.e., beneficial to the host) genes.…”