Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta). Issue 6 (12th September 2018)

• Record Type: Journal Article
• Authors: Iha, Cintia; Grassa, Christopher J.; Lyra, Goia de M.; Davis, Charles C.; Verbruggen, Heroen; Oliveira, Mariana C.
• Editors: Müller, K.
• Is Part Of: Journal of phycology. Volume 54:Issue 6(2018:Dec.)
• Page Start: 775
• Page End: 787
• Publication Date: 2018-09-12
• Subjects: chloroplast -- gene synteny -- genome architecture -- mitochondria -- phylogenomics -- plasmid‐derived sequences -- plasmids; Algae -- Periodicals; 579.8
• DOI: 10.1111/jpy.12765
• Languages: English
• ISSNs: 0022-3646

Abstract

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 trn L, and trn A and trn N. In chloroplast genomes, PDS insertions were in different positions, but generally found between psd D 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 leu C/ leu D 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 leu C/ leu D: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.