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

Author(s)

Iha, Cintia ^{[1, 2]} ; Grassa, Christopher J. ^[3] ; Lyra, Goia de M. ^{[3, 4]} ; Davis, Charles C. ^[3] ; Verbruggen, Heroen ^[1] ; Oliveira, Mariana C. ^[2]

Affiliation

^[1] Univ Melbourne, Sch BioSci, Melbourne, Vic 3010 - Australia

^[2] Univ Sao Paulo, Inst Biosci, Dept Bot, R Matao 277, BR-05508090 Sao Paulo, SP - Brazil

^[3] Harvard Univ Herbaria, Dept Organism & Evolutionary Biol, 22 Divin Ave, Cambridge, MA 02138 - USA

^[4] Univ Fed Bahia, Inst Biol, Lab Algas Marinhas, Rua Barao de Jeremoabo S-N, BR-40170115 Salvador, BA - Brazil

• Document type: Journal article
• Source: JOURNAL OF PHYCOLOGY; v. 54, n. 6, p. 775-787, DEC 2018.
• Web of Science Citations: 4

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. (AU)

• FAPESP's process: 15/50078-1 - Marine genomic: genome biology and evolution of key primary producers
• Grantee: Mariana Cabral de Oliveira
• Support Opportunities: Regular Research Grants
• FAPESP's process: 13/11833-3 - Diversity and phylogeny of red algae (Rhodophyta) of economic and ecological importance
• Grantee: Mariana Cabral de Oliveira
• Support Opportunities: BIOTA-FAPESP Program - Regular Research Grants