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

Journal of Phycology - Tập 54 Số 6 - Trang 775-787 - 2018
Cíntia Iha1,2, Christopher J. Grassa3, Goia de Mattos Lyra3,4, Charles C. Davis3, Heroen Verbruggen2, Mariana C. Oliveira1
1Department of Botany Institute of Biosciences University of São Paulo R Matão 277 São Paulo SP 05508‐090 Brazil
2School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia
3Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge Massachusetts 02138, USA
4Laboratório de Algas Marinhas Instituto de Biologia Universidade Federal da Bahia Rua Barão de Jeremoabo, s/n Salvador Bahia 40170‐115 Brazil

Tóm tắt

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.

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Journal of Phycology

Tập 54 Số 6

775-787

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