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Iha C, Grassa CJ, Lyra GDM, Davis CC, Verbruggen H, Oliveira MC. Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta). JOURNAL OF PHYCOLOGY 2018; 54:775-787. [PMID: 29989670 DOI: 10.1111/jpy.12765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 06/29/2018] [Indexed: 06/08/2023]
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.
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Affiliation(s)
- Cintia Iha
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Christopher J Grassa
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Goia de M Lyra
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
- Laboratório de Algas Marinhas, Instituto de Biologia, Universidade Federal da Bahia, Rua Barão de Jeremoabo, s/n, Salvador, Bahia, 40170-115, Brazil
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts, 02138, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Mariana C Oliveira
- Department of Botany, Institute of Biosciences, University of São Paulo, R Matão 277, São Paulo, SP, 05508-090, Brazil
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Lee J, Kim KM, Yang EC, Miller KA, Boo SM, Bhattacharya D, Yoon HS. Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes. Sci Rep 2016; 6:23744. [PMID: 27030297 PMCID: PMC4814812 DOI: 10.1038/srep23744] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 03/14/2016] [Indexed: 11/22/2022] Open
Abstract
The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.
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Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kyeong Mi Kim
- Marine Biodiversity Institute of Korea, Seocheon, 325-902, Korea
| | - Eun Chan Yang
- Marine Ecosystem Research Division, Korea Institute of Ocean Science & Technology, Ansan, 15627, Korea
| | - Kathy Ann Miller
- Herbarium, University of California at Berkeley, 1001 Valley Life Sciences Building 2465, Berkeley, California, 94720-2465, USA
| | - Sung Min Boo
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
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Abstract
It has been proposed that those plants which contain photosynthetic plastids surrounded by more than two membranes have arisen through secondary endosymbiotic events. Molecular evidence confirms this proposal, but the nature of the endosymbiont(s) and the number of endosymbioses remain unresolved. Whether plastids arose from one type of prokaryotic ancestor or multiple types is the subject of some controversy. In order to try to resolve this question, the plastid gene content and arrangement has been studied from a cryptomonad alga. Most of the gene clusters common to photosynthetic prokaryotes and plastids are preserved and seventeen genes which are not found on the plastid genomes of land plants have been found. Together with previously published phylogenetic analyses of plastid genes, the present data support the notion that the type of prokaryote involved in the initial endosymbiosis was from within the cyanobacterial assemblage and that an early divergence giving rise to the green plant lineage and the rhodophyte lineage resulted in the differences in plastid gene content and sequence between these two groups. Multiple secondary endosymbiotic events involving a eukaryotic (probably rhodophytic alga) and different hosts are hypothesized to have occurred subsequently, giving rise to the chromophyte, cryptophyte and euglenophyte lineages.
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Affiliation(s)
- S E Douglas
- Institute for Marine Biosciences, National Research Council, Halifax, Nova Scotia, Canada
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Abstract
We have discovered plasmids in 5 of 18 diatom species surveyed. In several species, more than one type of plasmid is present. Several of the plasmids show similarity by hybridization previously characterized plasmids in Cylindrotheca fusiformis (J. D. Jacobs et al., unpublished data). Additionally, there is similarity between the plasmids found in C. fusiformis and chloroplast DNA in three diatom species. These results add to the evidence that the plasmids have features of mobile genetic elements.
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Affiliation(s)
- M Hildebrand
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla 92093-0202
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