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Hammel A, Neupert J, Bock R. Optimized transgene expression in the red alga Porphyridium purpureum and efficient recombinant protein secretion into the culture medium. PLANT MOLECULAR BIOLOGY 2024; 114:18. [PMID: 38353826 PMCID: PMC10866757 DOI: 10.1007/s11103-024-01415-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024]
Abstract
Microalgae represent a promising but yet underexplored production platform for biotechnology. The vast majority of studies on recombinant protein expression in algae have been conducted in a single species, the green alga Chlamydomonas reinhardtii. However, due to epigenetic silencing, transgene expression in Chlamydomonas is often inefficient. Here we have investigated parameters that govern efficient transgene expression in the red microalga Porphyridium purpureum. Porphyridium is unique in that the introduced transformation vectors are episomally maintained as autonomously replicating plasmids in the nucleus. We show that full codon optimization to the preferred codon usage in the Porphyridium genome confers superior transgene expression, not only at the level of protein accumulation, but also at the level of mRNA accumulation, indicating that high translation rates increase mRNA stability. Our optimized expression constructs resulted in YFP accumulation to unprecedented levels of up to 5% of the total soluble protein. We also designed expression cassettes that target foreign proteins to the secretory pathway and lead to efficient protein secretion into the culture medium, thus simplifying recombinant protein harvest and purification. Our study paves the way to the exploration of red microalgae as expression hosts in molecular farming for recombinant proteins and metabolites.
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Affiliation(s)
- Alexander Hammel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie (MPI-MP), Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
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2
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Van Etten J, Cho CH, Yoon HS, Bhattacharya D. Extremophilic red algae as models for understanding adaptation to hostile environments and the evolution of eukaryotic life on the early earth. Semin Cell Dev Biol 2023; 134:4-13. [PMID: 35339358 DOI: 10.1016/j.semcdb.2022.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/20/2022] [Accepted: 03/04/2022] [Indexed: 01/08/2023]
Abstract
Extremophiles have always garnered great interest because of their exotic lifestyles and ability to thrive at the physical limits of life. In hot springs environments, the Cyanidiophyceae red algae are the only photosynthetic eukaryotes able to live under extremely low pH (0-5) and relatively high temperature (35ºC to 63ºC). These extremophiles live as biofilms in the springs, inhabit acid soils near the hot springs, and form endolithic populations in the surrounding rocks. Cyanidiophyceae represent a remarkable source of knowledge about the evolution of extremophilic lifestyles and their genomes encode specialized enzymes that have applied uses. Here we review the evolutionary origin, taxonomy, genome biology, industrial applications, and use of Cyanidiophyceae as genetic models. Currently, Cyanidiophyceae comprise a single order (Cyanidiales), three families, four genera, and nine species, including the well-known Cyanidioschyzon merolae and Galdieria sulphuraria. These algae have small, gene-rich genomes that are analogous to those of prokaryotes they live and compete with. There are few spliceosomal introns and evidence exists for horizontal gene transfer as a driver of local adaptation to gain access to external fixed carbon and to extrude toxic metals. Cyanidiophyceae offer a variety of commercial opportunities such as phytoremediation to detoxify contaminated soils or waters and exploitation of their mixotrophic lifestyles to support the efficient production of bioproducts such as phycocyanin and floridosides. In terms of exobiology, Cyanidiophyceae are an ideal model system for understanding the evolutionary effects of foreign gene acquisition and the interactions between different organisms inhabiting the same harsh environment on the early Earth. Finally, we describe ongoing research with C. merolae genetics and summarize the unique insights they offer to the understanding of algal biology and evolution.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
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Cyanophages as an important factor in the early evolution of oxygenic photosynthesis. Sci Rep 2022; 12:20581. [PMID: 36446879 PMCID: PMC9709159 DOI: 10.1038/s41598-022-24795-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Cyanophages are viruses that infect cyanobacteria. An interesting feature of many of them is the presence of psbA and psbD, genes that encode D1 and D2 proteins, respectively. The D1 and D2 are core proteins of the photosystem II (PSII) in cyanobacteria, algae and plants and influence the proper function of oxygenic photosynthesis (OP) in all oxyphototrophs on Earth. The frequent occurrence of psbA and psbD in cyanophages raises the question whether these genes coevolved with hosts during the early stages of cyanophage and cyanobacterial evolution, or whether they are direct descendants of genes adopted from the genomes of cyanobacterial hosts. The phylogeny of D1/D2 proteins encoded in the genomes of selected cyanophages and oxyphototrophs was reconstructed. In addition, common ancestral sequences of D1 and D2 proteins were predicted for cyanophages and oxyphototrophs. Based on this, the reconstruction of the 3D structures of D1 and D2 proteins was performed. In addition, the ratio of non-synonymous to synonymous (dN/dS) nucleotide substitutions in the coding sequences (CDSs) of psbA and psbD was determined. The results of the predicted spatial structures of the D1 and D2 proteins and purifying selection for the CDSs of psbA and psbD suggest that they belong to the ancient proteins, which may have formed the primordial PSII. It cannot be ruled out that they involved in water oxidation in cyanobacteria-like organisms at early stages of the evolution of life on Earth and coevolved with ancient cyanophages. The data are also discussed in the context of the origin of viruses.
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Wang S, Gao J, Chao H, Li Z, Pu W, Wang Y, Chen M. Comparative Chloroplast Genomes of Nicotiana Species (Solanaceae): Insights Into the Genetic Variation, Phylogenetic Relationship, and Polyploid Speciation. FRONTIERS IN PLANT SCIENCE 2022; 13:899252. [PMID: 35865282 PMCID: PMC9295722 DOI: 10.3389/fpls.2022.899252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/26/2022] [Indexed: 05/25/2023]
Abstract
Nicotiana L. is a genus rich in polyploidy, which represents an ideal natural system for investigating speciation, biodiversity, and phytogeography. Despite a wealth of phylogenetic work on this genus, a robust evolutionary framework with a dated molecular phylogeny for the genus is still lacking. In this study, the 19 complete chloroplast genomes of Nicotiana species were assembled, and five published chloroplast genomes of Nicotiana were retrieved for comparative analyses. The results showed that the 24 chloroplast genomes of Nicotiana, ranging from 155,327 bp (N. paniculata) to 156,142 bp (N. heterantha) in size, exhibited typical quadripartite structure. The chloroplast genomes were rather conserved in genome structure, GC content, RNA editing sites, and gene content and order. The higher GC content observed in the IR regions could be a result of the presence of abundant rRNA and tRNA genes, which contained a relatively higher GC content. A total of seven hypervariable regions, as new molecular markers for phylogenetic analysis, were uncovered. Based on 78 protein-coding genes, we constructed a well-supported phylogenetic tree, which was largely in agreement with previous studies, except for a slight conflict in several sections. Chloroplast phylogenetic results indicated that the progenitors of diploid N. sylvestris, N. knightiana, and the common ancestor of N. sylvestris and N. glauca might have donated the maternal genomes of allopolyploid N. tabacum, N. rustica, and section Repandae, respectively. Meanwhile, the diploid section Noctiflorae lineages (N. glauca) acted as the most likely maternal progenitor of section Suaveolentes. Molecular dating results show that the polyploid events range considerably in ~0.12 million (section Nicotiana) to ~5.77 million (section Repandae) years ago. The younger polyploids (N. tabacum and N. rustica) were estimated to have arisen ~0.120 and ~0.186 Mya, respectively. The older polyploids (section Repandae and Suaveolentes) were considered to have originated from a single polyploid event at ~5.77 and ~4.49 Mya, respectively. In summary, the comparative analysis of chloroplast genomes of Nicotiana species has not only revealed a series of new insights into the genetic variation and phylogenetic relationships in Nicotiana but also provided rich genetic resources for speciation and biodiversity research in the future.
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Affiliation(s)
- Shuaibin Wang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Junping Gao
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Haoyu Chao
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhaowu Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Wenxuan Pu
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Yaofu Wang
- Tobacco Research Institute of Technology Centre, China Tobacco Hunan Industrial Corporation, Changsha, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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Kim JI, Jo BY, Park MG, Yoo YD, Shin W, Archibald JM. Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:896138. [PMID: 35769291 PMCID: PMC9235467 DOI: 10.3389/fpls.2022.896138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Bok Yeon Jo
- Nakdonggang National Institute of Biological Resources, Sangju, South Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju, South Korea
| | - Yeong Du Yoo
- Department of Marine Biology, College of Ocean Sciences and Technology, Kunsan National University, Kunsan, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Dagnino-Leone J, Figueroa CP, Castañeda ML, Youlton AD, Vallejos-Almirall A, Agurto-Muñoz A, Pavón Pérez J, Agurto-Muñoz C. Phycobiliproteins: Structural aspects, functional characteristics, and biotechnological perspectives. Comput Struct Biotechnol J 2022; 20:1506-1527. [PMID: 35422968 PMCID: PMC8983314 DOI: 10.1016/j.csbj.2022.02.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 02/18/2022] [Accepted: 02/19/2022] [Indexed: 12/13/2022] Open
Abstract
Phycobiliproteins (PBPs) are fluorescent proteins of various colors, including fuchsia, purple-blue and cyan, that allow the capture of light energy in auxiliary photosynthetic complexes called phycobilisomes (PBS). PBPs have several highly preserved structural and physicochemical characteristics. In the PBS context, PBPs function is capture luminous energy in the 450–650 nm range and delivers it to photosystems allowing photosynthesis take place. Besides the energy harvesting function, PBPs also have shown to have multiple biological activities, including antioxidant, antibacterial and antitumours, making them an interesting focus for different biotechnological applications in areas like biomedicine, bioenergy and scientific research. Nowadays, the main sources of PBPs are cyanobacteria and micro and macro algae from the phylum Rhodophyta. Due to the diverse biological activities of PBPs, they have attracted the attention of different industries, such as food, biomedical and cosmetics. This is why a large number of patents related to the production, extraction, purification of PBPs and their application as cosmetics, biopharmaceuticals or diagnostic applications have been generated, looking less ecological impact in the natural prairies of macroalgae and less culture time or higher productivity in cyanobacteria to satisfy the markets and applications that require high amounts of these molecules. In this review, we summarize the main structural characteristics of PBPs, their biosynthesys and biotechnological applications. We also address current trends and future perspectives of the PBPs market.
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Affiliation(s)
- Jorge Dagnino-Leone
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
| | - Cristina Pinto Figueroa
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
| | - Mónica Latorre Castañeda
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
| | - Andrea Donoso Youlton
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
| | - Alejandro Vallejos-Almirall
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
| | - Andrés Agurto-Muñoz
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
| | - Jessy Pavón Pérez
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Ciencia y Tecnología de los Alimentos (CyTA), Facultad de Farmacia, Universidad de Concepción, Concepción 4030000 Chile
| | - Cristian Agurto-Muñoz
- Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Ciencia y Tecnología de los Alimentos (CyTA), Facultad de Farmacia, Universidad de Concepción, Concepción 4030000 Chile
- Corresponding author at: Grupo Interdisciplinario de Biotecnología Marina (GIBMAR), Centro de Biotecnología, Universidad de Concepción, Concepción 4030000, Chile.
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Kim D, Lee J, Cho CH, Kim EJ, Bhattacharya D, Yoon HS. Group II intron and repeat-rich red algal mitochondrial genomes demonstrate the dynamic recent history of autocatalytic RNAs. BMC Biol 2022; 20:2. [PMID: 34996446 PMCID: PMC8742464 DOI: 10.1186/s12915-021-01200-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Group II introns are mobile genetic elements that can insert at specific target sequences, however, their origins are often challenging to reconstruct because of rapid sequence decay following invasion and spread into different sites. To advance understanding of group II intron spread, we studied the intron-rich mitochondrial genome (mitogenome) in the unicellular red alga, Porphyridium. Results Analysis of mitogenomes in three closely related species in this genus revealed they were 3–6-fold larger in size (56–132 kbp) than in other red algae, that have genomes of size 21–43 kbp. This discrepancy is explained by two factors, group II intron invasion and expansion of repeated sequences in large intergenic regions. Phylogenetic analysis demonstrates that many mitogenome group II intron families are specific to Porphyridium, whereas others are closely related to sequences in fungi and in the red alga-derived plastids of stramenopiles. Network analysis of intron-encoded proteins (IEPs) shows a clear link between plastid and mitochondrial IEPs in distantly related species, with both groups associated with prokaryotic sequences. Conclusion Our analysis of group II introns in Porphyridium mitogenomes demonstrates the dynamic nature of group II intron evolution, strongly supports the lateral movement of group II introns among diverse eukaryotes, and reveals their ability to proliferate, once integrated in mitochondrial DNA. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01200-3.
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Affiliation(s)
- Dongseok Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, 41566, South Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Eun Jeung Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea.
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Kim H, Yang JH, Bustamante DE, Calderon MS, Mansilla A, Maggs CA, Hansen GI, Yoon HS. Organelle Genome Variation in the Red Algal Genus Ahnfeltia (Florideophyceae). Front Genet 2021; 12:724734. [PMID: 34646303 PMCID: PMC8503264 DOI: 10.3389/fgene.2021.724734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
The agarophyte Ahnfeltia (Ahnfeltiales, Rhodophyta) is a globally widespread genus with 11 accepted species names. Two of the most widespread species in this genus, A. plicata and A. fastigiata, may have diverged genetically due to past geographic changes and subsequent geographic isolation. To investigate this genomic and genetic diversity, we generated new plastid (ptDNAs) and mitochondrial genomes (mtDNAs) of these Ahnfeltia species from four different regions (A. plicata - Chile and UK and A. fastigiata - Korea and Oregon). Two architecture variations were found in the Ahnfeltia genomes: in ptDNA of A. fastigiata Oregon, the hypothetical pseudogene region was translocated, likely due to recombination with palindromic repeats or a gene transfer from a red algal plasmid. In mtDNA of A. fastigiata Korea, the composition of the group II intronic ORFs was distinct from others suggesting different scenarios of gain and loss of group II intronic ORFs. These features resulted in genome size differences between the two species. Overall gene contents of organelle genomes of Ahnfeltia were conserved. Phylogenetic analysis using concatenated genes from ptDNAs and mtDNAs supported the monophyly of the Ahnfeltiophycidae. The most probable individual gene trees showed that the Ahnfeltia populations were genetically diversified. These trees, the cox1 haplotype network, and a dN/dS analysis all supported the theory that these Ahnfeltia populations have diversified genetically in accordance with geographic distribution.
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Affiliation(s)
- Hocheol Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Danilo E Bustamante
- Instituto de Investigación para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Peru
| | - Martha S Calderon
- Laboratorio de Macroalgas Antárticas y Subantárticas, Universidad de Magallanes, Punta Arenas, Chile
| | - Andres Mansilla
- Laboratorio de Macroalgas Antárticas y Subantárticas, Universidad de Magallanes, Punta Arenas, Chile
| | - Christine A Maggs
- School of Biological Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Gayle I Hansen
- Marine Algal Biodiversity Research, Newport, OR, United States
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Kim H, Lee DY, Seo CW, Cho CH, Yoon HS. Complete plastid genome of Cumathamnion serrulatum (Ceramiales, Rhodophyta). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2009-2011. [PMID: 34189267 PMCID: PMC8208111 DOI: 10.1080/23802359.2021.1920489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We report the complete plastid genome of Cumathamnion serrulatum, also known as Delesseria serrulata. The plastid genome was 174,192 bp in size. Annotation showed there were 193 protein coding genes, three ribosomal RNAs, and 29 transfer RNAs. One intron was found, and the GC content was 27.2%. The maximum likelihood tree with the concatenated 177 plastid coding genes showed a strong monophyletic relationship to Membranoptera spp. within the Ceramiales.
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Affiliation(s)
- Hocheol Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Do-Yun Lee
- College of Pharmacy, Seoul National University, Seoul, Korea
| | - Chang Wan Seo
- School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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Characterization of ACE Inhibitory Peptides Prepared from Pyropia pseudolinearis Protein. Mar Drugs 2021; 19:md19040200. [PMID: 33916201 PMCID: PMC8066288 DOI: 10.3390/md19040200] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
More than 7000 red algae species have been classified. Although most of them are underused, they are a protein-rich marine resource. The hydrolysates of red algal proteins are good candidates for the inhibition of the angiotensin-I-converting enzyme (ACE). The ACE is one of the key factors for cardiovascular disease, and the inhibition of ACE activity is related to the prevention of high blood pressure. To better understand the relationship between the hydrolysates of red algal proteins and the inhibition of ACE activity, we attempted to identify novel ACE inhibitory peptides from Pyropia pseudolinearis. We prepared water soluble proteins (WSP) containing phycoerythrin, phycocyanin, allophycocyanin, and ribulose 1,5-bisphosphate carboxylase/oxygenase. In vitro analysis showed that the thermolysin hydrolysate of the WSP had high ACE inhibitory activity compared to that of WSP. We then identified 42 peptides in the hydrolysate by high-performance liquid chromatography and mass spectrometry. Among 42 peptides, 23 peptides were found in chloroplast proteins. We then synthesized the uncharacterized peptides ARY, YLR, and LRM and measured the ACE inhibitory activity. LRM showed a low IC50 value (0.15 μmol) compared to ARY and YLR (1.3 and 5.8 μmol). In silico analysis revealed that the LRM sequence was conserved in cpcA from Bangiales and Florideophyceae, indicating that the novel ACE inhibitory peptide LRM was highly conserved in red algae.
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Lateral Gene Transfer Mechanisms and Pan-genomes in Eukaryotes. Trends Parasitol 2020; 36:927-941. [DOI: 10.1016/j.pt.2020.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
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Park SI, Lee J. The complete mitochondrial genome of Pyropia pulchra (Bangiophyceae, Rhodophyta). Mitochondrial DNA B Resour 2020; 5:3157-3158. [PMID: 33458093 PMCID: PMC7782328 DOI: 10.1080/23802359.2020.1806132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyropia pulchra (Hollenberg) S.C. Lindstrom & Hughey is a foliose seaweed in Bangiales order distributed in North America. We assembled the complete mitochondrial genome sequence of Pyropia pulchra (33,190 bp), and annotated 26 protein-coding genes, 24 transfer RNAs, and 2 ribosomal RNAs. We analyzed a maximum likelihood tree using conserved 23 mitochondrial genes from Bangiales species. The mitochondrial phylogeny of Bangiales species shows a strong monophyletic relationship of genus Pyropia, and the taxonomic position of P. pulchra within the genus.
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Affiliation(s)
- Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University, Daegu, Korea
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Han KY, Maciszewski K, Graf L, Yang JH, Andersen RA, Karnkowska A, Yoon HS. Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization. JOURNAL OF PHYCOLOGY 2019; 55:1166-1180. [PMID: 31325913 DOI: 10.1111/jpy.12904] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/01/2019] [Indexed: 05/22/2023]
Abstract
Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non-intron-bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.
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Affiliation(s)
- Kwi Young Han
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
| | - Kacper Maciszewski
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Louis Graf
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
| | - Ji Hyun Yang
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, 98250, USA
| | - Anna Karnkowska
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Hwan Su Yoon
- Department of Biological Science, Sungkyunkwan University, Suwon, 16419, Korea
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14
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Kobras CM, Falush D. Adapting for life in the extreme. eLife 2019; 8:48999. [PMID: 31305242 PMCID: PMC6629370 DOI: 10.7554/elife.48999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 11/18/2022] Open
Abstract
Red algae have adapted to extreme environments by acquiring genes from bacteria and archaea.
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Affiliation(s)
- Carolin M Kobras
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Daniel Falush
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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15
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Rossoni AW, Price DC, Seger M, Lyska D, Lammers P, Bhattacharya D, Weber APM. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife 2019; 8:e45017. [PMID: 31149898 PMCID: PMC6629376 DOI: 10.7554/elife.45017] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/30/2019] [Indexed: 01/08/2023] Open
Abstract
The role and extent of horizontal gene transfer (HGT) in eukaryotes are hotly disputed topics that impact our understanding of the origin of metabolic processes and the role of organelles in cellular evolution. We addressed this issue by analyzing 10 novel Cyanidiales genomes and determined that 1% of their gene inventory is HGT-derived. Numerous HGT candidates share a close phylogenetic relationship with prokaryotes that live in similar habitats as the Cyanidiales and encode functions related to polyextremophily. HGT candidates differ from native genes in GC-content, number of splice sites, and gene expression. HGT candidates are more prone to loss, which may explain the absence of a eukaryotic pan-genome. Therefore, the lack of a pan-genome and cumulative effects fail to provide substantive arguments against our hypothesis of recurring HGT followed by differential loss in eukaryotes. The maintenance of 1% HGTs, even under selection for genome reduction, underlines the importance of non-endosymbiosis related foreign gene acquisition.
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Affiliation(s)
- Alessandro W Rossoni
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Dana C Price
- Department of Plant BiologyRutgers UniversityNew BrunswickUnited States
| | - Mark Seger
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | - Dagmar Lyska
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
| | - Peter Lammers
- Arizona Center for Algae Technology and InnovationArizona State UniversityMesaUnited States
| | | | - Andreas PM Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS)Heinrich Heine UniversityDüsseldorfGermany
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16
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Kumagai Y, Miyabe Y, Takeda T, Adachi K, Yasui H, Kishimura H. In Silico Analysis of Relationship between Proteins from Plastid Genome of Red Alga Palmaria sp. (Japan) and Angiotensin I Converting Enzyme Inhibitory Peptides. Mar Drugs 2019; 17:E190. [PMID: 30934583 PMCID: PMC6470614 DOI: 10.3390/md17030190] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/02/2022] Open
Abstract
Plastid proteins are one of the main components in red algae. In order to clarify the angiotensin I converting enzyme (ACE) inhibitory peptides from red alga Palmaria sp. (Japan), we determined the plastid genome sequence. The genome possesses 205 protein coding genes, which were classified as genetic systems, ribosomal proteins, photosystems, adenosine triphosphate (ATP) synthesis, metabolism, transport, or unknown. After comparing ACE inhibitory peptides between protein sequences and a database, photosystems (177 ACE inhibitory peptides) were found to be the major source of ACE inhibitory peptides (total of 751). Photosystems consist of phycobilisomes, photosystem I, photosystem II, cytochrome complex, and a redox system. Among them, photosystem I (53) and II (51) were the major source of ACE inhibitory peptides. We found that the amino acid sequence of apcE (14) in phycobilisomes, psaA (18) and psaB (13) in photosystem I, and psbB (11) and psbC (10) in photosystem II covered a majority of bioactive peptide sequences. These results are useful for evaluating the bioactive peptides from red algae.
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Affiliation(s)
- Yuya Kumagai
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Yoshikatsu Miyabe
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Tomoyuki Takeda
- Chair of Marine Chemical Resource Development, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Kohsuke Adachi
- Laboratory of Aquatic Product Utilization, Graduate School of Agriculture, Kochi University, Monobeotsu 200, Nankoku, Kochi 783-8502, Japan.
| | - Hajime Yasui
- Laboratory of Humans and the Ocean, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Hideki Kishimura
- Laboratory of Marine Chemical Resource Development, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
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17
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Boo GH, Hughey JR. Phylogenomics and multigene phylogenies decipher two new cryptic marine algae from California, Gelidium gabrielsonii and G. kathyanniae (Gelidiales, Rhodophyta). JOURNAL OF PHYCOLOGY 2019; 55:160-172. [PMID: 30341779 DOI: 10.1111/jpy.12802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 09/12/2018] [Indexed: 06/08/2023]
Abstract
Molecular surveys are leading to the discovery of many new cryptic species of marine algae. This is particularly true for red algal intertidal species, which exhibit a high degree of morphological convergence. DNA sequencing of recent collections of Gelidium along the coast of California, USA, identified two morphologically similar entities that differed in DNA sequence from existing species. To characterize the two new species of Gelidium and to determine their evolutionary relationships to other known taxa, phylogenomic, multigene analyses, and morphological observations were performed. Three complete mitogenomes and five plastid genomes were deciphered, including those from the new species candidates and the type materials of two closely related congeners. The mitogenomes contained 45 genes and had similar lengths (24,963-24,964 bp). The plastid genomes contained 232 genes and were roughly similar in size (175,499-177,099 bp). The organellar genomes showed a high level of gene synteny. The two Gelidium species are diminutive, turf-forming, and superficially resemble several long established species from the Pacific Ocean. The phylogenomic analysis, multigene phylogeny, and morphological evidence confirms the recognition and naming of two new species, describe herein as G. gabrielsonii and G. kathyanniae. On the basis of the monophyly of G. coulteri, G. gabrielsonii, G. galapagense, and G. kathyanniae, we suggest that this lineage likely evolved in California. Organellar genomes provide a powerful tool for discovering cryptic intertidal species and they continue to improve our understanding of the evolutionary biology of red algae and the systematics of the Gelidiales.
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Affiliation(s)
- Ga Hun Boo
- University Herbarium, University of California, 1001 Valley Life Sciences Building #2465, Berkeley, California, 94720, USA
| | - Jeffery R Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, 411 Central Ave., Salinas, California, 93901, USA
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18
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Figueroa-Martinez F, Jackson C, Reyes-Prieto A. Plastid Genomes from Diverse Glaucophyte Genera Reveal a Largely Conserved Gene Content and Limited Architectural Diversity. Genome Biol Evol 2019; 11:174-188. [PMID: 30534986 PMCID: PMC6330054 DOI: 10.1093/gbe/evy268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 12/30/2022] Open
Abstract
Plastid genome (ptDNA) data of Glaucophyta have been limited for many years to the genus Cyanophora. Here, we sequenced the ptDNAs of Gloeochaete wittrockiana, Cyanoptyche gloeocystis, Glaucocystis incrassata, and Glaucocystis sp. BBH. The reported sequences are the first genome-scale plastid data available for these three poorly studied glaucophyte genera. Although the Glaucophyta plastids appear morphologically “ancestral,” they actually bear derived genomes not radically different from those of red algae or viridiplants. The glaucophyte plastid coding capacity is highly conserved (112 genes shared) and the architecture of the plastid chromosomes is relatively simple. Phylogenomic analyses recovered Glaucophyta as the earliest diverging Archaeplastida lineage, but the position of viridiplants as the first branching group was not rejected by the approximately unbiased test. Pairwise distances estimated from 19 different plastid genes revealed that the highest sequence divergence between glaucophyte genera is frequently higher than distances between species of different classes within red algae or viridiplants. Gene synteny and sequence similarity in the ptDNAs of the two Glaucocystis species analyzed is conserved. However, the ptDNA of Gla. incrassata contains a 7.9-kb insertion not detected in Glaucocystis sp. BBH. The insertion contains ten open reading frames that include four coding regions similar to bacterial serine recombinases (two open reading frames), DNA primases, and peptidoglycan aminohydrolases. These three enzymes, often encoded in bacterial plasmids and bacteriophage genomes, are known to participate in the mobilization and replication of DNA mobile elements. It is therefore plausible that the insertion in Gla. incrassata ptDNA is derived from a DNA mobile element.
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Affiliation(s)
- Francisco Figueroa-Martinez
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,CONACyT-Universidad Autónoma Metropolitana Iztapalapa, Biotechnology Department, Mexico City, Mexico
| | - Christopher Jackson
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,School of Biosciences, University of Melbourne, Melbourne, Australia
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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19
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Lee J. Plasmid-Associated Organelle Genome Evolution In Red Algae. JOURNAL OF PHYCOLOGY 2018; 54:772-774. [PMID: 30614001 DOI: 10.1111/jpy.12797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon, 16419, Korea
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20
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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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21
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Lee JM, Song HJ, Park SI, Lee YM, Jeong SY, Cho TO, Kim JH, Choi HG, Choi CG, Nelson WA, Fredericq S, Bhattacharya D, Yoon HS. Mitochondrial and Plastid Genomes from Coralline Red Algae Provide Insights into the Incongruent Evolutionary Histories of Organelles. Genome Biol Evol 2018; 10:2961-2972. [PMID: 30364957 PMCID: PMC6279150 DOI: 10.1093/gbe/evy222] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2018] [Indexed: 11/14/2022] Open
Abstract
Mitochondria and plastids are generally uniparentally inherited and have a conserved gene content over hundreds of millions of years, which makes them potentially useful phylogenetic markers. Organelle single gene-based trees have long been the basis for elucidating interspecies relationships that inform taxonomy. More recently, high-throughput genome sequencing has enabled the construction of massive organelle genome databases from diverse eukaryotes, and these have been used to infer species relationships in deep evolutionary time. Here, we test the idea that despite their expected utility, conflicting phylogenetic signal may exist in mitochondrial and plastid genomes from the anciently diverged coralline red algae (Rhodophyta). We generated complete organelle genome data from five coralline red algae (Lithothamnion sp., Neogoniolithon spectabile, Renouxia sp., Rhodogorgon sp., and Synarthrophyton chejuensis) for comparative analysis with existing organelle genome data from two other species (Calliarthron tuberculosum and Sporolithon durum). We find strong evidence for incongruent phylogenetic signal from both organelle genomes that may be explained by incomplete lineage sorting that has maintained anciently derived gene copies or other molecular evolutionary processes such as hybridization or gene flow during the evolutionary history of coralline red algae.
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Affiliation(s)
- Jun Mo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Hae Jung Song
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - So Young Jeong
- Department of Marine Life Science, Chosun University, Gwangju, Korea
| | - Tae Oh Cho
- Department of Marine Life Science, Chosun University, Gwangju, Korea
| | - Ji Hee Kim
- Division of Life Sciences, Korea Polar Research Institute, KOPRI, Incheon, Korea
| | - Han-Gu Choi
- Division of Life Sciences, Korea Polar Research Institute, KOPRI, Incheon, Korea
| | - Chang Geun Choi
- Department of Ecological Engineering, Pukyong National University, Busan, Korea
| | - Wendy A Nelson
- National Institute for Water and Atmospheric Research, Wellington, New Zealand.,School of Biological Sciences, University of Auckland, New Zealand
| | - Suzanne Fredericq
- Biology Department, University of Louisiana at Lafayette, Lafayette, Louisiana
| | | | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
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22
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Robison TA, Grusz AL, Wolf PG, Mower JP, Fauskee BD, Sosa K, Schuettpelz E. Mobile Elements Shape Plastome Evolution in Ferns. Genome Biol Evol 2018; 10:2558-2571. [PMID: 30165616 PMCID: PMC6166771 DOI: 10.1093/gbe/evy189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
Plastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.
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Affiliation(s)
| | - Amanda L Grusz
- Department of Biology, University of Minnesota Duluth
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
| | - Paul G Wolf
- Department of Biology, Utah State University
| | - Jeffrey P Mower
- Department of Agronomy, Center for Plant Science Innovation, University of Nebraska
| | | | | | - Eric Schuettpelz
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Colombia
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23
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Replication of bacterial plasmids in the nucleus of the red alga Porphyridium purpureum. Nat Commun 2018; 9:3451. [PMID: 30150628 PMCID: PMC6110788 DOI: 10.1038/s41467-018-05651-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022] Open
Abstract
Rhodophytes (red algae) are a diverse group of algae with great ecological and economic importance. However, tools for post-genomic research on red algae are still largely lacking. Here, we report the development of an efficient genetic transformation system for the model rhodophyte Porphyridium purpureum. We show that transgenes can be expressed to unprecedented levels of up to 5% of the total soluble protein. Surprisingly, the transgenic DNA is maintained episomally, as extrachromosomal high-copy number plasmid. The bacterial replication origin confers replication in the algal nucleus, thus providing an intriguing example of a prokaryotic replication origin functioning in a eukaryotic system. The extended presence of bacterial episomal elements may provide an evolutionary explanation for the frequent natural occurrence of extrachromosomal plasmids in red algae, and may also have contributed to the high rate of horizontal gene transfer from bacteria to the nuclear genome of Porphyridium purpureum and other rhodophytes. Genetic tools for research on red algae (rhodophytes) are lacking. Here, Li and Bock present an efficient genetic transformation system for a model rhodophyte, and show that the transgenic DNA can be maintained as an extrachromosomal multi-copy plasmid in the algal nucleus.
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24
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Gabrielson PW, Hughey JR, Diaz-Pulido G. Genomics reveals abundant speciation in the coral reef building alga Porolithon onkodes (Corallinales, Rhodophyta). JOURNAL OF PHYCOLOGY 2018; 54:429-434. [PMID: 29920669 DOI: 10.1111/jpy.12761] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
An essential suite of coral reef ecosystem engineers is coralline red algae. Among these, the smooth, encrusting Porolithon onkodes has historically been considered the most important and common reef building species worldwide. We assess P. onkodes biodiversity by performing a genomic analysis of the lectotype specimen collected in 1892 from the Tami Islands, Gulf of Huon, east of New Guinea. Comparisons of DNA sequences from the lectotype specimen to those deposited in GenBank and to newly generated sequences from both field-collected and historical specimens demonstrate that at least 20 distinct species are passing under P. onkodes. We hypothesize that there were multiple evolutionary drivers including ecophysiology, hydrodynamic regimes, and biotic interactions as well as historical biogeography, which resulted in this high diversity of smooth, encrusting Porolithon species throughout the tropics. Our results emphasize the need to document the biodiversity, ecophysiology, and habitats of these tropical, reef-building algae in light of climate change and ocean acidification.
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Affiliation(s)
- Paul W Gabrielson
- Herbarium and Biology Department, University of North Carolina - Chapel Hill, Coker Hall, CB 3280, Chapel Hill, North Carolina, 27599-3280, USA
| | - Jeffery R Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, 411 Central Ave., Salinas, California, 93901, USA
| | - Guillermo Diaz-Pulido
- School of Environment and Science, Australian Rivers Institute-Coast and Estuaries, Griffith University, Nathan Campus, 170 Kessels Road, Brisbane, Queensland, 4111, Australia
- Australian Research Council Centre of Excellence for Coral Reef Studies, Townsville, Queensland, 4811, Australia
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25
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Guillory WX, Onyshchenko A, Ruck EC, Parks M, Nakov T, Wickett NJ, Alverson AJ. Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta). Genome Biol Evol 2018; 10:1504-1515. [PMID: 29850800 PMCID: PMC6007386 DOI: 10.1093/gbe/evy103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 01/23/2023] Open
Abstract
We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.
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Affiliation(s)
- Wilson X Guillory
- Department of Biological Sciences, University of Arkansas
- Department of Zoology, Southern Illinois University, Carbondale, IL
| | | | | | - Matthew Parks
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, Illinois
| | - Teofil Nakov
- Department of Biological Sciences, University of Arkansas
| | - Norman J Wickett
- Daniel F. and Ada L. Rice Plant Conservation Science Center, Chicago Botanic Garden, Glencoe, Illinois
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Cho CH, Choi JW, Lam DW, Kim KM, Yoon HS. Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats. PLoS One 2018; 13:e0196995. [PMID: 29738547 PMCID: PMC5940233 DOI: 10.1371/journal.pone.0196995] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/24/2018] [Indexed: 01/03/2023] Open
Abstract
The red algal subclass Nemaliophycidae includes both marine and freshwater taxa that contribute to more than half of the freshwater species in Rhodophyta. Given that these taxa inhabit diverse habitats, the Nemaliophycidae is a suitable model for studying environmental adaptation. For this purpose, we characterized plastid genomes of two freshwater species, Kumanoa americana (Batrachospermales) and Thorea hispida (Thoreales), and one marine species Palmaria palmata (Palmariales). Comparative genome analysis identified seven genes (ycf34, ycf35, ycf37, ycf46, ycf91, grx, and pbsA) that were different among marine and freshwater species. Among currently available red algal plastid genomes (127), four genes (pbsA, ycf34, ycf35, ycf37) were retained in most of the marine species. Among these, the pbsA gene, known for encoding heme oxygenase, had two additional copies (HMOX1 and HMOX2) that were newly discovered and were reported from previously red algal nuclear genomes. Each type of heme oxygenase had a different evolutionary history and special modifications (e.g., plastid targeting signal peptide). Based on this observation, we suggest that the plastid-encoded pbsA contributes to the iron controlling system in iron-deprived conditions. Thus, we highlight that this functional requirement may have prevented gene loss during the long evolutionary history of red algal plastid genomes.
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Affiliation(s)
- Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Daryl W. Lam
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Kyeong Mi Kim
- Marine Biodiversity Institute of Korea, Seocheon, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
- * E-mail:
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Yurchenko T, Ševčíková T, Strnad H, Butenko A, Eliáš M. The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite. Open Biol 2017; 6:rsob.160249. [PMID: 27906133 PMCID: PMC5133447 DOI: 10.1098/rsob.160249] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/31/2016] [Indexed: 01/26/2023] Open
Abstract
Acquisition of genes by plastid genomes (plastomes) via horizontal gene transfer (HGT) seems to be a rare phenomenon. Here, we report an interesting case of HGT revealed by sequencing the plastomes of the eustigmatophyte algae Monodopsis sp. MarTras21 and Vischeria sp. CAUP Q 202. These plastomes proved to harbour a unique cluster of six genes, most probably acquired from a bacterium of the phylum Bacteroidetes, with homologues in various bacteria, typically organized in a conserved uncharacterized putative operon. Sequence analyses of the six proteins encoded by the operon yielded the following annotation for them: (i) a novel family without discernible homologues; (ii) a new family within the superfamily of metallo-dependent hydrolases; (iii) a novel subgroup of the UbiA superfamily of prenyl transferases; (iv) a new clade within the sugar phosphate cyclase superfamily; (v) a new family within the xylose isomerase-like superfamily; and (vi) a hydrolase for a phosphate moiety-containing substrate. We suggest that the operon encodes enzymes of a pathway synthesizing an isoprenoid–cyclitol-derived compound, possibly an antimicrobial or other protective substance. To the best of our knowledge, this is the first report of an expansion of the metabolic capacity of a plastid mediated by HGT into the plastid genome.
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Affiliation(s)
- Tatiana Yurchenko
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic.,Faculty of Science, Institute of Environmental Technologies, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Tereza Ševčíková
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Hynek Strnad
- Institute of Molecular Genetics of the ASCR, v. v. i., Prague, Czech Republic
| | - Anzhelika Butenko
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Marek Eliáš
- Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic .,Faculty of Science, Institute of Environmental Technologies, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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Muñoz-Gómez SA, Mejía-Franco FG, Durnin K, Colp M, Grisdale CJ, Archibald JM, Slamovits CH. The New Red Algal Subphylum Proteorhodophytina Comprises the Largest and Most Divergent Plastid Genomes Known. Curr Biol 2017; 27:1677-1684.e4. [DOI: 10.1016/j.cub.2017.04.054] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 12/25/2022]
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Hughey JR, Hommersand MH, Gabrielson PW, Miller KA, Fuller T. Analysis of the complete plastomes of three species of Membranoptera (Ceramiales, Rhodophyta) from Pacific North America. JOURNAL OF PHYCOLOGY 2017; 53:32-43. [PMID: 27690326 DOI: 10.1111/jpy.12472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
Next generation sequence data were generated and used to assemble the complete plastomes of the holotype of Membranoptera weeksiae, the neotype (designated here) of M. tenuis, and a specimen examined by Kylin in making the new combination M. platyphylla. The three plastomes were similar in gene content and length and showed high gene synteny to Calliarthron, Grateloupia, Sporolithon, and Vertebrata. Sequence variation in the plastome coding regions were 0.89% between M. weeksiae and M. tenuis, 5.14% between M. weeksiae and M. platyphylla, and 5.18% between M. tenuis and M. platyphylla. We were unable to decipher the complete mitogenomes of the three species due to low coverage and structural problems; however, we assembled and analyzed, the cytochrome oxidase I, II, and III loci and found that M. weeksiae and M. tenuis differed in sequence by 1.3%, M. weeksiae and M. platyphylla by 8.4%, and M. tenuis and M. platyphylla by 8.1%. Evaluation of standard marker genes indicated that sequences from the rbcL, RuBisCO spacer, and CO1 genes closely approximated the pair-wise genetic distances observed between the plastomes of the three species of Membranoptera. A phylogenetic tree based on rbcL sequences showed that M. tenuis and M. weeksiae were sister taxa. Short rbcL sequences were obtained from type specimens of M. dimorpha, M. multiramosa, and M. edentata and confirmed their conspecificity with M. platyphylla. The data support the recognition of three species of Membranoptera occurring south of Alaska: M. platyphylla, M. tenuis, and M. weeksiae.
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Affiliation(s)
- Jeffery R Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, 411 Central Ave., Salinas, California, 93901, USA
| | - Max H Hommersand
- Department of Biology, University of North Carolina at Chapel Hill, CB# 3280, Coker Hall, Chapel Hill, North Carolina, 27599-3280, USA
| | - Paul W Gabrielson
- Herbarium and Department of Biology, University of North Carolina at Chapel Hill, CB# 3280, Coker Hall, Chapel Hill, North Carolina, 27599-3280, USA
| | - Kathy Ann Miller
- Herbarium, University of California at Berkeley, 1001 Valley Life Sciences Building 2465, Berkeley, California, 94720-2465, USA
| | - Timothy Fuller
- Division of Mathematics, Science, and Engineering, Hartnell College, 411 Central Ave., Salinas, California, 93901, USA
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Ng PK, Lin SM, Lim PE, Liu LC, Chen CM, Pai TW. Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae. BMC Genomics 2017; 18:40. [PMID: 28061748 PMCID: PMC5217408 DOI: 10.1186/s12864-016-3453-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/22/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined. RESULTS The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support. CONCLUSIONS Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of Gracilaria sensu lato complex and recognition of Hydropuntia as a genus distinct from Gracilaria sensu stricto.
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Affiliation(s)
- Poh-Kheng Ng
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Showe-Mei Lin
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, 50603 Malaysia
| | - Li-Chia Liu
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Chien-Ming Chen
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 20244 Taiwan
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, 20244 Taiwan
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31
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F Costa J, Lin SM, Macaya EC, Fernández-García C, Verbruggen H. Chloroplast genomes as a tool to resolve red algal phylogenies: a case study in the Nemaliales. BMC Evol Biol 2016; 16:205. [PMID: 27724867 PMCID: PMC5057469 DOI: 10.1186/s12862-016-0772-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/28/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Obtaining strongly supported phylogenies that permit confident taxonomic and evolutionary interpretations has been a challenge in algal biology. High-throughput sequencing has improved the capacity to generate data and yields more informative datasets. We sequenced and analysed the chloroplast genomes of 22 species of the order Nemaliales as a case study in the use of phylogenomics as an approach to achieve well-supported phylogenies of red algae. RESULTS Chloroplast genomes of the order Nemaliales are highly conserved, gene-dense and completely syntenic with very few cases of gene loss. Our ML estimation based on 195 genes recovered a completely supported phylogeny, permitting re-classification of the order at various taxonomic levels. Six families are recognised and the placement of several previously contradictory clades is resolved. Two new sub-orders are described, Galaxaurineae and Nemaliineae, based on the early-branching nature and monophyly of the groups, and presence or absence of a pericarp. Analyses of subsets of the data showed that >90 % bootstrap support can be achieved with datasets as small as 2500 nt and that fast and medium evolving genes perform much better when it comes to resolving phylogenetic relationships. CONCLUSIONS In this study we show that phylogenomics is an efficient and effective approach to investigate phylogenetic relationships. The six currently circumscribed Nemaliales families are clustered into two evolutionary lineages with strong statistical support based on chloroplast phylogenomic analyses. The conserved nature of red algal chloroplast genomes is a convenient and accessible source of data to resolve their ancient relationships.
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Affiliation(s)
- Joana F Costa
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Showe-Mei Lin
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Erasmo C Macaya
- Departamento de Oceanografıa, Universidad de Concepción, Casilla, 160-C, Chile
- Millennium Nucleus Ecology and Sustainable Management of Oceanic Island (ESMOI), Coquimbo, Chile
| | - Cindy Fernández-García
- Escuela de Biología, Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Universidad de Costa Rica, San Pedro, San José, 11501-2060, Costa Rica
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC, 3010, Australia
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32
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Lee J, Cho CH, Park SI, Choi JW, Song HS, West JA, Bhattacharya D, Yoon HS. Parallel evolution of highly conserved plastid genome architecture in red seaweeds and seed plants. BMC Biol 2016; 14:75. [PMID: 27589960 PMCID: PMC5010701 DOI: 10.1186/s12915-016-0299-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genomes that were available, including 48 from the red algae (17 complete and three partial genomes produced for this analysis) to elucidate the evolutionary history of these organelles. Results We found extreme conservation of plastid genome architecture in the major lineages of the multicellular Florideophyceae red algae. Only three minor structural types were detected in this group, which are explained by recombination events of the duplicated rDNA operons. A similar high level of structural conservation (although with different gene content) was found in seed plants. Three major plastid genome architectures were identified in representatives of 46 orders of angiosperms and three orders of gymnosperms. Conclusions Our results provide a comprehensive account of plastid gene loss and rearrangement events involving genome architecture within Archaeplastida and lead to one over-arching conclusion: from an ancestral pool of highly rearranged plastid genomes in red and green algae, the aquatic (Florideophyceae) and terrestrial (seed plants) multicellular lineages display high conservation in plastid genome architecture. This phenomenon correlates with, and could be explained by, the independent and widely divergent (separated by >400 million years) origins of complex sexual cycles and reproductive structures that led to the rapid diversification of these lineages. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0299-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- JunMo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyun Suk Song
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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