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Liu F, Wang Y, Huang H, Chen N. Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics. Front Microbiol 2023; 14:1203780. [PMID: 37396366 PMCID: PMC10307964 DOI: 10.3389/fmicb.2023.1203780] [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: 04/11/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
To understand the evolution of coscinodiscophycean diatoms, plastome sequences of six coscinodiscophycean diatom species were constructed and analyzed in this study, doubling the number of constructed plastome sequences in Coscinodiscophyceae (radial centrics). The platome sizes varied substantially in Coscinodiscophyceae, ranging from 119.1 kb of Actinocyclus subtilis to 135.8 kb of Stephanopyxis turris. Plastomes in Paraliales and Stephanopyxales tended to be larger than those in Rhizosoleniales and Coscinodiacales, which were due to the expansion of the inverted repeats (IRs) and to the marked increase of the large single copy (LSC). Phylogenomic analysis indicated that Paralia and Stephanopyxis clustered tightly to form the Paraliales-Stephanopyxales complex, which was sister to the Rhizosoleniales-Coscinodiscales complex. The divergence time between Paraliales and Stephanopyxales was estimated at 85 MYA in the middle Upper Cretaceous, indicating that Paraliales and Stephanopyxales appeared later than Coscinodiacales and Rhizosoleniales according to their phylogenetic relationships. Frequent losses of housekeeping protein-coding genes (PCGs) were observed in these coscinodiscophycean plastomes, indicating that diatom plastomes showed an ongoing reduction in gene content during evolution. Two acpP genes (acpP1 and acpP2) detected in diatom plastomes were found to be originated from an early gene duplication event occurred in the common progenitor after diatom emergence, rather than multiple independent gene duplications occurring in different lineages of diatoms. The IRs in Stephanopyxis turris and Rhizosolenia fallax-imbricata exhibited a similar trend of large expansion to the small single copy (SSC) and slightly small contraction from the LSC, which eventually led to the conspicuous increase in IR size. Gene order was highly conserved in Coscinodiacales, while multiple rearrangements were observed in Rhizosoleniales and between Paraliales and Stephanopyxales. Our results greatly expanded the phylogenetic breadth in Coscinodiscophyceae and gained novel insights into the evolution of plastomes in diatoms.
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Affiliation(s)
- Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yichao Wang
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
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2
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Irisarri I, Strassert JFH, Burki F. Phylogenomic Insights into the Origin of Primary Plastids. Syst Biol 2021; 71:105-120. [PMID: 33988690 DOI: 10.1093/sysbio/syab036] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and cyanobacteria, presumably in a common ancestor of the primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, plastid monophyly and non-monophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the monophyly of Archaeplastida hosts in four available phylogenomic datasets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes were investigated. Our analyses revealed a lack of support for host monophyly in the shorter individual datasets. However, when analyzed together under rigorous data curation and complex mixture models, the combined nuclear datasets supported the monophyly of primary photosynthetic eukaryotes (Archaeplastida) and revealed a putative association with plastid-lacking Picozoa. This study represents an important step towards better understanding deep eukaryotic evolution and the origin of plastids.
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Affiliation(s)
- Iker Irisarri
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Jürgen F H Strassert
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Science For Life Laboratory, Uppsala University, 75236 Sweden
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3
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The chloroplast genome sequence of the green macroalga Caulerpa okamurae (Ulvophyceae, Chlorophyta): Its structural features, organization and phylogenetic analysis. Mar Genomics 2020; 53:100752. [PMID: 32014385 DOI: 10.1016/j.margen.2020.100752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 12/05/2019] [Accepted: 01/24/2020] [Indexed: 11/20/2022]
Abstract
To clarify evolutionary characteristics, phylogenetic relationships as well as species identification of C. okamurae, we determined the cpDNA sequence of Caulerpa okamurae using de novo sequencing in the present study. The cpDNA of C. okamurae was 148,274 bp in length, and it lacked the inverted repeat commonly found in vascular green plants. The cpDNA of C. okamurae was highly compact with a gene density of 71.7%. Moreover, it was an AT-rich genome (65.5%) consisting 76 protein-coding genes (PCGs), 27 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 32 putative open reading frames (ORFs) and six introns. Additionally, the six introns were annotated in six genes as follows: psbA, rpoB, ftsH, psbD, atpF and cysA. The overall base composition of its cpDNA was 65.46% for AT. A total of 56 genes were encoded on the light strand, while all the other 50 chloroplast genes were encoded on the heavy strand. All of the PCGs had ATG as their start codon and employed TAA, TGA or TAG as their termination codon. Phylogenetic analyses suggested that the complete cpDNA sequence of C. okamurae fell in the Chlorophyta, Ulvophyceae, Bryopsidales, and Caulerpaceae and more resembled the cpDNAs of C. racemosa, C. cliftonii voucher and Tydemania expeditionis. Taken together, our data offered useful information for the studies of C.okamurae on evolutionary characteristics, phylogenetic relationships as well as species identification.
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4
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Cremen MCM, Leliaert F, Marcelino VR, Verbruggen H. Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta). Genome Biol Evol 2018; 10:1048-1061. [PMID: 29635329 PMCID: PMC5888179 DOI: 10.1093/gbe/evy063] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.
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Affiliation(s)
| | - Frederik Leliaert
- Botanic Garden Meise, 1860 Meise, Belgium.,Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Vanessa R Marcelino
- School of BioSciences, University of Melbourne, Parkville, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, New South Wales, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Australia
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5
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
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6
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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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7
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Turmel M, Otis C, Lemieux C. Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae. Sci Rep 2017; 7:994. [PMID: 28428552 PMCID: PMC5430533 DOI: 10.1038/s41598-017-01144-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/27/2017] [Indexed: 12/16/2022] Open
Abstract
The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.
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Affiliation(s)
- Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec (QC), Canada
| | - Christian Otis
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec (QC), Canada
| | - Claude Lemieux
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec (QC), Canada.
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8
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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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9
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Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov. Sci Rep 2016; 6:25367. [PMID: 27157793 PMCID: PMC4860620 DOI: 10.1038/srep25367] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/15/2016] [Indexed: 01/25/2023] Open
Abstract
The green plants (Viridiplantae) are an ancient group of eukaryotes comprising two main clades: the Chlorophyta, which includes a wide diversity of green algae, and the Streptophyta, which consists of freshwater green algae and the land plants. The early-diverging lineages of the Viridiplantae comprise unicellular algae, and multicellularity has evolved independently in the two clades. Recent molecular data have revealed an unrecognized early-diverging lineage of green plants, the Palmophyllales, with a unique form of multicellularity, and typically found in deep water. The phylogenetic position of this enigmatic group, however, remained uncertain. Here we elucidate the evolutionary affinity of the Palmophyllales using chloroplast genomic, and nuclear rDNA data. Phylogenetic analyses firmly place the palmophyllalean Verdigellas peltata along with species of Prasinococcales (prasinophyte clade VI) in the deepest-branching clade of the Chlorophyta. The small, compact and intronless chloroplast genome (cpDNA) of V. peltata shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov.
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10
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Turmel M, Otis C, Lemieux C. Dynamic Evolution of the Chloroplast Genome in the Green Algal Classes Pedinophyceae and Trebouxiophyceae. Genome Biol Evol 2015; 7:2062-82. [PMID: 26139832 PMCID: PMC4524492 DOI: 10.1093/gbe/evv130] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2015] [Indexed: 01/21/2023] Open
Abstract
Previous studies of trebouxiophycean chloroplast genomes revealed little information regarding the evolutionary dynamics of this genome because taxon sampling was too sparse and the relationships between the sampled taxa were unknown. We recently sequenced the chloroplast genomes of 27 trebouxiophycean and 2 pedinophycean green algae to resolve the relationships among the main lineages recognized for the Trebouxiophyceae. These taxa and the previously sampled members of the Pedinophyceae and Trebouxiophyceae are included in the comparative chloroplast genome analysis we report here. The 38 genomes examined display considerable variability at all levels, except gene content. Our results highlight the high propensity of the rDNA-containing large inverted repeat (IR) to vary in size, gene content and gene order as well as the repeated losses it experienced during trebouxiophycean evolution. Of the seven predicted IR losses, one event demarcates a superclade of 11 taxa representing 5 late-diverging lineages. IR expansions/contractions account not only for changes in gene content in this region but also for changes in gene order and gene duplications. Inversions also led to gene rearrangements within the IR, including the reversal or disruption of the rDNA operon in some lineages. Most of the 20 IR-less genomes are more rearranged compared with their IR-containing homologs and tend to show an accelerated rate of sequence evolution. In the IR-less superclade, several ancestral operons were disrupted, a few genes were fragmented, and a subgroup of taxa features a G+C-biased nucleotide composition. Our analyses also unveiled putative cases of gene acquisitions through horizontal transfer.
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Affiliation(s)
- Monique Turmel
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Christian Otis
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
| | - Claude Lemieux
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Québec, Canada
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11
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Verbruggen H, Costa JF. The plastid genome of the red alga Laurencia. JOURNAL OF PHYCOLOGY 2015; 51:586-589. [PMID: 26986672 DOI: 10.1111/jpy.12297] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/09/2015] [Indexed: 06/05/2023]
Abstract
We present the 174,935 nt long plastid genome of the red alga Laurencia sp. JFC0032. It is the third plastid genome characterized for the largest order of red algae (Ceramiales). The circular-mapping plastid genome is small compared to most florideophyte red algae, and our comparisons show a trend toward smaller plastid genome sizes in the family Rhodomelaceae, independent from a similar trend in Cyanidiophyceae. The Laurencia genome is densely packed with 200 annotated protein-coding genes (188 widely conserved, 3 open reading frames shared with other red algae and 9 hypothetical coding regions). It has 29 tRNAs, a single-copy ribosomal RNA cistron, a tmRNA, and the RNase P RNA.
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Affiliation(s)
- Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Joana F Costa
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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12
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Ševčíková T, Horák A, Klimeš V, Zbránková V, Demir-Hilton E, Sudek S, Jenkins J, Schmutz J, Přibyl P, Fousek J, Vlček Č, Lang BF, Oborník M, Worden AZ, Eliáš M. Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Sci Rep 2015; 5:10134. [PMID: 26017773 PMCID: PMC4603697 DOI: 10.1038/srep10134] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/31/2015] [Indexed: 01/15/2023] Open
Abstract
Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, the Limnista, exhibiting an unexpectedly elevated rate of plastid gene evolution. Our analyses also indicate that the root of the ochrophyte phylogeny falls between the recently redefined Khakista and Phaeista assemblages. Taking advantage of the expanded sampling of plastid genome sequences, we revisited the phylogenetic position of the plastid of Vitrella brassicaformis, a member of Alveolata with the least derived plastid genome known for the whole group. The results varied depending on the dataset and phylogenetic method employed, but suggested that the Vitrella plastids emerged from a deep ochrophyte lineage rather than being derived vertically from a hypothetical plastid-bearing common ancestor of alveolates and stramenopiles. Thus, we hypothesize that the plastid in Vitrella, and potentially in other alveolates, may have been acquired by an endosymbiosis of an early ochrophyte.
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Affiliation(s)
- Tereza Ševčíková
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Vladimír Klimeš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Veronika Zbránková
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Elif Demir-Hilton
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - Pavel Přibyl
- Centre for Algology and Biorefinery Research Centre of Competence, Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82 Třeboň, Czech Republic
| | - Jan Fousek
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - B Franz Lang
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal, Québec, H3C 3J7, Canada
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
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13
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Leliaert F, Lopez-Bautista JM. The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin. BMC Genomics 2015; 16:204. [PMID: 25879186 PMCID: PMC4487195 DOI: 10.1186/s12864-015-1418-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/28/2015] [Indexed: 12/31/2022] Open
Abstract
Background Species of Bryopsidales form ecologically important components of seaweed communities worldwide. These siphonous macroalgae are composed of a single giant tubular cell containing millions of nuclei and chloroplasts, and harbor diverse bacterial communities. Little is known about the diversity of chloroplast genomes (cpDNAs) in this group, and about the possible consequences of intracellular bacteria on genome composition of the host. We present the complete cpDNAs of Bryopsis plumosa and Tydemania expeditiones, as well as a re-annotated cpDNA of B. hypnoides, which was shown to contain a higher number of genes than originally published. Chloroplast genomic data were also used to evaluate phylogenetic hypotheses in the Chlorophyta, such as monophyly of the Ulvophyceae (the class in which the order Bryopsidales is currently classified). Results Both DNAs are circular and lack a large inverted repeat. The cpDNA of B. plumosa is 106,859 bp long and contains 115 unique genes. A 13 kb region was identified with several freestanding open reading frames (ORFs) of putative bacterial origin, including a large ORF (>8 kb) closely related to bacterial rhs-family genes. The cpDNA of T. expeditiones is 105,200 bp long and contains 125 unique genes. As in B. plumosa, several regions were identified with ORFs of possible bacterial origin, including genes involved in mobile functions (transposases, integrases, phage/plasmid DNA primases), and ORFs showing close similarity with bacterial DNA methyltransferases. The cpDNA of B. hypnoides differs from that of B. plumosa mainly in the presence of long intergenic spacers, and a large tRNA region. Chloroplast phylogenomic analyses were largely inconclusive with respect to monophyly of the Ulvophyceae, and the relationship of the Bryopsidales within the Chlorophyta. Conclusions The cpDNAs of B. plumosa and T. expeditiones are amongst the smallest and most gene dense chloroplast genomes in the core Chlorophyta. The presence of bacterial genes, including genes typically found in mobile elements, suggest that these have been acquired through horizontal gene transfer, which may have been facilitated by the occurrence of obligate intracellular bacteria in these siphonous algae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1418-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederik Leliaert
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA. .,Department of Biology, Marine Biology Research Group, Ghent University, Krijgslaan 281-S8, Ghent, 9000, Belgium.
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DePriest MS, Bhattacharya D, López-Bautista JM. The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One 2013; 8:e68246. [PMID: 23894297 PMCID: PMC3716797 DOI: 10.1371/journal.pone.0068246] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/26/2013] [Indexed: 11/20/2022] Open
Abstract
The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M.Lin & H.-Y.Liang (Halymeniaceae, Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta.
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Affiliation(s)
- Michael S DePriest
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, United States of America.
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