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Simon C, Fort A, Jouanneau D, McHale M, Sulpice R. Fast screening method to identify salinity tolerant strains of foliose Ulva species. Low salinity leads to increased organic matter of the biomass. JOURNAL OF APPLIED PHYCOLOGY 2024; 36:2161-2172. [PMID: 39050553 PMCID: PMC11263424 DOI: 10.1007/s10811-024-03222-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/21/2024] [Accepted: 02/25/2024] [Indexed: 07/27/2024]
Abstract
Sea lettuce (Ulva) is recognised for its potential in food, pharmaceutical, nutraceutical, biorefinery and bioremediation industries and is increasingly being cultivated. The requirements of those industries vary widely in terms of biomass composition. Ulva biomass composition and growth is known to be directly influenced by environmental factors, e.g., temperature, light, salinity, nutrient availability as well as by genetic factors and likely by microbiome composition. In order to select for the highest yielding strains in a given environment, we tested the suitability of common-garden experiments, i.e., the co-cultivation of different strains grown under shared conditions. Fifteen strains from six different foliose Ulva species were grown together under two different salinities, 35 ppt and 15 ppt. After 32 days, only U. australis strains remained at both salinities. If selection at low salinity was mostly based on survival, the selection process at seawater salinity was driven by competition, largely based on growth performance. Growth rates after a month were very similar at both salinities, suggesting the U. australis strains cope equally well in either condition. However, the composition of the biomass produced in both environments varied, with the content of all organic compounds being higher at low salinity, and the ash content being reduced in average by 66%. To summarize, this study provides an established bulk-selection protocol for efficiently screening large numbers of locally-sourced strains and highlights the potential of low salinity treatments for increased organic matter content, particularly in carbohydrates. Supplementary Information The online version contains supplementary material available at 10.1007/s10811-024-03222-0.
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Affiliation(s)
- Clara Simon
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
| | - Antoine Fort
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
- Department of Veterinary and Microbial Sciences, Technological University of The Shannon: Midlands, Athlone, Ireland
| | - Diane Jouanneau
- Sorbonne Université, CNRS, Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Roscoff, France
| | - Marcus McHale
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
| | - Ronan Sulpice
- School, Plant Systems Biology Lab, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, Galway, Ireland
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2
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Domozych DS, LoRicco JG. The extracellular matrix of green algae. PLANT PHYSIOLOGY 2023; 194:15-32. [PMID: 37399237 PMCID: PMC10762512 DOI: 10.1093/plphys/kiad384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Green algae display a wide range of extracellular matrix (ECM) components that include various types of cell walls (CW), scales, crystalline glycoprotein coverings, hydrophobic compounds, and complex gels or mucilage. Recently, new information derived from genomic/transcriptomic screening, advanced biochemical analyses, immunocytochemical studies, and ecophysiology has significantly enhanced and refined our understanding of the green algal ECM. In the later diverging charophyte group of green algae, the CW and other ECM components provide insight into the evolution of plants and the ways the ECM modulates during environmental stress. Chlorophytes produce diverse ECM components, many of which have been exploited for various uses in medicine, food, and biofuel production. This review highlights major advances in ECM studies of green algae.
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Affiliation(s)
- David S Domozych
- Department of Biology, Skidmore College, Saratoga Springs, NY 12866, USA
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3
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Glass SE, McCourt RM, Gottschalk SD, Lewis LA, Karol KG. Chloroplast genome evolution and phylogeny of the early-diverging charophycean green algae with a focus on the Klebsormidiophyceae and Streptofilum. JOURNAL OF PHYCOLOGY 2023; 59:1133-1146. [PMID: 37548118 DOI: 10.1111/jpy.13359] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 05/23/2023] [Indexed: 08/08/2023]
Abstract
The Klebsormidiophyceae are a class of green microalgae observed globally in both freshwater and terrestrial habitats. Morphology-based classification schemes of this class have been shown to be inadequate due to the simple morphology of these algae, the tendency of morphology to vary in culture versus field conditions, and rampant morphological homoplasy. Molecular studies revealing cryptic diversity have renewed interest in this group. We sequenced the complete chloroplast genomes of a broad series of taxa spanning the known taxonomic breadth of this class. We also sequenced the chloroplast genomes of three strains of Streptofilum, a recently discovered green algal lineage with close affinity to the Klebsormidiophyceae. Our results affirm the previously hypothesized polyphyly of the genus Klebsormidium as well as the polyphyly of the nominal species in this genus, K. flaccidum. Furthermore, plastome sequences strongly support the status of Streptofilum as a distinct, early-diverging lineage of charophytic algae sister to a clade comprising Klebsormidiophyceae plus Phragmoplastophyta. We also uncovered major structural alterations in the chloroplast genomes of species in Klebsormidium that have broad implications regarding the underlying mechanisms of chloroplast genome evolution.
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Affiliation(s)
- Sarah E Glass
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
- Department of Biological Sciences, Lehman College, The City University of New York, New York, New York, USA
| | - Richard M McCourt
- Academy of Natural Sciences of Drexel University, Philadelphia, Pennsylvania, USA
| | - Stephen D Gottschalk
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
- Department of Biological Sciences, Fordham University, Bronx, New York, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Kenneth G Karol
- Lewis B. and Dorothy Cullman Program for Molecular Systematics, The New York Botanical Garden, Bronx, New York, USA
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4
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Wegner L, Porth ML, Ehlers K. Multicellularity and the Need for Communication-A Systematic Overview on (Algal) Plasmodesmata and Other Types of Symplasmic Cell Connections. PLANTS (BASEL, SWITZERLAND) 2023; 12:3342. [PMID: 37765506 PMCID: PMC10536634 DOI: 10.3390/plants12183342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023]
Abstract
In the evolution of eukaryotes, the transition from unicellular to simple multicellular organisms has happened multiple times. For the development of complex multicellularity, characterized by sophisticated body plans and division of labor between specialized cells, symplasmic intercellular communication is supposed to be indispensable. We review the diversity of symplasmic connectivity among the eukaryotes and distinguish between distinct types of non-plasmodesmatal connections, plasmodesmata-like structures, and 'canonical' plasmodesmata on the basis of developmental, structural, and functional criteria. Focusing on the occurrence of plasmodesmata (-like) structures in extant taxa of fungi, brown algae (Phaeophyceae), green algae (Chlorophyta), and streptophyte algae, we present a detailed critical update on the available literature which is adapted to the present classification of these taxa and may serve as a tool for future work. From the data, we conclude that, actually, development of complex multicellularity correlates with symplasmic connectivity in many algal taxa, but there might be alternative routes. Furthermore, we deduce a four-step process towards the evolution of canonical plasmodesmata and demonstrate similarity of plasmodesmata in streptophyte algae and land plants with respect to the occurrence of an ER component. Finally, we discuss the urgent need for functional investigations and molecular work on cell connections in algal organisms.
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Affiliation(s)
- Linus Wegner
- Institute of Botany, Justus-Liebig University, D-35392 Giessen, Germany
| | | | - Katrin Ehlers
- Institute of Botany, Justus-Liebig University, D-35392 Giessen, Germany
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5
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Yang Z, Ma X, Wang Q, Tian X, Sun J, Zhang Z, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae. Nat Commun 2023; 14:5542. [PMID: 37696791 PMCID: PMC10495350 DOI: 10.1038/s41467-023-41137-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/23/2023] [Indexed: 09/13/2023] Open
Abstract
The Viridiplantae comprise two main clades, the Chlorophyta (including a diverse array of marine and freshwater green algae) and the Streptophyta (consisting of the freshwater charophytes and the land plants). Lineages sister to core Chlorophyta, informally refer to as prasinophytes, form a grade of mainly planktonic green algae. Recently, one of these lineages, Prasinodermophyta, which is previously grouped with prasinophytes, has been identified as the sister lineage to both Chlorophyta and Streptophyta. Resolving the deep relationships among green plants is crucial for understanding the historical impact of green algal diversity on marine ecology and geochemistry, but has been proven difficult given the ancient timing of the diversification events. Through extensive taxon and gene sampling, we conduct large-scale phylogenomic analyses to resolve deep relationships and reveal the Prasinodermophyta as the lineage sister to Chlorophyta, raising questions about the necessity of classifying the Prasinodermophyta as a distinct phylum. We unveil that incomplete lineage sorting is the main cause of discordance regarding the placement of Prasinodermophyta. Molecular dating analyses suggest that crown-group green plants and crown-group Prasinodermophyta date back to the Paleoproterozoic-Mesoproterozoic. Our study establishes a plausible link between oxygen levels in the Paleoproterozoic-Mesoproterozoic and the origin of Viridiplantae.
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Affiliation(s)
- Zhiping Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaolin Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jingyan Sun
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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6
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Massé A, Detang J, Duval C, Duperron S, Woo AC, Domart-Coulon I. Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities. Microorganisms 2023; 11:1318. [PMID: 37317290 DOI: 10.3390/microorganisms11051318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community's composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales' abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19-36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.
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Affiliation(s)
- Anaïs Massé
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Juliette Detang
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Charlotte Duval
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Sébastien Duperron
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
| | - Anthony C Woo
- Pôle Analyse de Données UAR 2700 2AD, Muséum National d'Histoire Naturelle (MNHN), 43 Rue Cuvier, 75005 Paris, France
| | - Isabelle Domart-Coulon
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum National d'Histoire Naturelle (MNHN), CNRS (UMR7245), CP54, 63 Rue Buffon, 75005 Paris, France
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7
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Rieseberg TP, Dadras A, Fürst-Jansen JMR, Dhabalia Ashok A, Darienko T, de Vries S, Irisarri I, de Vries J. Crossroads in the evolution of plant specialized metabolism. Semin Cell Dev Biol 2023; 134:37-58. [PMID: 35292191 DOI: 10.1016/j.semcdb.2022.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 12/25/2022]
Abstract
The monophyletic group of embryophytes (land plants) stands out among photosynthetic eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety, embryophytes account for the majority of the biomass on land and constitute an astounding biodiversity. What allowed for the massive radiation of this particular lineage? One of the defining features of all land plants is the production of an array of specialized metabolites. The compounds that the specialized metabolic pathways of embryophytes produce have diverse functions, ranging from superabundant structural polymers and compounds that ward off abiotic and biotic challenges, to signaling molecules whose abundance is measured at the nanomolar scale. These specialized metabolites govern the growth, development, and physiology of land plants-including their response to the environment. Hence, specialized metabolites define the biology of land plants as we know it. And they were likely a foundation for their success. It is thus intriguing to find that the closest algal relatives of land plants, freshwater organisms from the grade of streptophyte algae, possess homologs for key enzymes of specialized metabolic pathways known from land plants. Indeed, some studies suggest that signature metabolites emerging from these pathways can be found in streptophyte algae. Here we synthesize the current understanding of which routes of the specialized metabolism of embryophytes can be traced to a time before plants had conquered land.
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Affiliation(s)
- Tim P Rieseberg
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtsr. 1, 37077 Goettingen, Germany.
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8
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Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business. Semin Cell Dev Biol 2023; 134:27-36. [PMID: 35341677 DOI: 10.1016/j.semcdb.2022.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/20/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022]
Abstract
Ostreobium is a siphonous green alga in the Bryopsidales (Chlorophyta) that burrows into calcium carbonate (CaCO3) substrates. In this habitat, it lives under environmental conditions unusual for an alga (i.e., low light and low oxygen) and it is a major agent of carbonate reef bioerosion. In coral skeletons, Ostreobium can form conspicuous green bands recognizable by the naked eye and it is thought to contribute to the coral's nutritional needs. With coral reefs in global decline, there is a renewed focus on understanding Ostreobium biology and its roles in the coral holobiont. This review summarizes knowledge on Ostreobium's morphological structure, biodiversity and evolution, photosynthesis, mechanism of bioerosion and its role as a member of the coral holobiont. We discuss the resources available to study Ostreobium biology, lay out some of the uncharted territories in Ostreobium biology and offer perspectives for future research.
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9
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Liu F, Chen N, Wang H, Li J, Wang J, Qu F. Novel insights into chloroplast genome evolution in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta). FRONTIERS IN PLANT SCIENCE 2023; 14:1126175. [PMID: 37143870 PMCID: PMC10151680 DOI: 10.3389/fpls.2023.1126175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
To understand the evolutionary driving forces of chloroplast (or plastid) genomes (plastomes) in the green macroalgal genus Ulva (Ulvophyceae, Chlorophyta), in this study, we sequenced and constructed seven complete chloroplast genomes from five Ulva species, and conducted comparative genomic analysis of Ulva plastomes in Ulvophyceae. Ulva plastome evolution reflects the strong selection pressure driving the compactness of genome organization and the decrease of overall GC composition. The overall plastome sequences including canonical genes, introns, derived foreign sequences and non-coding regions show a synergetic decrease in GC content at varying degrees. Fast degeneration of plastome sequences including non-core genes (minD and trnR3), derived foreign sequences, and noncoding spacer regions was accompanied by the marked decrease of their GC composition. Plastome introns preferentially resided in conserved housekeeping genes with high GC content and long length, as might be related to high GC content of target site sequences recognized by intron-encoded proteins (IEPs), and to more target sites contained by long GC-rich genes. Many foreign DNA sequences integrated into different intergenic regions contain some homologous specific orfs with high similarity, indicating that they could have been derived from the same origin. The invasion of foreign sequences seems to be an important driving force for plastome rearrangement in these IR-lacking Ulva cpDNAs. Gene partitioning pattern has changed and distribution range of gene clusters has expanded after the loss of IR, indicating that genome rearrangement was more extensive and more frequent in Ulva plastomes, which was markedly different from that in IR-containing ulvophycean plastomes. These new insights greatly enhance our understanding of plastome evolution in ecologically important Ulva seaweeds.
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Affiliation(s)
- Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
- *Correspondence: Feng Liu, ;
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Hongshu Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Jiamin Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Jing Wang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Fan Qu
- Harbin University of Science and Technology, Weihai, Shandong, China
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10
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Simon C, McHale M, Sulpice R. Applications of Ulva Biomass and Strategies to Improve Its Yield and Composition: A Perspective for Ulva Aquaculture. BIOLOGY 2022; 11:1593. [PMID: 36358294 PMCID: PMC9687441 DOI: 10.3390/biology11111593] [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: 08/09/2022] [Revised: 10/10/2022] [Accepted: 10/23/2022] [Indexed: 09/08/2024]
Abstract
Sea lettuce (Ulva spp.), with its worldwide distribution and remarkable ability to grow rapidly under various conditions, represents an important natural resource that is still under-exploited. Its biomass can be used for a wide range of applications in the food/feed, pharmaceutical, nutraceutical, biofuel, and bioremediation industries. However, knowledge of the factors affecting Ulva biomass yield and composition is far from complete. Indeed, the respective contributions of the microbiome, natural genetic variation in Ulva species, environmental conditions and importantly, the interactions between these three factors on the Ulva biomass, have been only partially elucidated. Further investigation is important for the implementation of large-scale Ulva aquaculture, which requires stable and controlled biomass composition and yields. In this review, we document Ulva biomass composition, describe the uses of Ulva biomass and we propose different strategies for developing a sustainable and profitable Ulva aquaculture industry.
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Affiliation(s)
- Clara Simon
- Plant Systems Biology Laboratory, Ryan Institute & Marei Centre for Marine, Climate and Energy, School of Biological & Chemical Sciences, University of Galway, H91 TK33 Galway, Ireland
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11
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The Genome of the Marine Alga Ulva compressa (Chlorophyta) Reveals Protein-Coding Genes with Similarity to Plants and Green Microalgae, but Also to Animal, Bacterial, and Fungal Genes. Int J Mol Sci 2022; 23:ijms23137279. [PMID: 35806287 PMCID: PMC9266709 DOI: 10.3390/ijms23137279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
The genome of the marine alga Ulva compressa was assembled using long and short reads. The genome assembly was 80.8 Mb in size and encoded 19,207 protein-coding genes. Several genes encoding antioxidant enzymes and a few genes encoding enzymes that synthesize ascorbate and glutathione were identified, showing similarity to plant and bacterial enzymes. Additionally, several genes encoding signal transduction protein kinases, such as MAPKs, CDPKS, CBLPKs, and CaMKs, were also detected, showing similarity to plants, green microalgae, and bacterial proteins. Regulatory transcription factors, such as ethylene- and ABA-responsive factors, MYB, WRKY, and HSTF, were also present and showed similarity to plant and green microalgae transcription factors. Genes encoding enzymes that synthesize ACC and ABA-aldehyde were also identified, but oxidases that synthesize ethylene and ABA, as well as enzymes that synthesize other plant hormones, were absent. Interestingly, genes involved in plant cell wall synthesis and proteins related to animal extracellular matrix were also detected. Genes encoding cyclins and CDKs were also found, and CDKs showed similarity to animal and fungal CDKs. Few genes encoding voltage-dependent calcium channels and ionotropic glutamate receptors were identified as showing similarity to animal channels. Genes encoding Transient Receptor Potential (TRP) channels were not identified, even though TRPs have been experimentally detected, indicating that the genome is not yet complete. Thus, protein-coding genes present in the genome of U. compressa showed similarity to plant and green microalgae, but also to animal, bacterial, and fungal genes.
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12
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Hou Z, Ma X, Shi X, Li X, Yang L, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomic insights into a Mesoproterozoic-Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae). Nat Commun 2022; 13:1610. [PMID: 35318329 PMCID: PMC8941102 DOI: 10.1038/s41467-022-29282-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/09/2022] [Indexed: 01/09/2023] Open
Abstract
The Ulvophyceae, a major group of green algae, is of particular evolutionary interest because of its remarkable morphological and ecological diversity. Its phylogenetic relationships and diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- and concatenation-based approaches to reconstruct the phylogeny of the Ulvophyceae and to explore the sources of conflict in previous phylogenomic studies. The Ulvophyceae is recovered as a paraphyletic group, with the Bryopsidales being a sister group to the Chlorophyceae, and the remaining taxa forming a clade (Ulvophyceae sensu stricto). Molecular clock analyses with different calibration strategies emphasize the large impact of fossil calibrations, and indicate a Meso-Neoproterozoic origin of the Ulvophyceae (sensu stricto), earlier than previous estimates. The results imply that ulvophyceans may have had a profound influence on oceanic redox structures and global biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition. “Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
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Affiliation(s)
- Zheng Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xi Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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13
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Steinová J, Holien H, Košuthová A, Škaloud P. An Exception to the Rule? Could Photobiont Identity Be a Better Predictor of Lichen Phenotype than Mycobiont Identity? J Fungi (Basel) 2022; 8:jof8030275. [PMID: 35330277 PMCID: PMC8953480 DOI: 10.3390/jof8030275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 11/16/2022] Open
Abstract
With rare exceptions, the shape and appearance of lichen thalli are determined by the fungal partner; thus, mycobiont identity is normally used for lichen identification. However, it has repeatedly been shown in recent decades that phenotypic data often does not correspond with fungal gene evolution. Here, we report such a case in a three-species complex of red-fruited Cladonia lichens, two of which clearly differ morphologically, chemically, ecologically and in distribution range. We analysed 64 specimens of C. bellidiflora, C. polydactyla and C. umbricola, mainly collected in Europe, using five variable mycobiont-specific and two photobiont-specific molecular markers. All mycobiont markers exhibited very low variability and failed to separate the species. In comparison, photobiont identity corresponded better with lichen phenotype and separated esorediate C. bellidiflora from the two sorediate taxa. These results can be interpreted either as an unusual case of lichen photomorphs or as an example of recent speciation, in which phenotypic differentiation precedes the separation of the molecular markers. We hypothesise that association with different photobionts, which is probably related to habitat differentiation, may have triggered speciation in the mycobiont species.
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Affiliation(s)
- Jana Steinová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic;
- Correspondence:
| | - Håkon Holien
- Faculty of Biosciences and Aquaculture, Nord University, Pb 2501, NO-7729 Steinkjer, Norway;
| | - Alica Košuthová
- Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-104 05 Stockholm, Sweden;
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic;
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14
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Sasaki Y, Yoshikuni Y. Metabolic engineering for valorization of macroalgae biomass. Metab Eng 2022; 71:42-61. [PMID: 35077903 DOI: 10.1016/j.ymben.2022.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/18/2022]
Abstract
Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.
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Affiliation(s)
- Yusuke Sasaki
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, 060-8589, Japan.
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15
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Fournier GP, Parsons CW, Cutts EM, Tamre E. Standard Candles for Dating Microbial Lineages. Methods Mol Biol 2022; 2569:41-74. [PMID: 36083443 DOI: 10.1007/978-1-0716-2691-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.
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Affiliation(s)
- Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Chris W Parsons
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Elise M Cutts
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Erik Tamre
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
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16
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Lehtonen J, Horinouchi Y, Togashi T, Parker GA. Evolution of Anisogamy in Organisms with Parthenogenetic Gametes. Am Nat 2021; 198:360-378. [PMID: 34403316 DOI: 10.1086/715185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe two sexes are defined by the sizes of the gametes they produce, anisogamy being the state with two differing gamete sizes (hence, females and males). The origin of this divergence has received much research interest, both theoretically and empirically. The gamete dynamics (GD) theory is a widely accepted theoretical explanation for anisogamy, and green algae have been an important empirical testing ground for the theory. However, some green and brown algae produce parthenogenetic gametes (gametes that can develop without fusing with another gamete), in contrast to an assumption in GD theory that unfused gametes do not develop. Here, we construct a GD model accounting for parthenogenetic gametes. We find that under conditions of panmixia and highly efficient fertilization (i.e., conditions of classical GD models from 1972 onward), the results remain largely unaltered by parthenogametes. However, under gamete-limited conditions anisogamy evolves less easily in the new model, and a novel result emerges: whereas previous models typically predict the evolution of either anisogamy or small isogamy, the current model shows that large isogamy can evolve when parthenogenetic gametes evolve under conditions of inefficient fertilization. Our analyses uncover unexplored complications relating to sex ratios under this relatively uncharted gametic system. We discuss limitations these complications impose on our models and suggest avenues for future research. We compare model results to algae with parthenogenetic gametes in nature.
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17
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Gulbrandsen ØS, Andresen IJ, Krabberød AK, Bråte J, Shalchian-Tabrizi K. Phylogenomic analysis restructures the ulvophyceae. JOURNAL OF PHYCOLOGY 2021; 57:1223-1233. [PMID: 33721355 DOI: 10.1111/jpy.13168] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/26/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Here, we present new transcriptome sequencing data from seven species of Dasycladales (Ulvophyceae) and a phylogenomic analysis of the Chlorophyta with a particular focus on Ulvophyceae. We have focused on a broad selection of green algal groups and carefully selected genes suitable for reconstructing deep eukaryote evolutionary histories. Increasing the taxon sampling of Dasycladales restructures the Ulvophyceae by identifying Dasycladales as closely related to Scotinosphaerales and Oltmannsiellopsidales. Contrary to previous studies, we do not find support for a close relationship between Dasycladales and a group with Cladophorales and Trentepohliales. Instead, the latter group is sister to the remainder of the Ulvophyceae. Furthermore, our analyses show high and consistent statistical support for a sister relationship between Bryopsidales and Chlorophyceae in trees generated with both homogeneous and heterogeneous (heterotachy) evolutionary models. Our study provides a new framework for interpreting the evolutionary history of Ulvophyceae and the evolution of cellular morphologies.
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Affiliation(s)
- Øyvind Saetren Gulbrandsen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies Hus, Blindernveien 31, 0316, Oslo, Norway
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, Ås, Norway
| | - Ina Jungersen Andresen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies Hus, Blindernveien 31, 0316, Oslo, Norway
| | - Anders Kristian Krabberød
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies Hus, Blindernveien 31, 0316, Oslo, Norway
| | - Jon Bråte
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies Hus, Blindernveien 31, 0316, Oslo, Norway
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Kamran Shalchian-Tabrizi
- Centre for Integrative Microbial Evolution (CIME), Centre for Epigenetics, Development and Evolution (CEDE), Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Kristine Bonnevies Hus, Blindernveien 31, 0316, Oslo, Norway
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18
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Molecular Phylogeny of Unicellular Marine Coccoid Green Algae Revealed New Insights into the Systematics of the Ulvophyceae (Chlorophyta). Microorganisms 2021; 9:microorganisms9081586. [PMID: 34442668 PMCID: PMC8401757 DOI: 10.3390/microorganisms9081586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/17/2022] Open
Abstract
Most marine coccoid and sarcinoid green algal species have traditionally been placed within genera dominated by species from freshwater or soil habitats. For example, the genera Chlorocystis and Halochlorococcum contain exclusively marine species; however, their familial and ordinal affinities are unclear. They are characterized by a vegetative cell with lobated or reticulated chloroplast, formation of quadriflagellated zoospores and living epi- or endophytically within benthic macroalgae. They were integrated into the family Chlorochytriaceae which embraces all coccoid green algae with epi- or endophytic life phases. Later, they were excluded from the family of Chlorococcales based on studies of their life histories in culture, and transferred to their newly described order, Chlorocystidales of the Ulvophyceae. Both genera form a "Codiolum"-stage that serves as the unicellular sporophyte in their life cycles. Phylogenetic analyses of SSU and ITS rDNA sequences confirmed that these coccoid taxa belong to the Chlorocystidales, together with the sarcinoid genus Desmochloris. The biflagellated coccoid strains were members of the genus Sykidion, which represented its own order, Sykidiales, among the Ulvophyceae. Considering these results and the usage of the ITS-2/CBC approach revealed three species of Desmochloris, six of Chlorocystis, and three of Sykidion. Three new species and several new combinations were proposed.
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19
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Cai C, Gu K, Zhao H, Steinhagen S, He P, Wichard T. Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea. PLoS One 2021; 16:e0250968. [PMID: 34061855 PMCID: PMC8168861 DOI: 10.1371/journal.pone.0250968] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/18/2021] [Indexed: 11/18/2022] Open
Abstract
Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.
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Affiliation(s)
- Chuner Cai
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Kai Gu
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Hui Zhao
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Sophie Steinhagen
- Department of Marine Sciences-Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
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20
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Qi F, Zhao Y, Zhao N, Wang K, Li Z, Wang Y. Structural variation and evolution of chloroplast tRNAs in green algae. PeerJ 2021; 9:e11524. [PMID: 34131524 PMCID: PMC8176911 DOI: 10.7717/peerj.11524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/05/2021] [Indexed: 01/18/2023] Open
Abstract
As one of the important groups of the core Chlorophyta (Green algae), Chlorophyceae plays an important role in the evolution of plants. As a carrier of amino acids, tRNA plays an indispensable role in life activities. However, the structural variation of chloroplast tRNA and its evolutionary characteristics in Chlorophyta species have not been well studied. In this study, we analyzed the chloroplast genome tRNAs of 14 species in five categories in the green algae. We found that the number of chloroplasts tRNAs of Chlorophyceae is maintained between 28-32, and the length of the gene sequence ranges from 71 nt to 91 nt. There are 23-27 anticodon types of tRNAs, and some tRNAs have missing anticodons that are compensated for by other types of anticodons of that tRNA. In addition, three tRNAs were found to contain introns in the anti-codon loop of the tRNA, but the analysis scored poorly and it is presumed that these introns are not functional. After multiple sequence alignment, the Ψ-loop is the most conserved structural unit in the tRNA secondary structure, containing mostly U-U-C-x-A-x-U conserved sequences. The number of transitions in tRNA is higher than the number of transversions. In the replication loss analysis, it was found that green algal chloroplast tRNAs may have undergone substantial gene loss during the course of evolution. Based on the constructed phylogenetic tree, mutations were found to accompany the evolution of the Green algae chloroplast tRNA. Moreover, chloroplast tRNAs of Chlorophyceae are consistent with those of monocotyledons and gymnosperms in terms of evolutionary patterns, sharing a common multi-phylogenetic pattern and rooted in a rich common ancestor. Sequence alignment and systematic analysis of tRNA in chloroplast genome of Chlorophyceae, clarified the characteristics and rules of tRNA changes, which will promote the evolutionary relationship of tRNA and the origin and evolution of chloroplast.
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Affiliation(s)
- Fangbing Qi
- State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi’an, China
| | - Yajing Zhao
- State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi’an, China
| | - Ningbo Zhao
- State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi’an, China
| | - Kai Wang
- State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi’an, China
| | - Zhonghu Li
- State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi’an, China
| | - Yingjuan Wang
- State Key Laboratory of Biotechnology of Shannxi Province, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi’an, China
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21
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Li X, Hou Z, Xu C, Shi X, Yang L, Lewis LA, Zhong B. Large Phylogenomic Data sets Reveal Deep Relationships and Trait Evolution in Chlorophyte Green Algae. Genome Biol Evol 2021; 13:6265471. [PMID: 33950183 PMCID: PMC8271138 DOI: 10.1093/gbe/evab101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2021] [Indexed: 12/01/2022] Open
Abstract
The chlorophyte green algae (Chlorophyta) are species-rich ancient groups ubiquitous in various habitats with high cytological diversity, ranging from microscopic to macroscopic organisms. However, the deep phylogeny within core Chlorophyta remains unresolved, in part due to the relatively sparse taxon and gene sampling in previous studies. Here we contribute new transcriptomic data and reconstruct phylogenetic relationships of core Chlorophyta based on four large data sets up to 2,698 genes of 70 species, representing 80% of extant orders. The impacts of outgroup choice, missing data, bootstrap-support cutoffs, and model misspecification in phylogenetic inference of core Chlorophyta are examined. The species tree topologies of core Chlorophyta from different analyses are highly congruent, with strong supports at many relationships (e.g., the Bryopsidales and the Scotinosphaerales-Dasycladales clade). The monophyly of Chlorophyceae and of Trebouxiophyceae as well as the uncertain placement of Chlorodendrophyceae and Pedinophyceae corroborate results from previous studies. The reconstruction of ancestral scenarios illustrates the evolution of the freshwater-sea and microscopic–macroscopic transition in the Ulvophyceae, and the transformation of unicellular→colonial→multicellular in the chlorophyte green algae. In addition, we provided new evidence that serine is encoded by both canonical codons and noncanonical TAG code in Scotinosphaerales, and stop-to-sense codon reassignment in the Ulvophyceae has originated independently at least three times. Our robust phylogenetic framework of core Chlorophyta unveils the evolutionary history of phycoplast, cyto-morphology, and noncanonical genetic codes in chlorophyte green algae.
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Affiliation(s)
- Xi Li
- College of Life Sciences, Nanjing Normal University, China
| | - Zheng Hou
- College of Life Sciences, Nanjing Normal University, China
| | - Chenjie Xu
- College of Life Sciences, Nanjing Normal University, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, China
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, China
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22
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Miyamura S, Nakayama T, Mitsuhashi F, Nagumo T, Sato T, Motomura T, Hori T. Sex-specific Positioning of the Mating Structure in Scale-bearing Gametes of Monostroma angicava and Collinsiella cava (Ulvophyceae, Chlorophyta): A Possible Widespread Difference between Male and Female Gametes. JOURNAL OF PHYCOLOGY 2021; 57:510-527. [PMID: 33150600 DOI: 10.1111/jpy.13096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/02/2020] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
The gametes of chlorophytes can be divided into two morphological types (types α and β) based on the position of the mating structure relative to the flagella and eyespot. To elucidate the relationship between the morphological types and the sexes, we studied spatial relationships between the flagellar apparatus-eyespot-mating structures in biflagellate male and female gametes and their fate after fertilization in the anisogamous (Monostroma angicava) and the slightly anisogamous species (Collinsiella cava) using field emission scanning electron microscopy and transmission electron microscopy. The smaller male and larger female gametes of M. angicava had two basal bodies arranged at a 180° angle and the cell surface coated with square-shaped body scales, except for the flagella and mating structures. The mating structure of the female gamete was located on the same side of the flagellar beat plane as the eyespot (type β), whereas that of the male gamete was located on the opposite side (type α). This mating structure arrangement was also confirmed in C. cava. The initial fusion when male and female gametes were mixed involved the mating structures. In a fusing pair of gametes, each flagellum of one gamete lay alongside one flagellum of the other gamete. As fusion proceeded, the gamete pair transformed into a quadriflagellate planozygote, in which the four basal bodies were arranged in a cruciate pattern. The eyespots were positioned side-by-side on the same side of the cell. These results suggest that the two morphological types of gametes are intimately correlated with the particular sexes.
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Affiliation(s)
- Shinichi Miyamura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takeshi Nakayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | | | - Tamotsu Nagumo
- Echigo Natural History Laboratory, Ojiya, Niigata, 947-9941, Japan
| | - Tomonori Sato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - Terumitsu Hori
- Laboratory for Ginkgo Sciences, 2-5-23 Higashi, Tsukuba, Ibaraki, 305-0046, Japan
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23
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Fang J, Liu B, Liu G, Verbruggen H, Zhu H. Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:780054. [PMID: 34956275 PMCID: PMC8692980 DOI: 10.3389/fpls.2021.780054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 05/17/2023]
Abstract
Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26-36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD -GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.
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Affiliation(s)
- Jiao Fang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Huan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Huan Zhu,
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 PMCID: PMC7594059 DOI: 10.3390/v12101180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Correspondence: ; Tel.: +61-2-9351-5591
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 DOI: 10.1101/2020.06.08.141184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/26/2023] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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Tang Q, Pang K, Yuan X, Xiao S. A one-billion-year-old multicellular chlorophyte. Nat Ecol Evol 2020; 4:543-549. [PMID: 32094536 PMCID: PMC8668152 DOI: 10.1038/s41559-020-1122-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022]
Abstract
Chlorophytes (representing a clade within the Viridiplantae and a sister group of the Streptophyta) probably dominated marine export bioproductivity and played a key role in facilitating ecosystem complexity before the Mesozoic diversification of phototrophic eukaryotes such as diatoms, coccolithophorans and dinoflagellates. Molecular clock and biomarker data indicate that chlorophytes diverged in the Mesoproterozoic or early Neoproterozoic, followed by their subsequent phylogenetic diversification, multicellular evolution and ecological expansion in the late Neoproterozoic and Palaeozoic. This model, however, has not been rigorously tested with palaeontological data because of the scarcity of Proterozoic chlorophyte fossils. Here we report abundant millimetre-sized, multicellular and morphologically differentiated macrofossils from rocks approximately 1,000 million years ago. These fossils are described as Proterocladus antiquus new species and are interpreted as benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired macroscopic size, multicellularity and cellular differentiation nearly a billion years ago, much earlier than previously thought.
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Affiliation(s)
- Qing Tang
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA.
| | - Ke Pang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA.
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Jönsson M, Allahgholi L, Sardari RR, Hreggviðsson GO, Nordberg Karlsson E. Extraction and Modification of Macroalgal Polysaccharides for Current and Next-Generation Applications. Molecules 2020; 25:E930. [PMID: 32093097 PMCID: PMC7070867 DOI: 10.3390/molecules25040930] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 11/16/2022] Open
Abstract
Marine macroalgal (seaweed) polysaccharides are highly promising for next-generation applications in several industries. However, despite the reported comprehensive potential of these polysaccharides, commercial products are scarce on the market. Seaweed cultivations are increasing in number and production quantity, owing to an elevated global trend of utilization interest in seaweed. The extraction of polysaccharides from seaweed generally generates low yields, but novel methods are being developed to facilitate and improve the extraction processes. Current areas of applications for seaweed polysaccharides mainly take advantage of the physicochemical properties of certain polysaccharides, such as gelling, thickening and emulsifying. However, many of the numerous bioactivities reported are still only at research level and lack clinical evidence for commercialization. It has been suggested the construction of smaller units may generate better defined molecules that are more suitable for biomedical applications. Enzymatic modification is a promising tool for the generation of more defined, targeted biomolecules. This review covers; structural differences between the most predominant marine algal polysaccharides, extraction processes, modification alternatives, as well as a summary of current and potential next-generation application areas.
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Affiliation(s)
- Madeleine Jönsson
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
| | - Leila Allahgholi
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
| | - Roya R.R. Sardari
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
| | - Guðmundur O. Hreggviðsson
- Faculty of Life and Environmental Sciences, University of Iceland, Askja, IS-101 Reykjavík, Iceland;
- Matis Ohf, Vinlandsleid 12, IS-113 Reykjavik, Iceland
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, Post Office Box 124, 221 00 Lund, Sweden; (M.J.); (L.A.)
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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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Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci U S A 2020; 117:2551-2559. [PMID: 31911467 PMCID: PMC7007542 DOI: 10.1073/pnas.1910060117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | | | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Sofie D'hondt
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
- School of Biological Sciences, University of Western Australia, WA 6009, Australia
- Climate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium;
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Meise Botanic Garden, 1860 Meise, Belgium
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Repetti SI, Jackson CJ, Judd LM, Wick RR, Holt KE, Verbruggen H. The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. PeerJ 2020; 8:e8273. [PMID: 31915577 PMCID: PMC6944098 DOI: 10.7717/peerj.8273] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.
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Affiliation(s)
- Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | | | - Louise M Judd
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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Abstract
Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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Abstract
Algae are photosynthetic eukaryotes whose taxonomic breadth covers a range of life histories, degrees of cellular and developmental complexity, and diverse patterns of sexual reproduction. These patterns include haploid- and diploid-phase sex determination, isogamous mating systems, and dimorphic sexes. Despite the ubiquity of sexual reproduction in algae, their mating-type-determination and sex-determination mechanisms have been investigated in only a limited number of representatives. These include volvocine green algae, where sexual cycles and sex-determining mechanisms have shed light on the transition from mating types to sexes, and brown algae, which are a model for UV sex chromosome evolution in the context of a complex haplodiplontic life cycle. Recent advances in genomics have aided progress in understanding sexual cycles in less-studied taxa including ulvophyte, charophyte, and prasinophyte green algae, as well as in diatoms.
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Affiliation(s)
- James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
| | - Susana Coelho
- Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, CS 90074, F-29688 Roscoff, France;
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Arimoto A, Nishitsuji K, Higa Y, Arakaki N, Hisata K, Shinzato C, Satoh N, Shoguchi E. A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants. DNA Res 2019; 26:183-192. [PMID: 30918953 PMCID: PMC6476727 DOI: 10.1093/dnares/dsz002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/15/2019] [Indexed: 11/13/2022] Open
Abstract
Genome evolution and development of unicellular, multinucleate macroalgae (siphonous algae) are poorly known, although various multicellular organisms have been studied extensively. To understand macroalgal developmental evolution, we assembled the ∼26 Mb genome of a siphonous green alga, Caulerpa lentillifera, with high contiguity, containing 9,311 protein-coding genes. Molecular phylogeny using 107 nuclear genes indicates that the diversification of the class Ulvophyceae, including C. lentillifera, occurred before the split of the Chlorophyceae and Trebouxiophyceae. Compared with other green algae, the TALE superclass of homeobox genes, which expanded in land plants, shows a series of lineage-specific duplications in this siphonous macroalga. Plant hormone signalling components were also expanded in a lineage-specific manner. Expanded transport regulators, which show spatially different expression, suggest that the structural patterning strategy of a multinucleate cell depends on diversification of nuclear pore proteins. These results not only imply functional convergence of duplicated genes among green plants, but also provide insight into evolutionary roots of green plants. Based on the present results, we propose cellular and molecular mechanisms involved in the structural differentiation in the siphonous alga.
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Affiliation(s)
- Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yoshimi Higa
- Onna Village Fisheries Cooperative, Onna, Okinawa, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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Horinouchi Y, Yamaguchi M, Chibana H, Togashi T. Nuclear behavior and roles indicate that Codiolum phase is a sporophyte in Monostroma angicava (Ulotrichales, Ulvophyceae). JOURNAL OF PHYCOLOGY 2019; 55:534-542. [PMID: 30715731 DOI: 10.1111/jpy.12841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
The life-cycle system of Ulotrichales, a major order of Ulvophyceae, remains controversial because it is unclear whether the Codiolum phase, a characteristic unicellular diploid generation in ulotrichalean algae, is a zygote or a sporophyte. This controversy inhibits the understanding of the diversified life cycles in Ulvophyceae. To distinguish between zygotes and sporophytes, we have to examine not only whether diploid generations function as sporophytes, but also whether mitosis occurs before meiosis in diploid generations. However, the nuclear behavior in the Codiolum phases is largely unknown, probably because no suitable methods are available. Using fluorescent microscopy with ethidium bromide and transmission electron microscopy of cell-wall-dissected specimens, we report the nuclear behavior in the Codiolum phases of an ulotrichalean alga with a representative life cycle, Monostroma angicava. Each vegetative Codiolum phase had a single polyploid nucleus due to endoreduplication, a type of mitosis without nuclear division. During zoosporogenesis, the nucleus had a structure that would be a meiosis-specific complex. We quantitatively showed that Codiolum phases grew extremely large and produced numerous zoospores. Our results suggest that an event comparable to mitosis occurs before meiosis in the Codiolum phase of M. angicava. This nuclear behavior and the functions (growth and zoospore production abilities) correspond to those of sporophytes. Therefore, the life-cycle system of M. angicava is a heteromorphic haplo-diplontic cycle. This system appears to be widely adopted among other ulotrichalean algae.
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Affiliation(s)
- Yusuke Horinouchi
- Marine Biosystems Research Center, Chiba University, Kamogawa, 299-5502, Japan
| | - Masashi Yamaguchi
- Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Hiroji Chibana
- Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Tatsuya Togashi
- Marine Biosystems Research Center, Chiba University, Kamogawa, 299-5502, Japan
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A time travel story: metagenomic analyses decipher the unknown geographical shift and the storage history of possibly smuggled antique marble statues. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-1446-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Steinová J, Škaloud P, Yahr R, Bestová H, Muggia L. Reproductive and dispersal strategies shape the diversity of mycobiont-photobiont association in Cladonia lichens. Mol Phylogenet Evol 2019; 134:226-237. [PMID: 30797939 DOI: 10.1016/j.ympev.2019.02.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 02/16/2019] [Accepted: 02/17/2019] [Indexed: 11/27/2022]
Abstract
Ecological preferences, partner compatibility, or partner availability are known to be important factors shaping obligate and intimate lichen symbioses. We considered a complex of Cladonia species, traditionally differentiated by the extent of sexual reproduction and the type of vegetative propagules, to assess if the reproductive and dispersal strategies affect mycobiont-photobiont association patterns. In total 85 lichen thalli from 72 European localities were studied, two genetic markers for both Cladonia mycobionts and Asterochloris photobionts were analyzed. Variance partitioning analysis by multiple regression on distance matrices was performed to describe and partition variance in photobiont genetic diversity. Asexually reproducing Cladonia in our study were found to be strongly specific to their photobionts, associating with only two closely related Asterochloris species. In contrast, sexually reproducing lichens associated with seven unrelated Asterochloris lineages, thus being photobiont generalists. The reproductive mode had the largest explanatory power, explaining 44% of the total photobiont variability. Reproductive and dispersal strategies are the key factors shaping photobiont diversity in this group of Cladonia lichens. A strict photobiont specialisation observed in two studied species may steer both evolutionary flexibility and responses to ecological changes of these organisms, and considerably limit their distribution ranges.
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Affiliation(s)
- Jana Steinová
- Institute for Nanomaterials, Advanced Technologies and Innovations, Technical University of Liberec, Studentská 2, Liberec CZ-46117, Czech Republic; Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Praha 2 CZ-12801, Czech Republic.
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Praha 2 CZ-12801, Czech Republic
| | - Rebecca Yahr
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Helena Bestová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Praha 2 CZ-12801, Czech Republic
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, Trieste I-34127, Italy.
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Klimešová M, Rindi F, Škaloud P. DNA cloning demonstrates high genetic heterogeneity in populations of the subaerial green alga Trentepohlia (Trentepohliales, Chlorophyta). JOURNAL OF PHYCOLOGY 2019; 55:224-235. [PMID: 30481372 DOI: 10.1111/jpy.12817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 10/27/2018] [Indexed: 06/09/2023]
Abstract
Mats of the green alga Trentepohlia, a genus widely distributed in the tropics as well as temperate regions, have always been perceived as homogeneous (i.e., formed by only one species). As such, their general nature and specific feature play a supportive role in the species delimitation. However, the presence of morphologically dissimilar thalli was observed under the light microscope and when cultivating a piece of a single mat. To address this, we performed DNA cloning of the rbcL gene on mat fragments of T. abietina, T. annulata, T. jolithus and T. umbrina sampled in Europe to reveal if they are composed of one or more species. We revealed that more Trentepohlia haplotypes may coexist in a single mat. In consideration of this, we conclude that the use of material isolated in unialgal culture will be almost mandatory for a taxonomic reassessment of this complicated genus. Another direct implication of this problem is that herbarium specimens consisting of field-collected material should not be used for direct sequencing. We further hypothesize the reasons why multiple haplotypes of Trentepohlia occur more frequently in the tuft-like mats. Possibly, fragments and/or cells of other microalgae, including other species of Trentepohlia, might be retained in such mats more easily than in the crustose trentepohlialean mats.
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Affiliation(s)
- Michala Klimešová
- Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
| | - Fabio Rindi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Pavel Škaloud
- Faculty of Science, Charles University, Benátská 2, 128 00, Prague, Czech Republic
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Pescheck F. UV-A screening inCladophorasp. lowers internal UV-A availability and photoreactivation as compared to non-UV screening inUlva intestinalis. Photochem Photobiol Sci 2019; 18:413-423. [DOI: 10.1039/c8pp00432c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-A screening reduces UV-A-driven photoreactivation of UV-B-induced DNA damage in the green macroalgaCladophorasp.
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Affiliation(s)
- Frauke Pescheck
- Botanical Institute
- Christian-Albrechts-University of Kiel
- 24098 Kiel
- Germany
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Gong S, Li Z, Zhang F, Xiao Y, Cheng H. Symbiochlorum hainanensis gen. et sp. nov. (Ulvophyceae, Chlorophyta) isolated from bleached corals living in the South China Sea. JOURNAL OF PHYCOLOGY 2018; 54:811-817. [PMID: 30137670 DOI: 10.1111/jpy.12779] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/06/2018] [Indexed: 05/19/2023]
Abstract
Light/scanning electron/transmission microscopy-based morphological analyses and multiple nucleotide sequences-based molecular phylogenetic analyses are used to identify and assess the phylogenetic position of a new unidentified green alga isolated from bleached corals living in the South China Sea. This new unidentified green alga is a unicellular marine alga and has uninucleate vegetative cells and multiple chloroplasts with a pyrenoid. It can form aplanosporangium covered by cell walls and reproduces by releasing autospore. These features differ substantially from those of the two genera Ignatius and Pseudocharacium. Those two genera have been accommodated in the Ignatius clade. Nucleotide sequences of the nuclear small subunit ribosomal RNA gene (18S rRNA), internal transcribed spacer 2 of ribosomal RNA gene (ITS2) and ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit gene (rbcL, partial) are obtained and compared with published green algal sequences. The results from the morphology, ultrastructure, and multiple nucleotide sequences data support the placement of the new unidentified green alga in Ulvophyceae. This new unidentified isolate is described as Symbiochlorum hainanensis gen. et sp. nov., a new sister lineage to the Ignatius clade, Ulvophyceae, Chlorophyta.
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Affiliation(s)
- Sanqiang Gong
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Fengli Zhang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yilin Xiao
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Cheng
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
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Zheng F, Liu H, Jiang M, Xu Z, Wang Z, Wang C, Du F, Shen Z, Wang B. The complete mitochondrial genome of the Caulerpa lentillifera (Ulvophyceae, Chlorophyta): Sequence, genome content, organization structure and phylogenetic consideration. Gene 2018; 673:225-238. [PMID: 29933020 DOI: 10.1016/j.gene.2018.06.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 04/21/2018] [Accepted: 06/15/2018] [Indexed: 11/19/2022]
Abstract
The complete mitochondrial genome is greatly important for studies on genetic structure and phylogenetic relationship at various taxonomic levels. To obtain information about the evolutionary trends of mtDNA in the Ulvophyceae and also to gain insights into the phylogenetic relationships between ulvophytes and other chlorophytes, we determined the mtDNA sequence of Caulerpa lentillifera (sea grape) using de novo mitochondrial genome sequencing. The complete genomic DNA of C. lentillifera was circular and 209,034 bp in length, and it was the largest green-algal mitochondrial genome sequenced to date, with a low gene density of 65.2%, which is reminiscent of the "expanded" pattern of evolution exhibited by embryophyte mtDNAs. The C. lentillifera mtDNA consisted of a typical set of 17 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, three ribosomal RNA (rRNA) genes, 42 putative open reading frames (ORFs) and 29 introns, which had homologs in green-algal mtDNAs displaying an "ancestral" or a "reduced-derived" pattern of evolution. The overall base composition of its mitochondrial genome was 24.19% for A, 24.94% for T, 25.80% for G, 25.07% for C and 50.87% for GC. The mitochondrial genome of C. lentillifera was characterized by numerous small intergenic regions and introns, which was clearly different from other green algae. With the exception of the NADH dehydrogenase subunit 6 (ND6), ND1, ATP and three tRNA genes (tRNA-His, tRNA-Thr and tRNA-Ala), all other mitochondrial 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. To gain insights into the evolutionary trends of mtDNA in the Ulvophyceae, we inferred the complete mtDNA sequence of C. lentillifera, an ulvophyte belonging to a distinct, early-diverging lineage. Taken together, our data offered useful information for the studies on phylogenetic hypotheses and phylogenetic relationships of C. lentillifera within the Chlorophyta.
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Affiliation(s)
- Fengrong Zheng
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Hongzhan Liu
- Marine College of Shandong University, Weihai 264209, China.
| | - Meijing Jiang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongjun Xu
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Zongxing Wang
- First Institute of Oceanography SOA, Qingdao 266061, China
| | - Claire Wang
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Fei Du
- Qingdao Haiputao Organic Green Algae Research and Development Breed CO., LTD, Qingdao 266000, China
| | - Zhen Shen
- First Institute of Oceanography SOA, Qingdao 266061, China; Key laboratory of Marine Bioactive substance SOA, Qingdao 266061, China
| | - Bo Wang
- First Institute of Oceanography SOA, Qingdao 266061, China.
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Fang L, Leliaert F, Novis PM, Zhang Z, Zhu H, Liu G, Penny D, Zhong B. Improving phylogenetic inference of core Chlorophyta using chloroplast sequences with strong phylogenetic signals and heterogeneous models. Mol Phylogenet Evol 2018; 127:248-255. [PMID: 29885933 DOI: 10.1016/j.ympev.2018.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/26/2018] [Accepted: 06/04/2018] [Indexed: 01/09/2023]
Abstract
Phylogenetic relationships within the green algal phylum Chlorophyta have proven difficult to resolve. The core Chlorophyta include Chlorophyceae, Ulvophyceae, Trebouxiophyceae, Pedinophyceae and Chlorodendrophyceae, but the relationships among these classes remain unresolved and the monophyly of Ulvophyceae and Trebouxiophyceae are highly controversial. We analyzed a dataset of 101 green algal species and 73 protein-coding genes sampled from complete and partial chloroplast genomes, including six newly sequenced ulvophyte genomes (Blidingia minima NIES-1837, Ulothrix zonata, Halochlorococcum sp. NIES-1838, Scotinosphaera sp. NIES-154, Caulerpa brownii and Cephaleuros sp. HZ-2017). We applied the Tree Certainty (TC) score to quantify the level of incongruence between phylogenetic trees in chloroplast genomic datasets, and show that the conflicting phylogenetic trees of core Chlorophyta stem from the most GC-heterogeneous sites. With removing the most GC-heterogeneous sites, our chloroplast phylogenomic analyses using heterogeneous models consistently support monophyly of the Chlorophyceae and of the Trebouxiophyceae, but the Ulvophyceae was resolved as polyphyletic. Our analytical framework provides an efficient approach to reconstruct the optimal phylogenetic relationships by minimizing conflicting signals.
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Affiliation(s)
- Ling Fang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Frederik Leliaert
- Botanic Garden Meise, 1860 Meise, Belgium; Phycology Research Group, Biology Department, Ghent University, 9000 Ghent, Belgium
| | - Phil M Novis
- Allan Herbarium, Manaaki Whenua-Landcare Research, Lincoln 7640, New Zealand
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Huan Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guoxiang Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Mikhailyuk T, Lukešová A, Glaser K, Holzinger A, Obwegeser S, Nyporko S, Friedl T, Karsten U. New Taxa of Streptophyte Algae (Streptophyta) from Terrestrial Habitats Revealed Using an Integrative Approach. Protist 2018; 169:406-431. [PMID: 29860113 PMCID: PMC6071840 DOI: 10.1016/j.protis.2018.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 10/25/2022]
Abstract
Two new genera (Streptosarcina and Streptofilum) and three new species (Streptosarcina arenaria, S. costaricana and Streptofilum capillatum) of streptophyte algae were detected in cultures isolated from terrestrial habitats of Europe and Central America and described using an integrative approach. Additionally, a strain isolated from soil in North America was identified as Hormidiella parvula and proposed as an epitype of this species. The molecular phylogeny based on 18S rRNA and rbcL genes, secondary structure of ITS-2, as well as the morphology of vegetative and reproductive stages, cell ultrastructure, ecology and distribution of the investigated strains were assessed. The new genus Streptosarcina forms a sister lineage to the genus Hormidiella (Klebsormidiophyceae). Streptosarcina is characterized by packet-like (sarcinoid) and filamentous thalli with true branching and a cell organization typical for Klebsormidiophyceae. Streptofilum forms a separate lineage within Streptophyta. This genus represents an easily disintegrating filamentous alga which exhibits a cell coverage of unique structure: layers of submicroscopic scales of piliform shape covering the plasmalemma and exfoliate inside the mucilage envelope surrounding cells. The implications of the discovery of the new taxa for understanding evolutionary tendencies in the Streptophyta, a group of great evolutionary interest, are discussed.
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Affiliation(s)
- Tatiana Mikhailyuk
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Tereschenkivska Str. 2, Kyiv 01004, Ukraine.
| | - Alena Lukešová
- Biology Centre of the Czech Academy of Sciences, v.v.i., Institute of Soil Biology, Na Sádkách 7, České Budějovice CZ-37005, Czech Republic
| | - Karin Glaser
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
| | - Andreas Holzinger
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - Sabrina Obwegeser
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, A-6020 Innsbruck, Austria
| | - Svetlana Nyporko
- M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Tereschenkivska Str. 2, Kyiv 01004, Ukraine
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae, Georg-August University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Ulf Karsten
- Applied Ecology and Phycology, Institute of Biological Sciences, University of Rostock, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
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de Vries J, Gould SB. The monoplastidic bottleneck in algae and plant evolution. J Cell Sci 2018; 131:jcs.203414. [PMID: 28893840 DOI: 10.1242/jcs.203414] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plastids in plants and algae evolved from the endosymbiotic integration of a cyanobacterium by a heterotrophic eukaryote. New plastids can only emerge through fission; thus, the synchronization of bacterial division with the cell cycle of the eukaryotic host was vital to the origin of phototrophic eukaryotes. Most of the sampled algae house a single plastid per cell and basal-branching relatives of polyplastidic lineages are all monoplastidic, as are some non-vascular plants during certain stages of their life cycle. In this Review, we discuss recent advances in our understanding of the molecular components necessary for plastid division, including those of the peptidoglycan wall (of which remnants were recently identified in moss), in a wide range of phototrophic eukaryotes. Our comparison of the phenotype of 131 species harbouring plastids of either primary or secondary origin uncovers that one prerequisite for an algae or plant to house multiple plastids per nucleus appears to be the loss of the bacterial genes minD and minE from the plastid genome. The presence of a single plastid whose division is coupled to host cytokinesis was a prerequisite of plastid emergence. An escape from such a monoplastidic bottleneck succeeded rarely and appears to be coupled to the evolution of additional layers of control over plastid division and a complex morphology. The existence of a quality control checkpoint of plastid transmission remains to be demonstrated and is tied to understanding the monoplastidic bottleneck.
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Affiliation(s)
- Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada, B3H 4R2
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University, 40225 Düsseldorf, Germany
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Jackson C, Knoll AH, Chan CX, Verbruggen H. Plastid phylogenomics with broad taxon sampling further elucidates the distinct evolutionary origins and timing of secondary green plastids. Sci Rep 2018; 8:1523. [PMID: 29367699 PMCID: PMC5784168 DOI: 10.1038/s41598-017-18805-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/15/2017] [Indexed: 11/08/2022] Open
Abstract
Secondary plastids derived from green algae occur in chlorarachniophytes, photosynthetic euglenophytes, and the dinoflagellate genus Lepidodinium. Recent advances in understanding the origin of these plastids have been made, but analyses suffer from relatively sparse taxon sampling within the green algal groups to which they are related. In this study we aim to derive new insights into the identity of the plastid donors, and when in geological time the independent endosymbiosis events occurred. We use newly sequenced green algal chloroplast genomes from carefully chosen lineages potentially related to chlorarachniophyte and Lepidodinium plastids, combined with recently published chloroplast genomes, to present taxon-rich phylogenetic analyses to further pinpoint plastid origins. We integrate phylogenies with fossil information and relaxed molecular clock analyses. Our results indicate that the chlorarachniophyte plastid may originate from a precusor of siphonous green algae or a closely related lineage, whereas the Lepidodinium plastid originated from a pedinophyte. The euglenophyte plastid putatively originated from a lineage of prasinophytes within the order Pyramimonadales. Our molecular clock analyses narrow in on the likely timing of the secondary endosymbiosis events, suggesting that the event leading to Lepidodinium likely occurred more recently than those leading to the chlorarachniophyte and photosynthetic euglenophyte lineages.
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Affiliation(s)
- Christopher Jackson
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia.
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes. Curr Biol 2017; 27:3771-3782.e6. [PMID: 29199074 DOI: 10.1016/j.cub.2017.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/28/2022]
Abstract
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Kenny A Bogaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine, Québec City, QC G1V 0A6, Canada
| | - Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, New Kirk Building, Kelburn Parade, P.O. Box 600, Wellington 6012, New Zealand
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Juan M Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35484-0345, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Professors Walk, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium.
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Carvalho MC, Carneiro PBDM, Dellatorre FG, Gibilisco PE, Sachs J, Eyre BD. Bulk hydrogen stable isotope composition of seaweeds: Clear separation between Ulvophyceae and other classes. JOURNAL OF PHYCOLOGY 2017; 53:961-969. [PMID: 28653755 DOI: 10.1111/jpy.12558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 06/12/2017] [Indexed: 06/07/2023]
Abstract
Little is known about the bulk hydrogen stable isotope composition (δ2 H) of seaweeds. This study investigated the bulk δ2 H in several different seaweed species collected from three different beaches in Brazil, Australia, and Argentina. Here, we show that Ulvophyceae (a group of green algae) had lower δ2 H values (between -94‰ and -130‰) than red algae (Florideophyceae), brown algae (Phaeophyceae), and species from the class Bryopsidophyceae (another group of green algae). Overall the latter three groups of seaweeds had δ2 H values between -50‰ and -90‰. These findings were similar at the three different geographic locations. Observed differences in δ2 H values were probably related to differences in hydrogen (H) metabolism among algal groups, also observed in the δ2 H values of their lipids. The marked difference between the δ2 H values of Ulvophyecae and those of the other groups could be useful to trace the food source of food webs in coastal rocky shores, to assess the impacts of green tides on coastal ecosystems, and to help clarify aspects of their phylogeny. However, reference materials for seaweed δ2 H are required before the full potential of using the δ2 H of seaweeds for ecological studies can be exploited.
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Affiliation(s)
- Matheus C Carvalho
- Centre for Coastal Biogeochemistry Research, School of Environmental Science and Management, Southern Cross University, PO box 157, Lismore, New South Wales, Australia
| | - Pedro Bastos de Macedo Carneiro
- Laboratório de Macroalgas, Instituto de Ciências do Mar (LABOMAR), Universidade Federal do Ceará, Av. Abolição, 3207 Meireles. CEP: 60.165-081, Fortaleza, Ceará, Brazil
| | | | | | - Julian Sachs
- School of Oceanography, University of Washington, Seattle, Washington, USA
| | - Bradley D Eyre
- Centre for Coastal Biogeochemistry Research, School of Environmental Science and Management, Southern Cross University, PO box 157, Lismore, New South Wales, Australia
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Liu F, Melton JT, Bi Y. Mitochondrial genomes of the green macroalga Ulva pertusa (Ulvophyceae, Chlorophyta): novel insights into the evolution of mitogenomes in the Ulvophyceae. JOURNAL OF PHYCOLOGY 2017; 53:1010-1019. [PMID: 28677163 DOI: 10.1111/jpy.12561] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
To further understand the trends in the evolution of mitochondrial genomes (mitogenomes or mtDNAs) in the Ulvophyceae, the mitogenomes of two separate thalli of Ulva pertusa were sequenced. Two U. pertusa mitogenomes (Up1 and Up2) were 69,333 bp and 64,602 bp in length. These mitogenomes shared two ribosomal RNAs (rRNAs), 28 transfer RNAs (tRNAs), 29 protein-coding genes, and 12 open reading frames. The 4.7 kb difference in size was attributed to variation in intron content and tandem repeat regions. A total of six introns were present in the smaller U. pertusa mtDNA (Up2), while the larger mtDNA (Up1) had eight. The larger mtDNA had two additional group II introns in two genes (cox1 and cox2) and tandem duplication mutations in noncoding regions. Our results showed the first case of intraspecific variation in chlorophytan mitogenomes and provided further genomic data for the undersampled Ulvophyceae.
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Affiliation(s)
- Feng Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - James T Melton
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487-0345, USA
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
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48
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Cai C, Wang L, Zhou L, He P, Jiao B. Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis. PLoS One 2017; 12:e0184196. [PMID: 28863197 PMCID: PMC5581003 DOI: 10.1371/journal.pone.0184196] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 08/18/2017] [Indexed: 12/05/2022] Open
Abstract
Ulva flexuosa, one kind of green tide algae, has outbroken in the Yellow Sea of China during the past ten years. In the present study, we sequenced the chloroplast genome of U. flexuosa followed by annotation and comparative analysis. It indicated that the chloroplast genomes had high conservation among Ulva spp., and high rearrangement outside them. Though U. flexuosa was closer to U. linza than U. fasciata in phylogenetic tree, the average Ka/Ks between U. flexuosa and U. linza assessed by 67 protein-coding genes was higher than those between U. flexuosa and other species in Ulva spp., due to the variation of psbZ, psbM and ycf20. Our results laid the foundation for the future studies on the evolution of chloroplast genomes of Ulva, as well as the molecular identification of U. flexuosa varieties.
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Affiliation(s)
- Chuner Cai
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China
- Marine Biomedicine Institute, Second Military Medical University, Shanghai, China
| | - Lingke Wang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Lingjie Zhou
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Peimin He
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- National Demonstration Center for Experimental Fisheries Science Education (Shanghai Ocean University), Shanghai, China
- * E-mail: (PH); (BJ)
| | - Binghua Jiao
- Marine Biomedicine Institute, Second Military Medical University, Shanghai, China
- * E-mail: (PH); (BJ)
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49
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Verbruggen H, Marcelino VR, Guiry MD, Cremen MCM, Jackson CJ. Phylogenetic position of the coral symbiont Ostreobium (Ulvophyceae) inferred from chloroplast genome data. JOURNAL OF PHYCOLOGY 2017; 53:790-803. [PMID: 28394415 DOI: 10.1111/jpy.12540] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
The green algal genus Ostreobium is an important symbiont of corals, playing roles in reef decalcification and providing photosynthates to the coral during bleaching events. A chloroplast genome of a cultured strain of Ostreobium was available, but low taxon sampling and Ostreobium's early-branching nature left doubt about its phylogenetic position. Here, we generate and describe chloroplast genomes from four Ostreobium strains as well as Avrainvillea mazei and Neomeris sp., strategically sampled early-branching lineages in the Bryopsidales and Dasycladales respectively. At 80,584 bp, the chloroplast genome of Ostreobium sp. HV05042 is the most compact yet found in the Ulvophyceae. The Avrainvillea chloroplast genome is ~94 kbp and contains introns in infA and cysT that have nearly complete sequence identity except for an open reading frame (ORF) in infA that is not present in cysT. In line with other bryopsidalean species, it also contains regions with possibly bacteria-derived ORFs. The Neomeris data did not assemble into a canonical circular chloroplast genome but a large number of contigs containing fragments of chloroplast genes and showing evidence of long introns and intergenic regions, and the Neomeris chloroplast genome size was estimated to exceed 1.87 Mb. Chloroplast phylogenomics and 18S nrDNA data showed strong support for the Ostreobium lineage being sister to the remaining Bryopsidales. There were differences in branch support when outgroups were varied, but the overall support for the placement of Ostreobium was strong. These results permitted us to validate two suborders and introduce a third, the Ostreobineae.
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Affiliation(s)
- Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Vanessa R Marcelino
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Michael D Guiry
- AlgaeBase, Ryan Institute, National University of Ireland, Galway, H91 TK33, Ireland
| | - Ma Chiela M Cremen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Christopher J Jackson
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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50
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Dittami SM, Heesch S, Olsen JL, Collén J. Transitions between marine and freshwater environments provide new clues about the origins of multicellular plants and algae. JOURNAL OF PHYCOLOGY 2017; 53:731-745. [PMID: 28509401 DOI: 10.1111/jpy.12547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 04/19/2017] [Indexed: 05/03/2023]
Abstract
Marine-freshwater and freshwater-marine transitions have been key events in the evolution of life, and most major groups of organisms have independently undergone such events at least once in their history. Here, we first compile an inventory of bidirectional freshwater and marine transitions in multicellular photosynthetic eukaryotes. While green and red algae have mastered multiple transitions in both directions, brown algae have colonized freshwater on a maximum of six known occasions, and angiosperms have made the transition to marine environments only two or three times. Next, we review the early evolutionary events leading to the colonization of current habitats. It is commonly assumed that the conquest of land proceeded in a sequence from marine to freshwater habitats. However, recent evidence suggests that early photosynthetic eukaryotes may have arisen in subaerial or freshwater environments and only later colonized marine environments as hypersaline oceans were diluted to the contemporary level. Although this hypothesis remains speculative, it is important to keep these alternative scenarios in mind when interpreting the current habitat distribution of plants and algae. Finally, we discuss the roles of structural and functional adaptations of the cell wall, reactive oxygen species scavengers, osmoregulation, and reproduction. These are central for acclimatization to freshwater or to marine environments. We observe that successful transitions appear to have occurred more frequently in morphologically simple forms and conclude that, in addition to physiological studies of euryhaline species, comparative studies of closely related species fully adapted to one or the other environment are necessary to better understand the adaptive processes.
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Affiliation(s)
- Simon M Dittami
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
| | - Svenja Heesch
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Jonas Collén
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, 29688, Roscoff Cedex, France
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