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Fang J, Hu Y, Hu Z. Comparative analysis of codon usage patterns in 16 chloroplast genomes of suborder Halimedineae. BMC Genomics 2024; 25:945. [PMID: 39379800 PMCID: PMC11459826 DOI: 10.1186/s12864-024-10825-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 09/23/2024] [Indexed: 10/10/2024] Open
Abstract
The Halimedineae are marine green macroalgae that play crucial roles as primary producers in various habitats, including coral reefs, rocky shores, embayments, lagoons, and seagrass beds. Several tropical species have calcified thalli, which contribute significantly to the formation of coral reefs. In this study, we investigated the codon usage patterns and the main factors influencing codon usage bias in 16 chloroplast genomes of the suborder Halimedineae. Nucleotide composition analysis revealed that the codons of these species were enriched in A/U bases and preferred to end in A/U bases, and the distribution of GC content followed a trend of GC1 > GC2 > GC3. 30 optimal codons encoding 17 amino acids were identified, and most of the optimal codons and all of the over-expressed codons preferentially ended with A/U. The neutrality plot, effective number of codons (ENc) plot, and parity rule 2 (PR2) plot analysis indicated that natural selection played a major role in shaping codon usage bias of the most Halimedineae species. The genetic relationships based on their RSCU values and chloroplast protein-coding genes showed the closely related species have similar codon usage patterns. This study describes, for the first time, the codon usage patterns and characterization of Halimedineae chloroplast genomes, and provides new insights into the evolution of this suborder.
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Affiliation(s)
- Jiao Fang
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, Hubei, China.
| | - Yuquan Hu
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, College of Life Science, Jianghan University, Wuhan, Hubei, China
| | - Zhangfeng Hu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, Hubei, China.
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, College of Life Science, Jianghan University, Wuhan, Hubei, China.
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2
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Zhao H, Meng L, Hikida H, Ogata H. Eukaryotic genomic data uncover an extensive host range of mirusviruses. Curr Biol 2024; 34:2633-2643.e3. [PMID: 38806056 DOI: 10.1016/j.cub.2024.04.085] [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] [Received: 01/26/2024] [Revised: 04/10/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024]
Abstract
A recent marine metagenomic study has revealed the existence of a novel group of viruses designated mirusviruses, which are proposed to form an evolutionary link between two realms of double-stranded DNA viruses, Varidnaviria and Duplodnaviria. Metagenomic data suggest that mirusviruses infect microeukaryotes in the photic layer of the ocean, but their host range remains largely unknown. In this study, we investigated the presence of mirusvirus marker genes in 1,901 publicly available eukaryotic genome assemblies, mainly derived from unicellular eukaryotes, to identify potential hosts of mirusviruses. Mirusvirus marker sequences were identified in 915 assemblies spanning 227 genera across eight supergroups of eukaryotes. The habitats of the putative mirusvirus hosts included not only marine but also other diverse environments. Among the major capsid protein (MCP) signals in the genome assemblies, we identified 85 sequences that showed high sequence and structural similarities to reference mirusvirus MCPs. A phylogenetic analysis of these sequences revealed their distant evolutionary relationships with the seven previously reported mirusvirus clades. Most of the scaffolds with these MCP sequences encoded multiple mirusvirus homologs, suggesting that mirusviral infection contributes to the alteration of the host genome. We also identified three circular mirusviral genomes within the genomic data of the oil-producing thraustochytrid Schizochytrium sp. and the endolithic green alga Ostreobium quekettii. Overall, mirusviruses probably infect a wide spectrum of eukaryotes and are more diverse than previously reported.
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Affiliation(s)
- Hongda Zhao
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Lingjie Meng
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hiroyuki Hikida
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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3
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Sun W, Wei Z, Gu Y, Wang T, Liu B, Yan Y. Chloroplast genome structure analysis of Equisetum unveils phylogenetic relationships to ferns and mutational hotspot region. FRONTIERS IN PLANT SCIENCE 2024; 15:1328080. [PMID: 38665369 PMCID: PMC11044155 DOI: 10.3389/fpls.2024.1328080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/02/2024] [Indexed: 04/28/2024]
Abstract
Equisetum is one of the oldest extant group vascular plants and is considered to be the key to understanding vascular plant evolution. Equisetum is distributed almost all over the world and has a high degree of adaptability to different environments. Despite the fossil record of horsetails (Equisetum, Equisetaceae) dating back to the Carboniferous, the phylogenetic relationship of this genus is not well, and the chloroplast evolution in Equisetum remains poorly understood. In order to fill this gap, we sequenced, assembled, and annotated the chloroplast genomes of 12 species of Equisetum, and compared them to 13 previously published vascular plants chloroplast genomes to deeply examine the plastome evolutionary dynamics of Equisetum. The chloroplast genomes have a highly conserved quadripartite structure across the genus, but these chloroplast genomes have a lower GC content than other ferns. The size of Equisetum plastomes ranges from 130,773 bp to 133,684 bp and they encode 130 genes. Contraction/expansion of IR regions and the number of simple sequences repeat regions underlie large genomic variations in size among them. Comparative analysis revealed we also identified 13 divergence hotspot regions. Additionally, the genes accD and ycf1 can be used as potential DNA barcodes for the identification and phylogeny of the genus Equisetum. Twelve photosynthesis-related genes were specifically selected in Equisetum. Comparative genomic analyses implied divergent evolutionary patterns between Equisetum and other ferns. Phylogenomic analyses and molecular dating revealed a relatively distant phylogenetic relationship between Equisetum and other ferns, supporting the division of pteridophyte into Lycophytes, Equisetaceae and ferns. The results show that the chloroplast genome can be used to solve phylogenetic problems within or between Equisetum species, and also provide genomic resources for the study of Equisetum systematics and evolution.
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Affiliation(s)
- Weiyue Sun
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Zuoying Wei
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Yuefeng Gu
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Ting Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Guangzhou, China
| | - Baodong Liu
- Key Laboratory of Plant Biology, College of Heilongjiang Province, Harbin Normal University, Harbin, China
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Yuehong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orehid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
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Zhao H, Meng L, Hikida H, Ogata H. Eukaryotic genomic data uncover an extensive host range of mirusviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576163. [PMID: 38293090 PMCID: PMC10827195 DOI: 10.1101/2024.01.18.576163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
A recent marine metagenomic study has revealed the existence of a novel group of viruses designated mirusviruses, which are proposed to form an evolutionary link between two realms of double-stranded DNA viruses, Varidnaviria and Duplodnaviria. Metagenomic data suggest that mirusviruses infect microeukaryotes in the photic layer of the ocean, but their host range remains largely unknown. In this study, we investigated the presence of mirusvirus marker genes in publicly available 1,901 eukaryotic genome assemblies, mainly derived from unicellular eukaryotes, to identify potential hosts of mirusviruses. Mirusvirus marker sequences were identified in 1,348 assemblies spanning 284 genera across eight supergroups of eukaryotes. The habitats of the putative mirusvirus hosts included not only marine but also other diverse environments. Among the major capsid protein (MCP) signals in the genome assemblies, we identified 85 sequences that showed high sequence and structural similarities to reference mirusvirus MCPs. A phylogenetic analysis of these sequences revealed their distant evolutionary relationships with the seven previously reported mirusvirus clades. Most of the scaffolds with these MCP sequences encoded multiple mirusvirus homologs, underscoring the impact of mirusviral infection on the evolution of the host genome. We also identified three circular mirusviral genomes within the genomic data of the oil producing thraustochytrid Schizochytrium sp. and the endolithic green alga Ostreobium quekettii. Overall, mirusviruses probably infect a wide spectrum of eukaryotes and are more diverse than previously reported.
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Affiliation(s)
- Hongda Zhao
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Lingjie Meng
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Hiroyuki Hikida
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
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5
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Díaz-Tapia P, Rodríguez-Buján I, Maggs CA, Verbruggen H. Phylogenomic analysis of pseudocryptic diversity reveals the new genus Deltalsia (Rhodomelaceae, Rhodophyta). JOURNAL OF PHYCOLOGY 2023; 59:264-276. [PMID: 36504198 DOI: 10.1111/jpy.13311] [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: 07/01/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Molecular analyses, in combination with morphological studies, provide invaluable tools for delineating red algal taxa. However, molecular datasets are incomplete and taxonomic revisions are often required once additional species or populations are sequenced. The small red alga Conferva parasitica was described from the British Isles in 1762 and then reported from other parts of Europe. Conferva parasitica was traditionally included in the genus Pterosiphonia (type species P. cloiophylla in Schmitz and Falkenberg 1897), based on its morphological characters, and later transferred to Symphyocladia and finally to Symphyocladiella using molecular data from an Iberian specimen. However, although morphological differences have been observed between specimens of Symphyocladiella parasitica from northern and southern Europe they have yet to be investigated in a phylogenetic context. In this study, we collected specimens from both regions, studied their morphology and analyzed rbcL and cox1 DNA sequences. We determined the phylogenetic position of a British specimen using a phylogenomic approach based on mitochondrial and plastid genomes. Northern and southern European populations attributed to S. parasitica represent different species. Symphyocladiella arecina sp. nov. is proposed for specimens from southern Europe, but British specimens were resolved as a distant sister lineage to the morphologically distinctive Amplisiphonia, so we propose the new genus Deltalsia for this species. Our study highlights the relevance of using materials collected close to the type localities for taxonomic reassessments, and showcases the utility of genome-based phylogenies for resolving classification issues in the red algae.
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Affiliation(s)
- Pilar Díaz-Tapia
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
- Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de A Coruña, Paseo Marítimo Alcalde Francisco Vázquez, 10, 15001, A Coruña, Spain
| | - Iván Rodríguez-Buján
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
| | - Christine A Maggs
- Queen's University Marine Laboratory, Portaferry, Newtownards, BT22 1PF, UK
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Victoria, 3010, Australia
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Wetherbee R, Bringloe TT, van de Meene A, Andersen RA, Verbruggen H. Structure and formation of the perforated theca defining the Pelagophyceae (Heterokonta), and three new genera that substantiate the diverse nature of the class. JOURNAL OF PHYCOLOGY 2023; 59:126-151. [PMID: 36326615 DOI: 10.1111/jpy.13294] [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: 07/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The pelagophytes, a morphologically diverse class of marine heterokont algae, have been historically united only by DNA sequences. Recently we described a novel perforated theca (PT) encasing cells from the Pelagophyceae and hypothesized it may be the first morphological feature to define the class. Here we consolidate that observation, describing a PT for the first time in an additional seven pelagophyte genera, including three genera new to science. We established clonal cultures of pelagophytes collected from intertidal pools located around Australia, and established phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA and psbC gene sequences that led to the discovery of three new species: Wyeophycus julieharrissiae and Chromopallida australis form a distinct lineage along with Ankylochrysis lutea within the Pelagomonadales, while Pituiglomerulus capricornicus is sister genus to Chrysocystis fragilis in the Chrysocystaceae (Sarcinochrysidales). Using fixation by high-pressure freezing for electron microscope observations, a distinctive PT was observed in the three new genera described in this paper, as well as four genera not previously investigated: Chrysoreinhardia, Sargassococcus, Sungminbooa and Andersenia. The mechanism of PT formation is novel, being fabricated from rafts in Golgi-derived vesicles before being inserted into an established PT. Extracellular wall and/or mucilage layers assemble exterior to the PT in most pelagophytes, the materials likewise secreted by Golgi-derived vesicles, though the mechanism of secretion is novel. Secretory vesicles never fuse with the plasma membrane as in classic secretion and deposition, but rather relocate extracellularly beneath the PT and disintegrate, the contents having to pass through the PT prior to wall and/or mucilage synthesis. This study substantiates the diverse nature of pelagophytes, and provides further evidence that the PT is a sound morphological feature to define the Pelagophyceae, with all 14 of the 20 known genera studied to date by TEM possessing a PT.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Trevor T Bringloe
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Allison van de Meene
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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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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Phylotranscriptomic and Evolutionary Analyses of Oedogoniales (Chlorophyceae, Chlorophyta). DIVERSITY 2022. [DOI: 10.3390/d14030157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study determined the transcriptomes of eight Oedogoniales species, including six species from Oedogonium and two species from Oedocladium to conduct phylotranscriptomic and evolutionary analyses. 155,952 gene families and 192 single-copy orthogroups were detected. Phylotranscriptomic analyses based on single-copy orthogroups were conducted using supermatrix and coalescent-based approaches. The phylotranscriptomic analysis results revealed that Oedogonium is polyphyletic, and Oedocladium clustered with Oedogonium. Together with the transcriptomes of the OCC clade in the public database, the phylogenetic relationship of the three orders (Oedogoniales, Chaetophorales, Chaetopeltidales) is discussed. The non-synonymous (dN) to synonymous substitution (dS) ratios of single-copy orthogroups of the terrestrial Oedogoniales species using a branch model of phylogenetic analysis by maximum likelihood were estimated, which showed that 92 single-copy orthogroups were putative rapidly evolving genes. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses results revealed that some of the rapidly evolving genes were associated with photosynthesis, implying that terrestrial Oedogoniales species experienced rapid evolution to adapt to terrestrial habitats. The phylogenetic results combined with evolutionary analyses suggest that the terrestrialization process of Oedogoniales may have occured more than once.
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Fang J, Chen Y, Liu G, Verbruggen H, Zhu H. Chloroplast Genome Traits Correlate With Organismal Complexity and Ecological Traits in Chlorophyta. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.791166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A positive relationship between cell size and chloroplast genome size within chloroplast-bearing protists has been hypothesized in the past and shown in some case studies, but other factors influencing chloroplast genome size during the evolution of chlorophyte algae have been less studied. We study chloroplast genome size and GC content as a function of habitats and cell size of chlorophyte algae. The chloroplast genome size of green algae in freshwater, marine and terrestrial habitats was differed significantly, with terrestrial algae having larger chloroplast genome sizes in general. The most important contributor to these enlarged genomes in terrestrial species was the length of intergenic regions. There was no clear difference in the GC content of chloroplast genomes from the three habitats categories. Functional morphological categories also showed differences in chloroplast genome size, with filamentous algae having substantially larger genomes than other forms of algae, and foliose algae had lower GC content than other groups. Chloroplast genome size showed no significant differences among the classes Ulvophyceae, Trebouxiophyceae, and Chlorophyceae, but the GC content of Chlorophyceae chloroplast genomes was significantly lower than that of Ulvophyceae and Trebouxiophyceae. There was a certain positive relationship between chloroplast genome size and cell size for the Chlorophyta as a whole and within each of three major classes. Our data also confirmed previous reports that ancestral quadripartite architecture had been lost many times independently in Chlorophyta. Finally, the comparison of the phenotype of chlorophytes algae harboring plastids uncovered that most of the investigated Chlorophyta algae housed a single plastid per cell.
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Identification of polycistronic transcriptional units and non-canonical introns in green algal chloroplasts based on long-read RNA sequencing data. BMC Genomics 2021; 22:298. [PMID: 33892645 PMCID: PMC8063479 DOI: 10.1186/s12864-021-07598-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 04/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despite the architecture of chloroplast genome having been extensively studied in higher plants and several model species of algae, little is known about the transcriptional features of green algal chloroplast-encoded genes. RESULTS Based on full-length cDNA (Iso-Seq) sequencing, we identified widely co-transcribed polycistronic transcriptional units (PTUs) in the green alga Caulerpa lentillifera. In addition to clusters of genes from the same pathway, we identified a series of PTUs of up to nine genes whose function in the plastid is not understood. The RNA data further allowed us to confirm widespread expression of fragmented genes and conserved open reading frames, which are both important features in green algal chloroplast genomes. In addition, a newly fragmented gene specific to C. lentillifera was discovered, which may represent a recent gene fragmentation event in the chloroplast genome. With the newly annotated exon-intron boundary information, gene structural annotation was greatly improved across the siphonous green algae lineages. Our data also revealed a type of non-canonical Group II introns, with a deviant secondary structure and intronic ORFs lacking known splicing or mobility domains. These widespread introns have conserved positions in their genes and are excised precisely despite lacking clear consensus intron boundaries. CONCLUSION Our study fills important knowledge gaps in chloroplast genome organization and transcription in green algae, and provides new insights into expression of polycistronic transcripts, freestanding ORFs and fragmented genes in algal chloroplast genomes. Moreover, we revealed an unusual type of Group II intron with distinct features and conserved positions in Bryopsidales. Our data represents interesting additions to knowledge of chloroplast intron structure and highlights clusters of uncharacterized genes that probably play important roles in plastids.
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Wetherbee R, Bringloe TT, Costa JF, van de Meene A, Andersen RA, Verbruggen H. New pelagophytes show a novel mode of algal colony development and reveal a perforated theca that may define the class. JOURNAL OF PHYCOLOGY 2021; 57:396-411. [PMID: 32975327 DOI: 10.1111/jpy.13074] [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: 06/11/2020] [Revised: 07/20/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Pelagophytes (Heterokonta) are a morphologically diverse class of marine algae historically united only by DNA sequences. We established clonal cultures of sand-dwelling pelagophytes collected from intertidal pools around Australia. Phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA, and psbC sequences revealed two new genera, Gazia and Glomerochrysis, related to Aureoumbra in a distinct lineage within the Sarcinochrysidaceae (Pelagophyceae). The three new species (Gazia saundersii, Gazia australica, and Glomerochrysis psammophila), along with an Australian strain of Aureoumbra geitleri, are characterized by dominant benthic stages that differ significantly from one another, while occasionally producing classic heterokont zoospores. The benthic stage of Ga. saundersii has a novel development not observed in any other colonial alga, consisting of large, spherical colonies (up to 140 μm in diameter) containing c. 2,500 cells that eventually differentiate and segregate into a large number of daughter colonies that are subsequently liberated. Alternatively, colonies may differentiate into a mass of zoospores that escape and settle to develop into new colonies. In Gl. psammophila, cubic packets of cells form large sticky clusters that bind sand together, while Ga. australica and A. geitleri are unicellular species. Using fixation by high-pressure freezing, a distinctive perforated theca was observed by TEM in all genera of this lineage, and we hypothesize this unique covering may be the first morphological feature to characterize most, if not all, pelagophytes. This study substantiates the diverse nature of sand-dwelling pelagophytes as well as their mechanisms for thriving in a dynamic habitat.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Trevor T Bringloe
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Joana F Costa
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Allison van de Meene
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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12
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Iha C, Dougan KE, Varela JA, Avila V, Jackson CJ, Bogaert KA, Chen Y, Judd LM, Wick R, Holt KE, Pasella MM, Ricci F, Repetti SI, Medina M, Marcelino VR, Chan CX, Verbruggen H. Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Curr Biol 2021; 31:1393-1402.e5. [PMID: 33548192 DOI: 10.1016/j.cub.2021.01.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/21/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023]
Abstract
The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O2 availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium's adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allows it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching, and recovery.
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Affiliation(s)
- Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Katherine E Dougan
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, and APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Viridiana Avila
- Pennsylvania State University, University Park, PA 16802, USA
| | | | - Kenny A Bogaert
- Phycology Research Group, Ghent University, Krijgslaan 281 S8, 9000 Gent, Belgium
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia; London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Marisa M Pasella
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Francesco Ricci
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mónica Medina
- Pennsylvania State University, University Park, PA 16802, USA
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia.
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13
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Chen N, Sha LN, Wang YL, Yin LJ, Zhang Y, Wang Y, Wu DD, Kang HY, Zhang HQ, Zhou YH, Sun GL, Fan X. Variation in Plastome Sizes Accompanied by Evolutionary History in Monogenomic Triticeae (Poaceae: Triticeae). FRONTIERS IN PLANT SCIENCE 2021; 12:741063. [PMID: 34966398 PMCID: PMC8710740 DOI: 10.3389/fpls.2021.741063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/02/2021] [Indexed: 05/17/2023]
Abstract
To investigate the pattern of chloroplast genome variation in Triticeae, we comprehensively analyzed the indels in protein-coding genes and intergenic sequence, gene loss/pseudonization, intron variation, expansion/contraction in inverted repeat regions, and the relationship between sequence characteristics and chloroplast genome size in 34 monogenomic Triticeae plants. Ancestral genome reconstruction suggests that major length variations occurred in four-stem branches of monogenomic Triticeae followed by independent changes in each genus. It was shown that the chloroplast genome sizes of monogenomic Triticeae were highly variable. The chloroplast genome of Pseudoroegneria, Dasypyrum, Lophopyrum, Thinopyrum, Eremopyrum, Agropyron, Australopyrum, and Henradia in Triticeae had evolved toward size reduction largely because of pseudogenes elimination events and length deletion fragments in intergenic. The Aegilops/Triticum complex, Taeniatherum, Secale, Crithopsis, Herteranthelium, and Hordeum in Triticeae had a larger chloroplast genome size. The large size variation in major lineages and their subclades are most likely consequences of adaptive processes since these variations were significantly correlated with divergence time and historical climatic changes. We also found that several intergenic regions, such as petN-trnC and psbE-petL containing unique genetic information, which can be used as important tools to identify the maternal relationship among Triticeae species. Our results contribute to the novel knowledge of plastid genome evolution in Triticeae.
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Affiliation(s)
- Ning Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Li-Na Sha
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yi-Ling Wang
- College of Life Science, Shanxi Normal University, Shanxi, China
| | - Ling-Juan Yin
- Lijiang Nationality Secondary Specialized School, Lijiang, China
| | - Yue Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yi Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Dan-Dan Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hou-Yang Kang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hai-Qin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yong-Hong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Gen-Lou Sun
- Saint Mary’s University, Halifax, NS, Canada
- *Correspondence: Gen-Lou Sun,
| | - Xing Fan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xing Fan,
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14
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Massé A, Tribollet A, Meziane T, Bourguet-Kondracki ML, Yéprémian C, Sève C, Thiney N, Longeon A, Couté A, Domart-Coulon I. Functional diversity of microboring Ostreobium algae isolated from corals. Environ Microbiol 2020; 22:4825-4846. [PMID: 32990394 DOI: 10.1111/1462-2920.15256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 09/09/2020] [Accepted: 09/24/2020] [Indexed: 12/15/2022]
Abstract
The filamentous chlorophyte Ostreobium sp. dominates shallow marine carbonate microboring communities, and is one of the major agents of reef bioerosion. While its large genetic diversity has emerged, its physiology remains little known, with unexplored relationship between genotypes and phenotypes (endolithic versus free-living growth forms). Here, we isolated nine strains affiliated to two lineages of Ostreobium (>8% sequence divergence of the plastid gene rbcL), one of which was assigned to the family Odoaceae, from the fast-growing coral host Pocillopora acuta Lamarck 1816. Free-living isolates maintained their bioerosive potential, colonizing pre-bleached coral carbonate skeletons. We compared phenotypes, highlighting shifts in pigment and fatty acid compositions, carbon to nitrogen ratios and stable isotope compositions (δ13 C and δ15 N). Our data show a pattern of higher chlorophyll b and lower arachidonic acid (20:4ω6) content in endolithic versus free-living Ostreobium. Photosynthetic carbon fixation and nitrate uptake, quantified via 8 h pulse-labeling with 13 C-bicarbonate and 15 N-nitrate, showed lower isotopic enrichment in endolithic compared to free-living filaments. Our results highlight the functional plasticity of Ostreobium phenotypes. The isotope tracer approach opens the way to further study the biogeochemical cycling and trophic ecology of these cryptic algae at coral holobiont and reef scales.
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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, Paris, 75005, France.,IRD-Sorbonne Université (UPMC-CNRS-MNHN), Laboratoire IPSL-LOCEAN, 4 Place Jussieu, Tour 46-00, 5éme étage, Paris Cedex, 75005, France
| | - Aline Tribollet
- IRD-Sorbonne Université (UPMC-CNRS-MNHN), Laboratoire IPSL-LOCEAN, 4 Place Jussieu, Tour 46-00, 5éme étage, Paris Cedex, 75005, France
| | - Tarik Meziane
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle (MNHN), SU, UNICAEN, UA, CNRS (UMR7208), IRD; CP53, 61 rue Buffon, Paris, 75005, France
| | - Marie-Lise Bourguet-Kondracki
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Claude Yéprémian
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Charlotte Sève
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Najet Thiney
- Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle (MNHN), SU, UNICAEN, UA, CNRS (UMR7208), IRD; CP53, 61 rue Buffon, Paris, 75005, France
| | - Arlette Longeon
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Alain Couté
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
| | - Isabelle Domart-Coulon
- Molécules de Communication et Adaptation des Microorganismes (MCAM), Muséum national d'Histoire naturelle (MNHN), CNRS (UMR7245); CP54 63 Rue Buffon, Paris, 75005, France
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15
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Wu Z, Liao R, Yang T, Dong X, Lan D, Qin R, Liu H. Analysis of six chloroplast genomes provides insight into the evolution of Chrysosplenium (Saxifragaceae). BMC Genomics 2020; 21:621. [PMID: 32912155 PMCID: PMC7488271 DOI: 10.1186/s12864-020-07045-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/01/2020] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Chrysosplenium L. (Saxifragaceae) is a genus of plants widely distributed in Northern Hemisphere and usually found in moist, shaded valleys and mountain slopes. This genus is ideal for studying plant adaptation to low light conditions. Although some progress has been made in the systematics and biogeography of Chrysosplenium, its chloroplast genome evolution remains to be investigated. RESULTS To fill this gap, we sequenced the chloroplast genomes of six Chrysosplenium species and analyzed their genome structure, GC content, and nucleotide diversity. Moreover, we performed a phylogenetic analysis and calculated non-synonymous (Ka) /synonymous (Ks) substitution ratios using the combined protein-coding genes of 29 species within Saxifragales and two additional species as outgroups, as well as a pair-wise estimation for each gene within Chrysosplenium. Compared with the outgroups in Saxifragaceae, the six Chrysosplenium chloroplast genomes had lower GC contents; they also had conserved boundary regions and gene contents, as only the rpl32 gene was lost in four of the Chrysosplenium chloroplast genomes. Phylogenetic analyses suggested that the Chrysosplenium separated to two major clades (the opposite group and the alternate group). The selection pressure estimation (Ka/Ks ratios) of genes in the Chrysosplenium species showed that matK and ycf2 were subjected to positive selection. CONCLUSION This study provides genetic resources for exploring the phylogeny of Chrysosplenium and sheds light on plant adaptation to low light conditions. The lower average GC content and the lacking gene of rpl32 indicated selective pressure in their unique habitats. Different from results previously reported, our selective pressure estimation suggested that the genes related to photosynthesis (such as ycf2) were under positive selection at sites in the coding region.
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Affiliation(s)
- Zhihua Wu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Rui Liao
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Deqing Lan
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central University for Nationalities, Wuhan, 430074, Hubei, China.
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16
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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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17
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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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18
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Wetherbee R, Rossetto Marcelino V, Costa JF, Grant B, Crawford S, Waller RF, Andersen RA, Berry D, McFadden GI, Verbruggen H. A new marine prasinophyte genus alternates between a flagellate and a dominant benthic stage with microrhizoids for adhesion. JOURNAL OF PHYCOLOGY 2019; 55:1210-1225. [PMID: 31393007 DOI: 10.1111/jpy.12909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/13/2019] [Indexed: 06/10/2023]
Abstract
Prasinophytes (Chlorophyta) are a diverse, paraphyletic group of planktonic microalgae for which benthic species are largely unknown. Here, we report a sand-dwelling, marine prasinophyte with several novel features observed in clonal cultures established from numerous locations around Australia. The new genus and species, which we name Microrhizoidea pickettheapsiorum (Mamiellophyceae), alternates between a benthic palmelloid colony, where cell division occurs, and a planktonic flagellate. Flagellates are short lived, settle and quickly resorb their flagella, the basal bodies then nucleate novel tubular appendages, termed "microrhizoids", that lack an axoneme and function to anchor benthic cells to the substratum. To our knowledge, microrhizoids have not been observed in any other green alga or protist, are slightly smaller in diameter than flagella, generally contain nine microtubules, are long (3-5 times the length of flagella) and are not encased in scales. Following settlement, cell divisions result in a loose, palmelloid colony, each cell connected to the substratum by two microrhizoids. Flagellates are round to bean-shaped with two long, slightly uneven flagella. Both benthic cells and flagellates, along with their flagella, are encased in thin scales. Phylogenies based on the complete chloroplast genome of Microrhizoidea show that it is clearly a member of the Mamiellophyceae, most closely related to Dolichomastix tenuilepsis. More taxon-rich phylogenetic analyses of the 18S rRNA gene, including metabarcodes from the Tara Oceans and Ocean Sampling Day projects, confidently show the distinctive nature of Microrhizoidea, and that the described biodiversity of the Mamiellophyceae is a fraction of its real biodiversity. The discovery of a largely benthic prasinophyte changes our perspective on this group of algae and, along with the observation of other potential benthic lineages in environmental sequences, illustrates that benthic habitats can be a rich ground for algal biodiscovery.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Vanessa Rossetto Marcelino
- Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, 2145, Australia
| | - Joana F Costa
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brenna Grant
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Simon Crawford
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Drew Berry
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Geoffrey I McFadden
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
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19
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Morphological evolution and classification of the red algal order Ceramiales inferred using plastid phylogenomics. Mol Phylogenet Evol 2019; 137:76-85. [PMID: 31029748 DOI: 10.1016/j.ympev.2019.04.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 11/21/2022]
Abstract
The order Ceramiales contains about one third of red algal diversity and it was classically classified into four families according to morphology. The first phylogenies based on one or two molecular markers were poorly supported and failed to resolve these families as monophyletic. Nine families are currently recognized, but relationships within and among them are poorly understood. We produced a well-resolved phylogeny for the Ceramiales using plastid genomes for 80 (28 newly sequenced) representative species of the major lineages. Three of the previously recognized families were resolved as independent monophyletic lineages: Ceramiaceae, Wrangeliaceae and Rhodomelaceae. By contrast, our results indicated that the other six families require reclassification. We propose the new order Inkyuleeales, a new circumscription of the Callithamniaceae to include the Spyridiaceae, and a new concept of the Delesseriaceae that includes the Sarcomeniaceae and the Dasyaceae. We also investigated the evolution of the thallus structure, which has been important in the classical delineation of families. The ancestor of the Ceramiales was a monosiphonous filament that evolved into more complex morphologies several times independently during the evolutionary history of this hyperdiverse lineage.
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20
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Marcelino VR, Wille M, Hurt AC, González-Acuña D, Klaassen M, Schlub TE, Eden JS, Shi M, Iredell JR, Sorrell TC, Holmes EC. Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes. BMC Biol 2019; 17:31. [PMID: 30961590 PMCID: PMC6454771 DOI: 10.1186/s12915-019-0649-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Antibiotic resistance is rendering common bacterial infections untreatable. Wildlife can incorporate and disperse antibiotic-resistant bacteria in the environment, such as water systems, which in turn serve as reservoirs of resistance genes for human pathogens. Anthropogenic activity may contribute to the spread of bacterial resistance cycling through natural environments, including through the release of human waste, as sewage treatment only partially removes antibiotic-resistant bacteria. However, empirical data supporting these effects are currently limited. Here we used bulk RNA-sequencing (meta-transcriptomics) to assess the diversity and expression levels of functionally viable resistance genes in the gut microbiome of birds with aquatic habits in diverse locations. RESULTS We found antibiotic resistance genes in birds from all localities, from penguins in Antarctica to ducks in a wastewater treatment plant in Australia. Comparative analysis revealed that birds feeding at the wastewater treatment plant carried the greatest resistance gene burden, including genes typically associated with multidrug resistance plasmids as the aac(6)-Ib-cr gene. Differences in resistance gene burden also reflected aspects of bird ecology, taxonomy, and microbial function. Notably, ducks, which feed by dabbling, carried a higher abundance and diversity of resistance genes than turnstones, avocets, and penguins, which usually prey on more pristine waters. CONCLUSIONS These transcriptome data suggest that human waste, even if it undergoes treatment, might contribute to the spread of antibiotic resistance genes to the wild. Differences in microbiome functioning across different bird lineages may also play a role in the antibiotic resistance burden carried by wild birds. In summary, we reveal the complex factors explaining the distribution of resistance genes and their exchange routes between humans and wildlife, and show that meta-transcriptomics is a valuable tool to access functional resistance genes in whole microbial communities.
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Affiliation(s)
- Vanessa R Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia. .,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia. .,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Daniel González-Acuña
- Laboratorio de Parásitos y Enfermedades de Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad de Concepción, 3349001, Concepción, Chile
| | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3216, Australia
| | - Timothy E Schlub
- Faculty of Medicine and Health, Sydney School of Public Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia.,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jonathan R Iredell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,Westmead Institute for Medical Research, Westmead, NSW, 2145, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia.,School of Life & Environmental Sciences, Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
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21
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Cvetkovska M, Orgnero S, Hüner NPA, Smith DR. The enigmatic loss of light-independent chlorophyll biosynthesis from an Antarctic green alga in a light-limited environment. THE NEW PHYTOLOGIST 2019; 222:651-656. [PMID: 30506801 DOI: 10.1111/nph.15623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Marina Cvetkovska
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Shane Orgnero
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Norman P A Hüner
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7, Canada
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22
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Cremen MCM, Leliaert F, Marcelino VR, Verbruggen H. Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta). Genome Biol Evol 2018; 10:1048-1061. [PMID: 29635329 PMCID: PMC5888179 DOI: 10.1093/gbe/evy063] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 12/15/2022] Open
Abstract
Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales). We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogenetic methods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.
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Affiliation(s)
| | - Frederik Leliaert
- Botanic Garden Meise, 1860 Meise, Belgium.,Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Vanessa R Marcelino
- School of BioSciences, University of Melbourne, Parkville, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, New South Wales, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Australia
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23
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Cremen MCM, Leliaert F, West J, Lam DW, Shimada S, Lopez-Bautista JM, Verbruggen H. Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses. Mol Phylogenet Evol 2018; 130:397-405. [PMID: 30227214 DOI: 10.1016/j.ympev.2018.09.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/04/2018] [Accepted: 09/10/2018] [Indexed: 01/12/2023]
Abstract
The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders - Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. A new classification scheme is proposed, which includes the merger of the families Pseudocodiaceae, Rhipiliaceae and Udoteaceae into a more broadly circumscribed Halimedaceae, and the establishment of tribes for the different lineages found therein. In addition, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on our phylogeny.
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Affiliation(s)
- Ma Chiela M Cremen
- School of BioSciences, University of Melbourne, Parkville, 3010 Victoria, Australia.
| | - Frederik Leliaert
- Botanic Garden Meise, 1860 Meise, Belgium; Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - John West
- School of BioSciences, University of Melbourne, Parkville, 3010 Victoria, Australia
| | - Daryl W Lam
- Department of Biological Sciences, The University of Alabama, 35487 AL, USA
| | - Satoshi Shimada
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo 112-8610, Japan
| | | | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, 3010 Victoria, Australia
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24
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Zhang YJ, Zhu C, Ding Y, Yan ZW, Li GH, Lan Y, Wen JF, Chen B. Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton. BMC Genomics 2018; 19:469. [PMID: 29914356 PMCID: PMC6006717 DOI: 10.1186/s12864-018-4845-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/31/2018] [Indexed: 01/24/2023] Open
Abstract
Background Eukaryotic cells contain a huge variety of internally specialized subcellular compartments. Stoichiogenomics aims to reveal patterns of elements usage in biological macromolecules. However, the stoichiogenomic characteristics and how they adapt to various subcellular microenvironments are still unknown. Results Here we first updated the definition of stoichiogenomics. Then we applied it to subcellular research, and detected distinctive nitrogen content of nuclear and hydrogen, sulfur content of extracellular proteomes. Specially, we found that acidic amino acids (AAs) content of cytoskeletal proteins is the highest. The increased charged AAs are mainly caused by the eukaryotic originated cytoskeletal proteins. Functional subdivision of the cytoskeleton showed that activation, binding/association, and complexes are the three largest functional categories. Electrostatic interaction analysis showed an increased electrostatic interaction between both primary sequences and PPI interfaces of 3D structures, in the cytoskeleton. Conclusions This study creates a blueprint of subcellular stoichiogenomic characteristics, and explains that charged AAs of the cytoskeleton increased greatly in evolution, which offer material basis for the eukaryotic cytoskeletal proteins to act in two ways of electrostatic interactions, and further perform their activation, binding/association and complex formation. Electronic supplementary material The online version of this article (10.1186/s12864-018-4845-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Juan Zhang
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China
| | - Chengxu Zhu
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Yiran Ding
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Zheng-Wen Yan
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China
| | - Yang Lan
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China.
| | - Bin Chen
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China.
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25
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Zhang Z, An M, Miao J, Gu Z, Liu C, Zhong B. The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolution. BMC PLANT BIOLOGY 2018; 18:53. [PMID: 29614974 PMCID: PMC5883279 DOI: 10.1186/s12870-018-1273-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/27/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The ice alga Chlamydomonas sp. ICE-L is the main contributor to primary productivity in Antarctic sea ice ecosystems and is well adapted to the extremely harsh environment. However, the adaptive mechanism of Chlamydomonas sp. ICE-L to sea-ice environment remains unclear. To study the adaptive strategies in Chlamydomonas sp. ICE-L, we investigated the molecular evolution of chloroplast photosynthetic genes that are essential for the accumulation of carbohydrate and energy living in Antarctic sea ice. RESULTS The 60 chloroplast protein-coding genes of Chlamydomonas sp. ICE-L were obtained, and the branch-site test detected significant signatures of positive selection on atpB, psaB, and rbcL genes in Chlamydomonas sp. ICE-L associated with the photosynthetic machinery. These positively selected genes were further identified as being under convergent evolution between Chlamydomonas sp. ICE-L and the halotolerant alga Dunaliella salina. CONCLUSIONS Our study provides evidence that the phototrophic component of Chlamydomonas sp. ICE-L exhibits adaptive evolution under extreme environment. The positive Darwinian selection operates on the chloroplast protein-coding genes of Antarctic ice algae adapted to extreme environment following functional-specific and lineages-specific patterns. In addition, three positively selected genes with convergent substitutions in Chlamydomonas sp. ICE-L were identified, and the adaptive modifications in these genes were in functionally important regions of the proteins. Our study provides a foundation for future experiments on the biochemical and physiological impacts of photosynthetic genes in green algae.
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Affiliation(s)
- Zhenhua Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Meiling An
- Medical College, Qingdao University, Qingdao, China
| | - Jinlai Miao
- Medical College, Qingdao University, Qingdao, China
- Key Laboratory of Marine Bioactive Substance, The First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Zhiqiang Gu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Bojian Zhong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.
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26
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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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27
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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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28
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Díaz-Tapia P, Maggs CA, West JA, Verbruggen H. Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta). JOURNAL OF PHYCOLOGY 2017; 53:920-937. [PMID: 28561261 DOI: 10.1111/jpy.12553] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined). The majority of branches were resolved with full bootstrap support. We then added 266 rbcL, 125 18S rRNA gene and 143 cox1 sequences to construct a comprehensive phylogeny containing nearly half of all known species in the family (407 species in 89 genera). These analyses suggest the same subdivision into higher-level lineages, but included many branches with moderate or poor support. The circumscription for nine of the 13 previously described tribes was supported, but the Lophothalieae, Polysiphonieae, Pterosiphonieae and Herposiphonieae required revision, and five new tribes and one resurrected tribe were segregated from them. Rhizoid anatomy is highlighted as a key diagnostic character for the morphological delineation of several lineages. This work provides the most extensive phylogenetic analysis of the Rhodomelaceae to date and successfully resolves the relationships among major clades of the family. Our data show that organellar genomes obtained through high-throughput sequencing produce well-resolved phylogenies of difficult groups, and their more general application in algal systematics will likely permit deciphering questions about classification at many taxonomic levels.
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Affiliation(s)
- Pilar Díaz-Tapia
- Coastal Biology Research Group, Faculty of Sciences and Centre for Advanced Scientific Research (CICA), University of A Coruña, 15071, A Coruña, Spain
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Poole, Dorset, BH12 5BB, UK
| | - Christine A Maggs
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Poole, Dorset, BH12 5BB, UK
| | - John A West
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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29
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Marcelino VR, Morrow KM, Oppen MJH, Bourne DG, Verbruggen H. Diversity and stability of coral endolithic microbial communities at a naturally high
p
CO
2
reef. Mol Ecol 2017; 26:5344-5357. [DOI: 10.1111/mec.14268] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 12/15/2022]
Affiliation(s)
| | - Kathleen M. Morrow
- Department of Molecular, Cellular and Biomedical Sciences University of New Hampshire Durham NH USA
- Australian Institute of Marine Science Townsville Qld Australia
| | - Madeleine J. H. Oppen
- School of Biosciences University of Melbourne Melbourne Vic. Australia
- Australian Institute of Marine Science Townsville Qld Australia
| | - David G. Bourne
- Australian Institute of Marine Science Townsville Qld Australia
- College of Science and Engineering James Cook University Townville Qld Australia
| | - Heroen Verbruggen
- School of Biosciences University of Melbourne Melbourne Vic. Australia
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30
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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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31
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Rossetto Marcelino V, Verbruggen H. Reference datasets of tufA and UPA markers to identify algae in metabarcoding surveys. Data Brief 2017; 11:273-276. [PMID: 28243624 PMCID: PMC5320050 DOI: 10.1016/j.dib.2017.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/15/2017] [Accepted: 02/06/2017] [Indexed: 11/18/2022] Open
Abstract
The data presented here are related to the research article “Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae” (Marcelino and Verbruggen, 2016) [1]. Here we provide reference datasets of the elongation factor Tu (tufA) and the Universal Plastid Amplicon (UPA) markers in a format that is ready-to-use in the QIIME pipeline (Caporaso et al., 2010) [2]. In addition to sequences previously available in GenBank, we included newly discovered endolithic algae lineages using both amplicon sequencing (Marcelino and Verbruggen, 2016) [1] and chloroplast genome data (Marcelino et al., 2016; Verbruggen et al., in press) [3], [4]. We also provide a script to convert GenBank flatfiles into reference datasets that can be used with other markers. The tufA and UPA reference datasets are made publicly available here to facilitate biodiversity assessments of microalgal communities.
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Affiliation(s)
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia
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32
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Smith DR. Does Cell Size Impact Chloroplast Genome Size? FRONTIERS IN PLANT SCIENCE 2017; 8:2116. [PMID: 29312382 PMCID: PMC5735124 DOI: 10.3389/fpls.2017.02116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/28/2017] [Indexed: 05/11/2023]
Abstract
There is a strong positive relationship between nuclear genome size and cell size across the eukaryotic domain, but the cause and effect of this relationship is unclear. A positive coupling of cell size and DNA content has also been recorded for various bacteria, suggesting that, with some exceptions, this association might be universal throughout the tree of life. However, the link between cell size and genome size has not yet been thoroughly explored with respect to chloroplasts, or organelles as a whole, largely because of a lack data on cell morphology and organelle DNA content. Here, I speculate about a potential positive scaling of cell size and chloroplast genome size within different plastid-bearing protists, including ulvophyte, prasinophyte, and trebouxiophyte green algae. I provide examples in which large and small chloroplast DNAs occur alongside large and small cell sizes, respectively, as well as examples where this trend does not hold. Ultimately, I argue that a relationship between cellular architecture and organelle genome architecture is worth exploring, and encourage researchers to keep an open mind on this front.
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