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Zwonitzer KD, Tressel LG, Wu Z, Kan S, Broz AK, Mower JP, Ruhlman TA, Jansen RK, Sloan DB, Havird JC. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proc Natl Acad Sci U S A 2024; 121:e2317240121. [PMID: 38427600 DOI: 10.1073/pnas.2317240121] [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: 10/12/2023] [Accepted: 01/22/2024] [Indexed: 03/03/2024] Open
Abstract
Nuclear and organellar genomes can evolve at vastly different rates despite occupying the same cell. In most bilaterian animals, mitochondrial DNA (mtDNA) evolves faster than nuclear DNA, whereas this trend is generally reversed in plants. However, in some exceptional angiosperm clades, mtDNA substitution rates have increased up to 5,000-fold compared with closely related lineages. The mechanisms responsible for this acceleration are generally unknown. Because plants rely on homologous recombination to repair mtDNA damage, we hypothesized that mtDNA copy numbers may predict evolutionary rates, as lower copy numbers may provide fewer templates for such repair mechanisms. In support of this hypothesis, we found that copy number explains 47% of the variation in synonymous substitution rates of mtDNA across 60 diverse seed plant species representing ~300 million years of evolution. Copy number was also negatively correlated with mitogenome size, which may be a cause or consequence of mutation rate variation. Both relationships were unique to mtDNA and not observed in plastid DNA. These results suggest that homologous recombinational repair plays a role in driving mtDNA substitution rates in plants and may explain variation in mtDNA evolution more broadly across eukaryotes. Our findings also contribute to broader questions about the relationships between mutation rates, genome size, selection efficiency, and the drift-barrier hypothesis.
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Affiliation(s)
- Kendra D Zwonitzer
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Lydia G Tressel
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shenglong Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
- Marine College, Shandong University, Weihai 264209, China
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Tracey A Ruhlman
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
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Yang P, Guo K, Yang Y, Lyu M, Liu J, Li X, Feng Y. Phylogeny and genetic variations of the three genome compartments in haptophytes shed light on the rapid evolution of coccolithophores. Gene 2023; 887:147716. [PMID: 37604324 DOI: 10.1016/j.gene.2023.147716] [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: 04/14/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Haptophyte algae, including coccolithophores, play key roles in global carbon cycling and ecosystem. They exhibit exceptional morphological and functional diversity. However, their phylogeny is mostly based on short markers and genome researches are always limited to few species, hindering a better understanding about their evolution and diversification. In this study, by assembling 69 new plastid genomes, 65 new mitochondrial genomes, and 55 nuclear drafts, we systematically analyzed their genome variations and built the most comprehensive phylogenies in haptophytes and Noelaerhabdaceae, with the latter is the family of the model coccolithophore Emiliania huxleyi. The haptophyte genomes vary significantly in size, gene content, and structure. We detected phylogenetic incongruence of Prymnesiales between genome compartments. In Noelaerhabdaceae, by including Reticulofenestra sessilis and a proper outgroup, we found R. sessilis was not the basal taxon of this family. Noelaerhabdaceae strains have very similar genomic features and conserved sequences, but different gene content and dynamic structure. We speculate that was caused by DNA double-strand break repairs. Our results provide valuable genetic resources and new insights into the evolution of haptophytes, especially coccolithophores.
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Affiliation(s)
- Penghao Yang
- Fudan University, Shanghai 200433, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Kangning Guo
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yuqing Yang
- Fudan University, Shanghai 200433, China; Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin 300380, China
| | - Jingwen Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Xiaobo Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China
| | - Yanlei Feng
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310030, China; Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang 310024, China.
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3
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Roitman S, Rozenberg A, Lavy T, Brussaard CPD, Kleifeld O, Béjà O. Isolation and infection cycle of a polinton-like virus virophage in an abundant marine alga. Nat Microbiol 2023; 8:332-346. [PMID: 36702941 DOI: 10.1038/s41564-022-01305-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/13/2022] [Indexed: 01/27/2023]
Abstract
Virophages are small double stranded DNA (dsDNA) viruses that can only replicate in a host by co-infecting with another virus. Marine algae are commonly associated with virophage-like elements such as Polinton-like viruses (PLVs) that remain largely uncharacterized. Here we isolated a PLV that co-infects the alga Phaeocystis globosa with the Phaeocystis globosa virus-14T (PgV-14T), a close relative of the "Phaeocystis globosa virus-virophage" genomic sequence. We name this PLV 'Gezel-14T. Gezel is phylogenetically distinct from the Lavidaviridae family where all known virophages belong. Gezel-14T co-infection decreases the fitness of its viral host by reducing burst sizes of PgV-14T, yet insufficiently to spare the cellular host population. Genomic screens show Gezel-14T-like PLVs integrated into Phaeocystis genomes, suggesting that these widespread viruses are capable of integration into cellular host genomes. This system presents an opportunity to better understand the evolution of eukaryotic dsDNA viruses as well as the complex dynamics and implications of viral parasitism.
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Affiliation(s)
- Sheila Roitman
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Tali Lavy
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Corina P D Brussaard
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, The Netherlands
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Oded Kleifeld
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
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4
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Tilney CL, Hubbard KA. Expression of nuclear-encoded, haptophyte-derived ftsH genes support extremely rapid PSII repair and high-light photoacclimation in Karenia brevis (Dinophyceae). HARMFUL ALGAE 2022; 118:102295. [PMID: 36195421 DOI: 10.1016/j.hal.2022.102295] [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: 05/17/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 06/16/2023]
Abstract
Karenia brevis, a neurotoxic dinoflagellate that produces brevetoxins, is endemic to the Gulf of Mexico and can grow at high irradiances typical of surface waters found there. To build upon a growing number of studies addressing high-light tolerance in K. brevis, specific photobiology and molecular mechanisms underlying this capacity were evaluated in culture. Since photosystem II (PSII) repair cycle activity can be crucial to high light tolerance in plants and algae, the present study assessed this capacity in K. brevis and characterized the ftsH-like genes which are fundamental to this process. Compared with cultures grown in low-light, cultures grown in high-light showed a 65-fold increase in PSII photoinactivation, a ∼50-fold increase in PSII repair, enhanced nonphotochemical quenching (NPQ), and depressed Fv/Fm. Repair rates were among the fastest reported in phytoplankton. Publicly available K. brevis transcriptomes (MMETSP) were queried for ftsH-like sequences and refined with additional sequencing from two K. brevis strains. The genes were phylogenetically related to haptophyte orthologs, implicating acquisition during tertiary endosymbiosis. RT-qPCR of three of the four ftsH-like homologs revealed that poly-A tails predominated in all homologs, and that the most highly expressed homolog had a 5' splice leader and amino-acid motifs characteristic of chloroplast targeting, indicating nuclear encoding for this plastid-targeted gene. High-light cultures showed a ∼1.5-fold upregulation in mRNA expression of the thylakoid-associated genes. Overall, in conjunction with NPQ mechanisms, rapid PSII repair mediated by a haptophyte-derived ftsH prevents chronic photoinhibition in K. brevis. Our findings continue to build the case that high-light photobiology-supported by the acquisition and maintenance of tertiary endosymbiotic genes-is critical to the success of K. brevis in the Gulf of Mexico.
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Affiliation(s)
- Charles L Tilney
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA; Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, Québec, G5M 1L7, Canada.
| | - Katherine A Hubbard
- Fish and Wildlife Research Institute, Florida Fish and Wildlife Conservation Commission, St. Petersburg, FL, 33701, USA
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Fang J, Xu X, Chen Q, Lin A, Lin S, Lei W, Zhong C, Huang Y, He Y. The complete mitochondrial genome of Isochrysis galbana harbors a unique repeat structure and a specific trans-spliced cox1 gene. Front Microbiol 2022; 13:966219. [PMID: 36238593 PMCID: PMC9551565 DOI: 10.3389/fmicb.2022.966219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The haptophyte Isochrysis galbana is considered as a promising source for food supplements due to its rich fucoxanthin and polyunsaturated fatty acids content. Here, the I. galbana mitochondrial genome (mitogenome) was sequenced using a combination of Illumina and PacBio sequencing platforms. This 39,258 bp circular mitogenome has a total of 46 genes, including 20 protein-coding genes, 24 tRNA genes and two rRNA genes. A large block of repeats (~12.7 kb) was segregated in one region of the mitogenome, accounting for almost one third of the total size. A trans-spliced gene cox1 was first identified in I. galbana mitogenome and was verified by RNA-seq and DNA-seq data. The massive expansion of tandem repeat size and cis- to trans-splicing shift could be explained by the high mitogenome rearrangement rates in haptophytes. Strict SNP calling based on deep transcriptome sequencing data suggested the lack of RNA editing in both organelles in this species, consistent with previous studies in other algal lineages. To gain insight into haptophyte mitogenome evolution, a comparative analysis of mitogenomes within haptophytes and among eight main algal lineages was performed. A core gene set of 15 energy and metabolism genes is present in haptophyte mitogenomes, consisting of 1 cob, 3 cox, 7 nad, 2 atp and 2 ribosomal genes. Gene content and order was poorly conserved in this lineage. Haptophyte mitogenomes have lost many functional genes found in many other eukaryotes including rps/rpl, sdh, tat, secY genes, which make it contain the smallest gene set among all algal taxa. All these implied the rapid-evolving and more recently evolved mitogenomes of haptophytes compared to other algal lineages. The phylogenetic tree constructed by cox1 genes of 204 algal mitogenomes yielded well-resolved internal relationships, providing new evidence for red-lineages that contained plastids of red algal secondary endosymbiotic origin. This newly assembled mitogenome will add to our knowledge of general trends in algal mitogenome evolution within haptophytes and among different algal taxa.
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Affiliation(s)
- Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
- *Correspondence: Jingping Fang,
| | - Xiuming Xu
- College of Life Science, Fujian Normal University, Fuzhou, China
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Xiuming Xu,
| | - Qinchang Chen
- College of Life Science, Fujian Normal University, Fuzhou, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
| | - Aiting Lin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Wen Lei
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Cairong Zhong
- College of Life Science, Fujian Normal University, Fuzhou, China
- Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, China
| | - Yongji Huang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Yongjin He
- College of Life Science, Fujian Normal University, Fuzhou, China
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6
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ddRAD Sequencing-Based Scanning of Genetic Variants in Sargassum fusiforme. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10070958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Sargassum fusiforme is a commercially important brown seaweed that has experienced significant population reduction both from heavy exploitation and degradation of the environment. Cultivated breed strains are also in a state of population mixing. These population stressors make it necessary to investigate the population genetics to discover best practices to conserve and breed this seaweed. In this study, the genetic diversity and population structure of S. fusiforme were investigated by the genome-wide SNP data acquired from double digest restriction site-associated DNA sequencing (ddRAD-seq). We found a low genetic diversity and a slight population differentiation within and between wild and cultivated populations, and the effective population size of S. fusiforme had experienced a continuous decline. Tajima’s D analysis showed the population contraction in wild populations may be related to copper pollution which showed a consistent trend with the increase of the sea surface temperature. The potential selection signatures may change the timing or level of gene expression, and further experiments are needed to investigate the effect of the mutation on relevant pathways. These results suggest an urgent need to manage and conserve S. fusiforme resources and biodiversity considering the accelerating change of the environment.
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Liang Y, Choi HG, Zhang S, Hu ZM, Duan D. The organellar genomes of Silvetia siliquosa (Fucales, Phaeophyceae) and comparative analyses of the brown algae. PLoS One 2022; 17:e0269631. [PMID: 35709195 PMCID: PMC9202911 DOI: 10.1371/journal.pone.0269631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/24/2022] [Indexed: 11/18/2022] Open
Abstract
The brown alga Silvetia siliquosa (Tseng et Chang) Serrão, Cho, Boo & Brawly is endemic to the Yellow-Bohai Sea and southwestern Korea. It is increasingly endangered due to habitat loss and excessive collection. Here, we sequenced the mitochondrial (mt) and chloroplast (cp) genomes of S. siliquosa. De novo assembly showed that the mt-genome was 36,036 bp in length, including 38 protein-coding genes (PCGs), 26 tRNAs, and 3 rRNAs, and the cp-genome was 124,991 bp in length, containing 139 PCGs, 28 tRNAs, and 6 rRNAs. Gene composition, gene number, and gene order of the mt-genome and cp-genome were very similar to those of other species in Fucales. Phylogenetic analysis revealed a close genetic relationship between S. siliquosa and F. vesiculosus, which diverged approximately 8 Mya (5.7-11.0 Mya), corresponding to the Late Miocene (5.3-11.6 Ma). The synonymous substitution rate of mitochondrial genes of phaeophycean species was 1.4 times higher than that of chloroplast genes, but the cp-genomes were more structurally variable than the mt-genomes, with numerous gene losses and rearrangements among the different orders in Phaeophyceae. This study reports the mt- and cp-genomes of the endangered S. siliquosa and improves our understanding of its phylogenetic position in Phaeophyceae and of organellar genomic evolution in brown algae.
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Affiliation(s)
- Yanshuo Liang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Han-Gil Choi
- Faculty of Biological Science and Institute for Environmental Science, Wonkwang University, Iksan, Korea
| | - Shuangshuang Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zi-Min Hu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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8
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Gibson K, Song H, Chen N. Metabarcoding analysis of microbiome dynamics during a Phaeocystis globosa bloom in the Beibu Gulf, China. HARMFUL ALGAE 2022; 114:102217. [PMID: 35550291 DOI: 10.1016/j.hal.2022.102217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 06/15/2023]
Abstract
Phaeocystis globosa is an ecologically important haptophyte that can form harmful algal blooms (HABs). In this study, we used 16S rDNA V3-V4 amplicon sequencing data to explore the ecological mechanisms underlying a P. globosa bloom in the Beibu Gulf, China. Using field samples collected from three time points of a bloom, we observed a distinct succession in the bacteria, archaea and phytoplankton community composition throughout the bloom. We also observed temporal variation in response to the bloom at the nucleotide level, which supports a previously underappreciated amount of intragroup variation in the niches taken up by microbes during HABs. We developed a preliminary model for the development and progression of the P. globosa bloom using the spatial-temporal dynamics of P. globosa and the bacteria, archaea, phytoplankton and environmental variables. We also identified microbes with putative interactions with P. globosa during the bloom by identifying microbes correlated with P. globosa in interaction networks, identifying particle-associated microbes and exploring the P. globosa colony microbiome using sequences from whole P. globosa colonies collected during the bloom. This study revealed novel insight into the development of P. globosa HABs and many testable hypotheses that will guide future research on the mechanisms of P. globosa HABs.
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Affiliation(s)
- Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada
| | - Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.
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9
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Liu S, Wang Y, Xu Q, Zhang M, Chen N. Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation. BMC Genomics 2021; 22:746. [PMID: 34654361 PMCID: PMC8520197 DOI: 10.1186/s12864-021-07999-z] [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: 03/06/2021] [Accepted: 09/03/2021] [Indexed: 12/05/2022] Open
Abstract
Background Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as “super barcode” in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi. Results In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya. Conclusions The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07999-z.
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Affiliation(s)
- Shuya Liu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yichao Wang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Qing Xu
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjia Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.,University of Chinese Academy of Sciences, Beijing, 10039, China
| | - Nansheng Chen
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 266071, Qingdao, China. .,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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10
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Mmonwa KL, Barker NP, McQuaid CD, Teske PR. Coastal dunefields maintain pre-Holocene genetic structure in a rocky shore red alga. JOURNAL OF PHYCOLOGY 2021; 57:1542-1553. [PMID: 33982309 DOI: 10.1111/jpy.13182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 04/20/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Most intertidal algae have limited dispersal potential, and areas that lack hard substratum suitable for attachment are thus expected to isolate regional populations from each other. Here, we used nuclear and mitochondrial genetic data to compare genetic structure in two co-distributed intertidal red algae with different dispersal potential along the South African coastline. Gelidium pristoides is divided into a south-eastern and a south-western evolutionary lineage separated by extensive, continuous sandy shoreline habitat adjacent to coastal dunefields. In contrast, Hypnea spicifera is genetically homogeneous throughout its range. In G. pristoides, the genetic breaks are associated with contemporary coastal dunefields. The age of the divergence event suggests that this may reflect the effect of older dispersal barriers, and that genetic structure was subsequently maintained by the formation of contemporary coastal dunefields.
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Affiliation(s)
- Kolobe Lucas Mmonwa
- Research and Monitoring, KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa
| | - Nigel Paul Barker
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, South Africa
| | - Christopher David McQuaid
- Coastal Research Group, Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Peter Rodja Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
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11
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Paudel YP, Hu Z, Khatiwada JR, Fan L, Pradhan S, Liu B, Qin W. Chloroplast genome analysis of Chrysotila dentata. Gene 2021; 804:145871. [PMID: 34363887 DOI: 10.1016/j.gene.2021.145871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022]
Abstract
Chrysotila dentata is an ecologically important marine alga contributing to the coccolith formation. In this study, a complete chloroplast (cp DNA) genome of Chrysotila dentata was sequenced by using Illumina Hiseq and was analyzed with the help of a bioinformatics tool CPGAVAS2. The circular chloroplast genome of Chrysotila dentata has a size of 109,017 bp with two inverted repeats (IRs) regions (4513 bp each) which is a common feature in most land plants and algal species. The Chrysotila dentata cp genome consists of 61 identified protein-coding genes, 30 tRNA genes and 6 rRNAs with 21 microsatellites. The phylogenetic relationship with other select algal species revealed a close phylogeny of Chrysotila dentata with Phaeocystis antarctica. This is the first report of the cp genome analysis of genus Chrysotila and the results from this study will be helpful for understanding the genetic structure and function of chloroplast in other species of Chrysotila.
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Affiliation(s)
- Yagya Prasad Paudel
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada; Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Zixuan Hu
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Janak Raj Khatiwada
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Lu Fan
- School of Civil Engineering, Architecture and Environment, Hubei University of Technology, Wuhan 430068, China
| | - Shreeti Pradhan
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, ON P7B 5E1, Canada.
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12
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Song H, Chen Y, Liu F, Chen N. Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications. Front Microbiol 2021; 12:676447. [PMID: 34276607 PMCID: PMC8283788 DOI: 10.3389/fmicb.2021.676447] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/31/2021] [Indexed: 01/04/2023] Open
Abstract
The haptophyte Phaeocystis globosa is a well-known species for its pivotal role in global carbon and sulfur cycles and for its capability of forming harmful algal blooms (HABs) with serious ecological consequences. Its mitochondrial genome (mtDNA) sequence has been reported in 2014 but it remains incomplete due to its long repeat sequences. In this study, we constructed the first full-length mtDNA of P. globosa, which was a circular genome with a size of 43,585 bp by applying the PacBio single molecular sequencing method. The mtDNA of this P. globosa strain (CNS00066), which was isolated from the Beibu Gulf, China, encoded 19 protein-coding genes (PCGs), 25 tRNA genes, and two rRNA genes. It contained two large repeat regions of 6.7 kb and ∼14.0 kb in length, respectively. The combined length of these two repeat regions, which were missing from the previous mtDNA assembly, accounted for almost half of the entire mtDNA and represented the longest repeat region among all sequenced haptophyte mtDNAs. In this study, we tested the hypothesis that repeat unit amplification is a driving force for different mtDNA sizes. Comparative analysis of mtDNAs of five additional P. globosa strains (four strains obtained in this study, and one strain previously published) revealed that all six mtDNAs shared identical numbers of genes but with dramatically different repeat regions. A homologous repeat unit was identified but with hugely different numbers of copies in all P. globosa strains. Thus, repeat amplification may represent an important driving force of mtDNA evolution in P. globosa.
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Affiliation(s)
- Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,School of Earth and Planetary, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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13
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Song H, Chen Y, Gibson K, Liu S, Yu Z, Chen N. High genetic diversity of the harmful algal bloom species Phaeocystis globosa revealed using the molecular marker COX1. HARMFUL ALGAE 2021; 107:102065. [PMID: 34456022 DOI: 10.1016/j.hal.2021.102065] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 06/13/2023]
Abstract
Accumulating evidence indicates that the haptophyte species Phaeocystis globosa, which plays an important role in climate control and may cause harmful algal blooms (HABs), displays a rich genetic diversity that may be responsible for differences in colonial sizes, different toxicity during blooms, and differential optimum growth temperature. In this project, we demonstrated that COX1 can be used as an effective molecular marker for its low intra-genome variations and high resolution in differentiating different P. globosa strains. Analyzing 57 P. globosa strains and seven field samples revealed high P. globosa genetic diversity with at least seven distinct clades. This study not only demonstrated for the first time that the common molecular marker COX1 can be used for differentiating P. globosa strains with high-resolution, and for tracking dynamics of different P. globosa strains during bloom development, but also revealed that P. globosa had high genetic diversity in the field.
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Affiliation(s)
- Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 10049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kate Gibson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, BC, Canada
| | - Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 10049, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, BC, Canada.
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14
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Wang X, Song H, Wang Y, Chen N. Research on the biology and ecology of the harmful algal bloom species Phaeocystis globosa in China: Progresses in the last 20 years. HARMFUL ALGAE 2021; 107:102057. [PMID: 34456018 DOI: 10.1016/j.hal.2021.102057] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/09/2021] [Accepted: 05/22/2021] [Indexed: 06/13/2023]
Abstract
Chinese researchers have made substantial progresses in research on the harmful algal bloom (HAB) species Phaeocystis globosa since the first P. globosa bloom outbreak in the Chinese coastal waters in 1997. However, as many results, especially the earlier ones, were published in non-English literature, much of the research on P. globosa biology, ecology, and biogeochemistry made by Chinese researchers have been unknown to colleagues from other countries. We review current knowledge on taxonomy, morphology, genetics, physiology, survival strategies and mitigation of P. globosa gained by Chinese researchers from the past two decades. P. globosa is the only Phaeocystis species that causes blooms in the Chinese waters, although other Phaeocystis species including P. jahnii and P. cordata have been detected in Chinese coastal regions. P. globosa has a complex life history with at least two morphotypes including a haploid flagellate and a diploid colonial cell. Colonial P. globosa blooms typically occur in winter after a diatom bloom in coastal waters of the South China Sea. P. globosa in Chinese coastal waters usually has extremely large colonial sizes, up to 3 cm in diameter, an order of magnitude greater than that observed in European coastal waters. The development of giant colonies is associated with enhanced sinking rate, limited nutrient diffusion, as well as decreased stability of colonies. The Chinese P. globosa strains also showed strong genetic diversity and physiological plasticity, being able to grow and develop into colonies at higher temperature and irradiance relative to that in European waters. High genetic diversity of P. globosa was revealed by developing high-resolution and high-specificity molecular markers including Phaeocystis globosa chloroplast 1 (pgcp1). Due to the severe impact of P. globosa on ecology and economy, much effort has been made to mitigate P. globosa blooms including the application of modified clays. Overall, P. globosa in the Chinese waters demonstrate unique genetic, phenotypical and physiological features that differ from P. globosa in other ocean regions. Further studies are needed to explore how environmental factors trigger the occurrence of P. globosa blooms and ascertain the impact of P. globosa blooms on the environment.
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Affiliation(s)
- Xiaodong Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yan Wang
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby V5A 1S6, British Columbia, Canada.
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15
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Plastid genomes and phylogenomics of liverworts (Marchantiophyta): Conserved genome structure but highest relative plastid substitution rate in land plants. Mol Phylogenet Evol 2021; 161:107171. [PMID: 33798674 DOI: 10.1016/j.ympev.2021.107171] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 01/04/2023]
Abstract
With some 7300 species of small nonvascular spore-producing plants, liverworts represent one of the major lineages of land plants. Although multi-locus molecular phylogenetic studies have elucidated relationships of liverworts at different taxonomic categories, the backbone phylogeny of liverworts is still to be fully resolved, especially for the placement of Ptilidiales and the relationships within Jungermanniales and Marchantiales. Here, we provided phylogenomic inferences of liverworts based on 42 newly sequenced and 24 published liverwort plastid genomes representing all but two orders of liverworts, and characterized the evolution of the plastome in liverworts. The structure of the plastid genome is overall conserved across the phylogeny of liverworts, with only two structural variants detected from simple thalloids, besides 18 out of 43 liverwort genera showing intron variations in their plastomes. Complex thalloid liverworts maintain the most plastid genes, and seem to undergo fewer gene deletions and pseudogenization events than other liverworts. Plastid phylogenetic inferences yielded mostly robustly supported relationships, and consistently resolved Ptilidiales as the sister to Porellales. The relative ratio of silent substitutions across the three genetic compartments (i.e., 1:15:10, for mitochondrial:plastid:nuclear) suggests that liverwort plastid genes have the potential to evolve faster than their nuclear counterparts, unlike in any other major land plant lineages where the mutation rate of nuclear genes overwhelm those of their plastid and mitochondrial counterparts.
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16
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Zhang M, Cui Z, Liu F, Chen N. Definition of a High-Resolution Molecular Marker for Tracking the Genetic Diversity of the Harmful Algal Species Eucampia zodiacus Through Comparative Analysis of Mitochondrial Genomes. Front Microbiol 2021; 12:631144. [PMID: 33841358 PMCID: PMC8024477 DOI: 10.3389/fmicb.2021.631144] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
The cosmopolitan phytoplankton species Eucampia zodiacus is a common harmful algal bloom (HAB) species that have been found to cause HABs in essentially all coastal regions except the Polar regions. However, molecular information for this HAB species is limited with only a few molecular markers. In this project, we constructed the mitochondrial genome (mtDNA) of E. zodiacus, which was also the first mtDNA constructed for any species in the order Hemiaulales that includes 145 reported species (including two additional HAB species Cerataulina bicornis and Cerataulina pelagica). Comparative analysis of eight E. zodiacus strains revealed that they could not be distinguished using common molecular markers, suggesting that common molecular markers do not have adequate resolution for distinguishing E. zodiacus strains. However, these E. zodiacus strains could be distinguished using whole mtDNAs, suggesting the presence of different genotypes due to evolutionary divergence. Through comparative analysis of the mtDNAs of multiple E. zodiacus strains, we identified a new molecular marker ezmt1 that could adequately distinguish different E. zodiacus strains isolated in various coastal regions in China. This molecular marker ezmt1, which was ∼400 bp in size, could be applied to identify causative genotypes during E. zodiacus HABs through tracking the dynamic changes of genetic diversity of E. zodiacus in HABs.
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Affiliation(s)
- Mengjia Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Zongmei Cui
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Oceanology, University of Chinese Academy of Sciences, Beijing, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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17
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Song H, Liu F, Li Z, Xu Q, Chen Y, Yu Z, Chen N. Development of a high-resolution molecular marker for tracking Phaeocystis globosa genetic diversity through comparative analysis of chloroplast genomes. HARMFUL ALGAE 2020; 99:101911. [PMID: 33218437 DOI: 10.1016/j.hal.2020.101911] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/28/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
The phytoplankton Phaeocystis globosa thrives in a wide range of marine regions and plays an important role in climate control. It can also form harmful algal blooms (HABs) that threaten environments and impact important coastal infrastructures. Mechanisms underlying the formation of P. globosa blooms still remain poorly understood. Accumulating evidence suggests that P. globosa has high genetic diversity and different P. globosa strains may have differential contributions to the development of P. globosa blooms. However, due to the lack of molecular markers with adequate resolution for distinguishing P. globosa genetic diversity, such differential contributions by different P. globosa strains could not be accurately ascertained. As such, high-resolution molecular markers need to be developed and applied to distinguish P. globosa genetic diversity. In this study, we undertook to define high-resolution molecular marker by assembling and comparing the whole chloroplast genomes of P. globosa strains isolated from different regions of the world. Through comparative analysis of P. globosa cpDNAs and detection of single nucleotide variations (SNVs), a molecular marker pgcp1 with improved resolution was developed. The pgcp1 demonstrated the highest resolution compared with other regions including 18S rDNA V4 region, 28S rDNA D1-D2 region and rbcL region, through genetic distance and phylogenetic analysis of 13 P. globosa strains. Molecular analysis of environmental samples and strains collected in multiple expeditions from a wide range of ocean regions including multiple regions in China, Vietnam, Thailand and Western Pacific using pgcp1 as the molecular marker displayed high genetic diversity of P. globosa with at least four major P. globosa clades. In conclusion, we have developed pgcp1 as a high-resolution molecular marker for the harmful algal bloom species P. globosa, which can be used to track intra-species genetic diversity and dynamics of P. globosa during bloom development.
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Affiliation(s)
- Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zelin Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Ocean University of China, Qingdao 266100, China
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiming Yu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada.
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18
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Fang J, Lin A, Yuan X, Chen Y, He W, Huang J, Zhang X, Lin G, Zhang J, Xue T. The complete chloroplast genome of Isochrysis galbana and comparison with related haptophyte species. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101989] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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19
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Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC PLANT BIOLOGY 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
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Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
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20
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Rizkallah MR, Frickenhaus S, Trimborn S, Harms L, Moustafa A, Benes V, Gäbler-Schwarz S, Beszteri S. Deciphering Patterns of Adaptation and Acclimation in the Transcriptome of Phaeocystis antarctica to Changing Iron Conditions 1. JOURNAL OF PHYCOLOGY 2020; 56:747-760. [PMID: 32068264 DOI: 10.1111/jpy.12979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 01/21/2020] [Indexed: 06/10/2023]
Abstract
The haptophyte Phaeocystis antarctica is endemic to the Southern Ocean, where iron supply is sporadic and its availability limits primary production. In iron fertilization experiments, P. antarctica showed a prompt and steady increase in cell abundance compared to heavily silicified diatoms along with enhanced colony formation. Here we utilized a transcriptomic approach to investigate molecular responses to alleviation of iron limitation in P. antarctica. We analyzed the transcriptomic response before and after (14 h, 24 h and 72 h) iron addition to a low-iron acclimated culture. After iron addition, we observed indicators of a quick reorganization of cellular energetics, from carbohydrate catabolism and mitochondrial energy production to anabolism. In addition to typical substitution responses from an iron-economic toward an iron-sufficient state for flavodoxin (ferredoxin) and plastocyanin (cytochrome c6 ), we found other genes utilizing the same strategy involved in nitrogen assimilation and fatty acid desaturation. Our results shed light on a number of adaptive mechanisms that P. antarctica uses under low iron, including the utilization of a Cu-dependent ferric reductase system and indication of mixotrophic growth. The gene expression patterns underpin P. antarctica as a quick responder to iron addition.
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Affiliation(s)
| | - Stephan Frickenhaus
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Centre for Industrial Mathematics, University of Bremen, Bibliothekstrasse 1, 28359 Postfach 330440, 28334, Bremen, Germany
| | - Scarlett Trimborn
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Department of Marine Botany, University of Bremen, Bibliothekstrasse 1, 28359 Postfach 330440, 28334, Bremen, Germany
| | - Lars Harms
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Herrstrasse 231, 26129, Oldenburg, Germany
| | - Ahmed Moustafa
- Department of Biology, American University in Cairo, P.O. Box 74, 11835, Cairo, Egypt
| | - Vladimir Benes
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Steffi Gäbler-Schwarz
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Sara Beszteri
- Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
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21
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Hu Y, Xing W, Hu Z, Liu G. Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes. Genes (Basel) 2020; 11:genes11010115. [PMID: 31968709 PMCID: PMC7016891 DOI: 10.3390/genes11010115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 01/30/2023] Open
Abstract
We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.
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Affiliation(s)
- Yuxin Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyue Xing
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence: ; Tel.: +86-027-6878-0576
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Hovde BT, Deodato CR, Andersen RA, Starkenburg SR, Barlow SB, Cattolico RA. Chrysochromulina: Genomic assessment and taxonomic diagnosis of the type species for an oleaginous algal clade. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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23
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Qi X, Kuo LY, Guo C, Li H, Li Z, Qi J, Wang L, Hu Y, Xiang J, Zhang C, Guo J, Huang CH, Ma H. A well-resolved fern nuclear phylogeny reveals the evolution history of numerous transcription factor families. Mol Phylogenet Evol 2018; 127:961-977. [PMID: 29981932 DOI: 10.1016/j.ympev.2018.06.043] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/27/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
Ferns account for 80% of nonflowering vascular plant species and are the sister lineage of seed plants. Recent molecular phylogenetics have greatly advanced understanding of fern tree of life, but relationships among some major lineages remain unclear. To better resolve the phylogenetic relationships of ferns, we generated transcriptomes from 125 ferns and two lycophytes, with three additional public datasets, to represent all 11 orders and 85% of families of ferns. Our nuclear phylogeny provides strong supports for the monophyly of all four subclasses and nearly all orders and families, and for relationships among these lineages. The only exception is Gleicheniales, which was highly supported as being paraphyletic with Dipteridaceae sister to a clade with Gleicheniaceae + Hymenophyllales. In addition, new and strongly supported phylogenetic relationships are found for suborders and families in Polypodiales. We provide the first dated fern phylogenomic tree using many nuclear genes from a large majority of families, with an estimate for separation of the ancestors of ferns and seed plants in early Devonian at ∼400 Mya and subsequent gradual divergences of fern orders from ∼380 to 200 Mya. Moreover, the newly obtained fern phylogeny provides a framework for gene family analyses, which indicate that the vast majority of transcription factor families found in seed plants were already present in the common ancestor of extant vascular plants. In addition, fern transcription factor genes show similar duplication patterns to those in seed plants, with some showing stable copy number and others displaying independent expansions in both ferns and seed plants. This study provides a robust phylogenetic and gene family evolution framework, as well as rich molecular resources for understanding the morphological and functional evolution in ferns.
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Affiliation(s)
- Xinping Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | | | - Chunce Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Hao Li
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Zhongyang Li
- College of Life and Environmental Sciences, Gannan Normal University, Ganzhou, Jiangxi 341000, China
| | - Ji Qi
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Linbo Wang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianying Xiang
- College of Biodiversity Conservation and Utilization, Southwest Forestry University, 300 Bailong Road, Kunming 650224, China
| | - Caifei Zhang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, Center for Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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Spalink D, Stoffel K, Walden GK, Hulse-Kemp AM, Hill TA, Van Deynze A, Bohs L. Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae). Mol Phylogenet Evol 2018; 126:293-302. [PMID: 29702214 DOI: 10.1016/j.ympev.2018.04.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 04/20/2018] [Accepted: 04/20/2018] [Indexed: 11/17/2022]
Abstract
The integration of genomics and phylogenetics allows new insight into the structure of gene tree discordance, the relationships among gene position, gene history, and rate of evolution, as well as the correspondence of gene function, positive selection, and gene ontology enrichment across lineages. We explore these issues using the tribe Capsiceae (Solanaceae), which is comprised of the genera Lycianthes and Capsicum (peppers). In combining the annotated genomes of Capsicum with newly sequenced transcriptomes of four species of Lycianthes and Capsicum, we develop phylogenies for 6747 genes, and construct a backbone species tree using both concordance and explicit phylogenetic network approaches. We quantify phylogenetic discordance among individual gene trees, measure their rates of synonymous and nonsynonymous substitution, and test whether they were positively selected along any branch of the phylogeny. We then map these genes onto the annotated Capsicum genome and test whether rates of evolution, gene history, and gene ontology vary significantly with gene position. We observed substantial discordance among gene trees. A bifurcating species tree placing Capsicum within a paraphyletic Lycianthes was supported over all phylogenetic networks. Rates of synonymous and nonsynonymous substitution varied 41-fold and 130-fold among genes, respectively, and were significantly lower in pericentromeric regions. We found that results of concordance tree analyses vary depending on the subset of genes used, and that genes within the pericentromeric regions only capture a portion of the observed discordance. We identified 787 genes that have been positively selected throughout the diversification history of Capsiceae, and discuss the importance of these genes as targets for investigation of economically important traits in the domesticated peppers.
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Affiliation(s)
- Daniel Spalink
- Department of Biology, University of Utah, Salt Lake City, UT, USA.
| | - Kevin Stoffel
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Genevieve K Walden
- Department of Biology, University of Utah, Salt Lake City, UT, USA; Plant Pest Diagnostics Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832-1448 USA
| | - Amanda M Hulse-Kemp
- Department of Plant Sciences, University of California, Davis, CA, USA; USDA-ARS, Genomics and Bioinformatics Research Unit, Raleigh, NC, USA
| | - Theresa A Hill
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Lynn Bohs
- Department of Biology, University of Utah, Salt Lake City, UT, USA
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Kim JI, Yoon HS, Yi G, Shin W, Archibald JM. Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements. BMC Genomics 2018; 19:275. [PMID: 29678149 PMCID: PMC5910586 DOI: 10.1186/s12864-018-4626-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cryptophytes are an ecologically important group of algae comprised of phototrophic, heterotrophic and osmotrophic species. This lineage is of great interest to evolutionary biologists because their plastids are of red algal secondary endosymbiotic origin. Cryptophytes have a clear phylogenetic affinity to heterotrophic eukaryotes and possess four genomes: host-derived nuclear and mitochondrial genomes, and plastid and nucleomorph genomes of endosymbiotic origin. RESULTS To gain insight into cryptophyte mitochondrial genome evolution, we sequenced the mitochondrial DNAs of five species and performed a comparative analysis of seven genomes from the following cryptophyte genera: Chroomonas, Cryptomonas, Hemiselmis, Proteomonas, Rhodomonas, Storeatula and Teleaulax. The mitochondrial genomes were similar in terms of their general architecture, gene content and presence of a large repeat region. However, gene order was poorly conserved. Characteristic features of cryptophyte mtDNAs included large syntenic clusters resembling α-proteobacterial operons that encode bacteria-like rRNAs, tRNAs, and ribosomal protein genes. The cryptophyte mitochondrial genomes retain almost all genes found in many other eukaryotes including the nad, sdh, cox, cob, and atp genes, with the exception of sdh2 and atp3. In addition, gene cluster analysis showed that cryptophytes possess a gene order closely resembling the jakobid flagellates Jakoba and Reclinomonas. Interestingly, the cox1 gene of R. salina, T. amphioxeia, and Storeatula species was found to contain group II introns encoding a reverse transcriptase protein, as did the cob gene of Storeatula species CCMP1868. CONCLUSIONS These newly sequenced genomes increase the breadth of data available from algae and will aid in the identification of general trends in mitochondrial genome evolution. While most of the genomes were highly conserved, extensive gene arrangements have shuffled gene order, perhaps due to genome rearrangements associated with hairpin-containing mobile genetic elements, tRNAs with palindromic sequences, and tandem repeat sequences. The cox1 and cob gene sequences suggest that introns have recently been acquired during cryptophyte evolution. Comparison of phylogenetic trees based on plastid and mitochondrial genome data sets underscore the different evolutionary histories of the host and endosymbiont components of present-day cryptophytes.
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Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, South Korea
| | - Gangman Yi
- Department of Multimedia Engineering, Dongguk University, Seoul, 04620, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea.
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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Turmel M, Otis C, Lemieux C. Divergent copies of the large inverted repeat in the chloroplast genomes of ulvophycean green algae. Sci Rep 2017; 7:994. [PMID: 28428552 PMCID: PMC5430533 DOI: 10.1038/s41598-017-01144-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/27/2017] [Indexed: 12/16/2022] Open
Abstract
The chloroplast genomes of many algae and almost all land plants carry two identical copies of a large inverted repeat (IR) sequence that can pair for flip-flop recombination and undergo expansion/contraction. Although the IR has been lost multiple times during the evolution of the green algae, the underlying mechanisms are still largely unknown. A recent comparison of IR-lacking and IR-containing chloroplast genomes of chlorophytes from the Ulvophyceae (Ulotrichales) suggested that differential elimination of genes from the IR copies might lead to IR loss. To gain deeper insights into the evolutionary history of the chloroplast genome in the Ulvophyceae, we analyzed the genomes of Ignatius tetrasporus and Pseudocharacium americanum (Ignatiales, an order not previously sampled), Dangemannia microcystis (Oltmannsiellopsidales), Pseudoneochloris marina (Ulvales) and also Chamaetrichon capsulatum and Trichosarcina mucosa (Ulotrichales). Our comparison of these six chloroplast genomes with those previously reported for nine ulvophyceans revealed unsuspected variability. All newly examined genomes feature an IR, but remarkably, the copies of the IR present in the Ignatiales, Pseudoneochloris, and Chamaetrichon diverge in sequence, with the tRNA genes from the rRNA operon missing in one IR copy. The implications of this unprecedented finding for the mechanism of IR loss and flip-flop recombination are discussed.
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Affiliation(s)
- Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec (QC), Canada
| | - Christian Otis
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec (QC), Canada
| | - Claude Lemieux
- Institut de Biologie Intégrative et des Systèmes, Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Québec (QC), Canada.
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27
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Xu X, Fei D, Han H, Liu H, Zhang J, Zhou Y, Xu C, Wang H, Cao H, Zhang H. Comparative characterization analysis of synonymous codon usage bias in classical swine fever virus. Microb Pathog 2017; 107:368-371. [PMID: 28416383 DOI: 10.1016/j.micpath.2017.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 04/01/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
Abstract
Classical swine fever virus (CSFV) is responsible for the highly contagious viral disease of swine, and causes great economic loss in the swine-raising industry. Considering the significance of CSFV, a systemic analysis was performed to study its codon usage patterns. In this study, using the complete genome sequences of 76 CSFV representing three genotypes, we firstly analyzed the relative nucleotide composition, effective number of codon (ENC) and synonymous codon usage in CSFV genomes. The results showed that CSFV is GC-moderate genome and the third-ended codons are not preferentially used. Every ENC values in CSFV genomes are >50, indicating that the codon usage bias is comparatively slight. Subsequently, we performed the correspondence analysis (COA) to investigate synonymous codon usage variation among all of the CSFV genomes. We found that codon usage bias in these CSFV genomes is greatly influenced by G + C mutation, which suggests that mutational pressure may be the main factor determining the codon usage biases. Moreover, most of the codon usage bias among different CSFV ORFs is directly related to the nucleotide composition. Other factors, such as hydrophobicity and aromaticity, also influence the codon usage variation among CSFV genomes. Our study represents the most comprehensive analysis of codon usage patterns in CSFV genome and provides a basic understanding of the mechanisms for its codon usage bias.
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Affiliation(s)
- Xin Xu
- College of Animal Medicine, Northeast Agricultural University, Harbin 150030, China; Heilongjiang Institute of Veterinary Science, Qiqihar 161005, China; College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Dongliang Fei
- College of Animal Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Huansheng Han
- College of Animal Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Honggui Liu
- College of Animal Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Jiayong Zhang
- College of Animal Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Yulong Zhou
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Chuang Xu
- College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China
| | - Hongbin Wang
- College of Animal Medicine, Northeast Agricultural University, Harbin 150030, China.
| | - Hongwei Cao
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China.
| | - Hua Zhang
- College of Life Science and Technology, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; College of Animal Science and Veterinary Medicine, HeiLongJiang BaYi Agricultural University, Daqing 163319, China; Biotechnology Center, HeiLongJiang BaYi Agricultural University, Daqing 163319, China.
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Tajima N, Saitoh K, Sato S, Maruyama F, Ichinomiya M, Yoshikawa S, Kurokawa K, Ohta H, Tabata S, Kuwata A, Sato N. Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms). Curr Genet 2016; 62:887-896. [DOI: 10.1007/s00294-016-0598-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 03/25/2016] [Accepted: 03/26/2016] [Indexed: 10/21/2022]
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Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae. Sci Rep 2015; 5:14465. [PMID: 26403826 PMCID: PMC4585924 DOI: 10.1038/srep14465] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 08/28/2015] [Indexed: 01/16/2023] Open
Abstract
The forfeiting of photosynthetic capabilities has occurred independently many times throughout eukaryotic evolution. But almost all non-photosynthetic plants and algae still retain a colorless plastid and an associated genome, which performs fundamental processes apart from photosynthesis. Unfortunately, little is known about the forces leading to photosynthetic loss; this is largely because there is a lack of data from transitional species. Here, we compare the plastid genomes of two “transitional” green algae: the photosynthetic, mixotrophic Auxenochlorella protothecoides and the non-photosynthetic, obligate heterotroph Prototheca wickerhamii. Remarkably, the plastid genome of A. protothecoides is only slightly larger than that of P. wickerhamii, making it among the smallest plastid genomes yet observed from photosynthetic green algae. Even more surprising, both algae have almost identical plastid genomic architectures and gene compositions (with the exception of genes involved in photosynthesis), implying that they are closely related. This close relationship was further supported by phylogenetic and substitution rate analyses, which suggest that the lineages giving rise to A. protothecoides and P. wickerhamii diverged from one another around six million years ago.
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Raven JA. Implications of mutation of organelle genomes for organelle function and evolution. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5639-50. [PMID: 26077836 DOI: 10.1093/jxb/erv298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK †School of Plant Biology, University of Western Australia, M048, 35 Stirling Highway, Crawley, WA 6009, Australia
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31
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Abstract
The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission.
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Abstract
Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to be greater than that of the mitochondrial genome. This assumption is based on early, pioneering studies of land plant molecular evolution, which uncovered higher rates of synonymous substitution in plastid versus mitochondrial DNAs. However, much of the plastid-containing eukaryotic diversity falls outside of land plants, and the patterns of plastid DNA evolution for embryophytes do not necessarily reflect those of other groups. Recent analyses of plastid and mitochondrial substitution rates in diverse lineages have uncovered very different trends than those recorded for land plants. Here, I explore these new data and argue that for many protists the plastid mutation rate is lower than that of the mitochondrion, including groups with primary or secondary plastids as well as nonphotosynthetic algae. These findings have far-reaching implications for how we view plastid genomes and how their sequences are used for evolutionary analyses, and might ultimately reflect a general tendency toward more efficient DNA repair mechanisms in plastids than in mitochondria.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON, Canada
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33
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Sloan DB. Using plants to elucidate the mechanisms of cytonuclear co-evolution. THE NEW PHYTOLOGIST 2015; 205:1040-6. [PMID: 25729802 DOI: 10.1111/nph.12835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The presence of both cytoplasmic and nuclear genomes within eukaryotic cells raises fascinating questions about co-evolution between genomic compartments that experience fundamentally different mutation rates and modes of inheritance. The highly mutagenic environments found in the mitochondria of some eukaryotes have generated interest in the role that mitochondrial mutation accumulation plays in phenomena such as intracellular gene transfer, compensatory evolution in the nucleus and the evolution of reproductive isolation. Although plant systems have played an important historical role in the study of cytonuclear co-evolution, they remain underutilized in many respects. In particular, the enormous natural variation in DNA substitution rates, gene content and genome architecture in plant mitochondria - much of which has even been found within a single genus – provides opportunities to resolve longstanding evolutionary questions about the consequences of mitochondrial mutation accumulation. This review summarizes some of the classic questions about cytonuclear co-evolution that could be addressed by taking advantage of the variation in plants and highlights a recent analysis of the effect of mitochondrial mutation accumulation on rates of molecular evolution in the nucleus.
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34
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Dornburg A, Townsend JP, Friedman M, Near TJ. Phylogenetic informativeness reconciles ray-finned fish molecular divergence times. BMC Evol Biol 2014; 14:169. [PMID: 25103329 PMCID: PMC4236503 DOI: 10.1186/s12862-014-0169-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/21/2014] [Indexed: 11/24/2022] Open
Abstract
Background Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. Results We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Conclusions Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.
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Affiliation(s)
- Alex Dornburg
- Department of Ecology and Evolutionary Biology, Yale University, New Haven 06520, Connecticut, USA.
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Hovde BT, Starkenburg SR, Hunsperger HM, Mercer LD, Deodato CR, Jha RK, Chertkov O, Monnat RJ, Cattolico RA. The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles. BMC Genomics 2014; 15:604. [PMID: 25034814 PMCID: PMC4226036 DOI: 10.1186/1471-2164-15-604] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/09/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation. RESULTS The complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent 'CheY-like' two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes--algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs)--a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade. CONCLUSION The Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.
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Smith DR, Jackson CJ, Reyes-Prieto A. Nucleotide substitution analyses of the glaucophyte Cyanophora suggest an ancestrally lower mutation rate in plastid vs mitochondrial DNA for the Archaeplastida. Mol Phylogenet Evol 2014; 79:380-4. [PMID: 25017510 DOI: 10.1016/j.ympev.2014.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 06/28/2014] [Accepted: 07/02/2014] [Indexed: 10/25/2022]
Abstract
A lot is known about the evolution and architecture of plastid, mitochondrial, and nuclear genomes, but surprisingly little is known about their relative rates of mutation. Most available relative-rate data come from seed plants, which, with few exceptions, have a mitochondrial mutation rate that is lower than those of the plastid and nucleus. But new findings from diverse plastid-bearing lineages have shown that for some eukaryotes the mitochondrial mutation rate is an order of magnitude greater than those of the plastid and nucleus. Here, we explore for the first time relative rates of mutation within the Glaucophyta-one of three main lineages that make up the Archaeplastida (or Plantae sensu lato). Nucleotide substitution analyses from distinct isolates of the unicellular glaucophyte Cyanophora paradoxa reveal 4-5-fold lower rates of mutation in the plastid and nucleus than the mitochondrion, which is similar to the mutational pattern observed in red algae and haptophytes, but opposite to that of seed plants. These data, together with data from previous reports, suggest that for much of the known photosynthetic eukaryotic diversity, plastid DNA mutations occur less frequently than those in mitochondrial DNA.
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Affiliation(s)
- David Roy Smith
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada.
| | - Christopher J Jackson
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada; Integrated Microbiology Program, Canadian Institute for Advanced Research, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, NB E3B 5A3, Canada; Integrated Microbiology Program, Canadian Institute for Advanced Research, Canada
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Nishimura Y, Kamikawa R, Hashimoto T, Inagaki Y. An intronic open reading frame was released from one of group II introns in the mitochondrial genome of the haptophyte Chrysochromulina sp. NIES-1333. Mob Genet Elements 2014; 4:e29384. [PMID: 25054084 PMCID: PMC4091101 DOI: 10.4161/mge.29384] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 05/27/2014] [Accepted: 05/27/2014] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial (mt) genome sequences, which often bear introns, have been sampled from phylogenetically diverse eukaryotes. Thus, we can anticipate novel insights into intron evolution from previously unstudied mt genomes. We here investigated the origins and evolution of three introns in the mt genome of the haptophyte Chrysochromulina sp. NIES-1333, which was sequenced completely in this study. All the three introns were characterized as group II, on the basis of predicted secondary structure, and the conserved sequence motifs at the 5′ and 3′ termini. Our comparative studies on diverse mt genomes prompt us to propose that the Chrysochromulina mt genome laterally acquired the introns from mt genomes in distantly related eukaryotes. Many group II introns harbor intronic open reading frames for the proteins (intron-encoded proteins or IEPs), which likely facilitate the splicing of their host introns. However, we propose that a “free-standing,” IEP-like protein, which is not encoded within any introns in the Chrysochromulina mt genome, is involved in the splicing of the first cox1 intron that lacks any open reading frames.
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Affiliation(s)
- Yuki Nishimura
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan ; Graduate School of Systems and Information Engineering; University of Tsukuba; Tsukuba, Japan
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies; Kyoto University; Kyoto, Japan ; Graduate School of Global Environmental Studies; Kyoto University; Kyoto, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan ; Center for Computational Sciences; University of Tsukuba; Tsukuba, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba, Japan ; Center for Computational Sciences; University of Tsukuba; Tsukuba, Japan
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