1
|
Timanikova N, Fletcher K, Han JW, van West P, Woodward S, Kim GH, Küpper FC, Wenzel M. Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens. Environ Microbiol 2024; 26:e16656. [PMID: 38818657 DOI: 10.1111/1462-2920.16656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
Seaweeds are important components of marine ecosystems with emerging potential in aquaculture and as sources of biofuel, food products and pharmacological compounds. However, an increasingly recognised threat to natural and industrial seaweed populations is infection with parasitic single-celled eukaryotes from the relatively understudied oomycete lineage. Here we examine the eukaryomes of diverse brown, red and green marine macroalgae collected from polar (Baffin Island), cold-temperate (Falkland Islands) and tropical (Ascension Island) locations, with a focus on oomycete and closely related diatom taxa. Using 18S rRNA gene amplicon sequencing, we show unexpected genetic and taxonomic diversity of the eukaryomes, a strong broad-brush association between eukaryome composition and geographic location, and some evidence of association between eukaryome structure and macroalgal phylogenetic relationships (phylosymbiosis). However, the oomycete fraction of the eukaryome showed disparate patterns of diversity and structure, highlighting much weaker association with geography and no evidence of phylosymbiosis. We present several novel haplotypes of the most common oomycete Eurychasma dicksonii and report for the first time a cosmopolitan distribution and absence of host specificity of this important pathogen. This indicates rich diversity in macroalgal oomycete pathogens and highlights that these pathogens may be generalist and highly adaptable to diverse environmental conditions.
Collapse
Affiliation(s)
| | - Kyle Fletcher
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Oceanlab, University of Aberdeen, Newburgh, UK
- Aberdeen Oomycete Laboratory, International Centre for Aquaculture Research and Development, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jon-Wong Han
- Kongju National University, Gongju, South Chungcheong Province, South Korea
| | - Pieter van West
- Aberdeen Oomycete Laboratory, International Centre for Aquaculture Research and Development, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Steve Woodward
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Gwang-Hoon Kim
- Kongju National University, Gongju, South Chungcheong Province, South Korea
| | - Frithjof C Küpper
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
- Kongju National University, Gongju, South Chungcheong Province, South Korea
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen, UK
- Department of Chemistry and Biochemistry, San Diego State University, California, San Diego, California, USA
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| |
Collapse
|
2
|
Cahoon AB, Johnson KM, Brown SM, Manoylov KM, Nienow JA. The chloroplast and mitochondrial genomes of two Gomphonema parvulum (Bacillariophyta) environmental isolates from South Carolina (United States) and Virginia (United States). JOURNAL OF PHYCOLOGY 2024; 60:299-307. [PMID: 38433431 DOI: 10.1111/jpy.13415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/24/2023] [Accepted: 11/24/2023] [Indexed: 03/05/2024]
Abstract
Gomphonema parvulum is a cosmopolitan freshwater diatom that is used as an indicator in water quality biomonitoring. In this study, we report the culturing of two geographically separated isolates from southeastern North America, their morphology, and the sequencing and assembly of their mitochondrial and chloroplast genomes. Morphologically, both strains fit G. parvulum sensu lato, but the frustules from a protected habitat in South Carolina were smaller than those cited in the historic data of this species from the same location as well as a second culture from Virginia. Phylogenetic analyses using the rbcL gene placed both within a clade with G. parvulum. Genetic markers, including full chloroplast and mitochondrial genomes and the nuclear small subunit rRNA gene region were assembled from each isolate. The organellar genomes of the two strains varied slightly in size due to small differences in intergenic regions with chloroplast genomes of 121,035 bp and 121,482 bp and mitochondrial genomes of 34,639 bp and 34,654 bp. The intraspecific pairwise identities of the chloroplast and mitochondrial genomes of these two isolates were 97.9% and 95.4%, respectively. Multigene phylogenetic analysis demonstrated a close relationship between G. parvulum, Gomphoneis minuta, and Didymosphenia geminata.
Collapse
Affiliation(s)
- A Bruce Cahoon
- Department of Natural Sciences, The University of Virginia's College at Wise, Wise, Virginia, USA
| | - Katherine M Johnson
- Department of Biological and Environmental Sciences, Georgia College & State University, Milledgeville, Georgia, USA
| | - Sydney M Brown
- Department of Biological and Environmental Sciences, Georgia College & State University, Milledgeville, Georgia, USA
| | - Kalina M Manoylov
- Department of Biological and Environmental Sciences, Georgia College & State University, Milledgeville, Georgia, USA
| | - James A Nienow
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
| |
Collapse
|
3
|
Du F, Li Y, Xu K. Phylogeny and Evolution of Cocconeiopsis (Cocconeidaceae) as Revealed by Complete Chloroplast and Mitochondrial Genomes. Int J Mol Sci 2023; 25:266. [PMID: 38203438 PMCID: PMC10778710 DOI: 10.3390/ijms25010266] [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: 11/20/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The genus Cocconeiopsis was separated from Navicula, but its systematic position is in debate. We sequenced the complete chloroplast and mitochondrial genome of Cocconeidaceae for the first time with Cocconeiopsis kantsiensis and investigated its phylogeny and evolutionary history. Results showed that the plastid genome was 140,415 bp long with 167 genes. The mitochondrial genome was 43,732 bp long with 66 genes. Comparative analysis showed that the plastid genome structure of C. kantsiensis was most similar to those of three Navicula species and Halamphora americana, and its size was significantly smaller than that of a monoraphid species. Its mitochondrial genome was similar to that of related species except for Phaeodactylum tricornutum. The multigene phylogeny reconstruction showed that Cocconeiopsis was sister to Didymosphenia but distant from Naviculaceae. The two-gene phylogenetic analysis containing 255 species showed Cocconeiopsis was sister to Cocconeis, and distant from Naviculaceae as well. Divergence time estimation indicates the common ancestor of cocconeid species occurred about 62.8 Ma and Cocconeiopsis diverged with monoraphid Cocconeis about 58.9 Ma. Our results support the assignment of Cocconeiopsis to Cocconeidaceae and that monoraphid cocconeids were likely evolved from the lineage of Cocconeiopsis.
Collapse
Affiliation(s)
- Feichao Du
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.D.); (Y.L.)
- Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhang Li
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.D.); (Y.L.)
- Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Kuidong Xu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (F.D.); (Y.L.)
- Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Laoshan Laboratory, Qingdao 266237, China
| |
Collapse
|
4
|
Liu F, Wang Y, Huang H, Chen N. Evolutionary dynamics of plastomes in coscinodiscophycean diatoms revealed by comparative genomics. Front Microbiol 2023; 14:1203780. [PMID: 37396366 PMCID: PMC10307964 DOI: 10.3389/fmicb.2023.1203780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
To understand the evolution of coscinodiscophycean diatoms, plastome sequences of six coscinodiscophycean diatom species were constructed and analyzed in this study, doubling the number of constructed plastome sequences in Coscinodiscophyceae (radial centrics). The platome sizes varied substantially in Coscinodiscophyceae, ranging from 119.1 kb of Actinocyclus subtilis to 135.8 kb of Stephanopyxis turris. Plastomes in Paraliales and Stephanopyxales tended to be larger than those in Rhizosoleniales and Coscinodiacales, which were due to the expansion of the inverted repeats (IRs) and to the marked increase of the large single copy (LSC). Phylogenomic analysis indicated that Paralia and Stephanopyxis clustered tightly to form the Paraliales-Stephanopyxales complex, which was sister to the Rhizosoleniales-Coscinodiscales complex. The divergence time between Paraliales and Stephanopyxales was estimated at 85 MYA in the middle Upper Cretaceous, indicating that Paraliales and Stephanopyxales appeared later than Coscinodiacales and Rhizosoleniales according to their phylogenetic relationships. Frequent losses of housekeeping protein-coding genes (PCGs) were observed in these coscinodiscophycean plastomes, indicating that diatom plastomes showed an ongoing reduction in gene content during evolution. Two acpP genes (acpP1 and acpP2) detected in diatom plastomes were found to be originated from an early gene duplication event occurred in the common progenitor after diatom emergence, rather than multiple independent gene duplications occurring in different lineages of diatoms. The IRs in Stephanopyxis turris and Rhizosolenia fallax-imbricata exhibited a similar trend of large expansion to the small single copy (SSC) and slightly small contraction from the LSC, which eventually led to the conspicuous increase in IR size. Gene order was highly conserved in Coscinodiacales, while multiple rearrangements were observed in Rhizosoleniales and between Paraliales and Stephanopyxales. Our results greatly expanded the phylogenetic breadth in Coscinodiscophyceae and gained novel insights into the evolution of plastomes in diatoms.
Collapse
Affiliation(s)
- Feng Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Yichao Wang
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Hailong Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, China
| | - Nansheng Chen
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Marine Ecology and Environmental Science Laboratory, Laoshan Laboratory, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| |
Collapse
|
5
|
Wang Y, Wang J, Chen Y, Liu S, Zhao Y, Chen N. Comparative Analysis of Bacillariophyceae Chloroplast Genomes Uncovers Extensive Genome Rearrangements Associated with Speciation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10024. [PMID: 36011659 PMCID: PMC9408514 DOI: 10.3390/ijerph191610024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/07/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The Bacillariophyceae is a species-rich, ecologically significant class of Bacillariophyta. Despite their critical importance in marine ecosystems as primary producers and in the development of harmful algal blooms (HABs), taxonomic research on Bacillariophyceae species has been hindered because of their limited morphological features, plasticity of morphologies, and the low resolution of common molecular markers. Hence molecular markers with improved resolution are urgently needed. Organelle genomes, which can be constructed efficiently with the recent development of high throughput DNA sequencing technologies and the advancement of bioinformatics tools, have been proposed as super barcodes for their higher resolution for distinguishing different species and intra-species genomic variations. In this study, we tested the value of full-length chloroplast genomes (cpDNAs) as super barcodes for distinguishing diatom species, by constructing cpDNAs of 11 strains of the class Bacillariophyceae, including Nitzschia ovalis, Nitzschia traheaformis, Cylindrotheca spp., Psammodictyon constrictum, Bacillaria paxillifer, two strains of Haslea tsukamotoi, Haslea avium, Navicula arenaria, and Pleurosigma sp. Comparative analysis of cpDNAs revealed that cpDNAs were not only adequate for resolving different species, but also for enabling recognition of high levels of genome rearrangements between cpDNAs of different species, especially for species of the genera Nitzschia, Cylindrotheca, Navicula and Haslea. Additionally, comparative analysis suggested that the positioning of species in the genus Haslea should be transferred to the genus Navicula. Chloroplast genome-based evolutionary analysis suggested that the Bacillariophyceae species first appeared during the Cretaceous period and the diversity of species rose after the mass extinction about 65 Mya. This study highlighted the value of cpDNAs in research on the biodiversity and evolution of Bacillariophyceae species, and, with the construction of more cpDNAs representing additional genera, deeper insight into the biodiversity and evolutionary relationships of Bacillariophyceae species will be gained.
Collapse
Affiliation(s)
- Yichao Wang
- 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 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jing Wang
- 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 100049, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - 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
| | - Yongfang Zhao
- Laboratory of Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, 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, BC V5A 1S6, Canada
| |
Collapse
|
6
|
Kim JI, Jo BY, Park MG, Yoo YD, Shin W, Archibald JM. Evolutionary Dynamics and Lateral Gene Transfer in Raphidophyceae Plastid Genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:896138. [PMID: 35769291 PMCID: PMC9235467 DOI: 10.3389/fpls.2022.896138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The Raphidophyceae is an ecologically important eukaryotic lineage of primary producers and predators that inhabit marine and freshwater environments worldwide. These organisms are of great evolutionary interest because their plastids are the product of eukaryote-eukaryote endosymbiosis. To obtain deeper insight into the evolutionary history of raphidophycean plastids, we sequenced and analyzed the plastid genomes of three freshwater and three marine species. Our comparison of these genomes, together with the previously reported plastid genome of Heterosigma akashiwo, revealed unexpected variability in genome structure. Unlike the genomes of other analyzed species, the plastid genome of Gonyostomum semen was found to contain only a single rRNA operon, presumably due to the loss of genes from the inverted repeat (IR) region found in most plastid genomes. In contrast, the marine species Fibrocapsa japonica contains the largest IR region and overall plastid genome for any raphidophyte examined thus far, mainly due to the presence of four large gene-poor regions and foreign DNA. Two plastid genes, tyrC in F. japonica and He. akashiwo and serC in F. japonica, appear to have arisen via lateral gene transfer (LGT) from diatoms, and several raphidophyte open reading frames are demonstrably homologous to sequences in diatom plasmids and plastid genomes. A group II intron in the F. japonica psbB gene also appears to be derived by LGT. Our results provide important insights into the evolutionary history of raphidophyte plastid genomes via LGT from the plastids and plasmid DNAs of diatoms.
Collapse
Affiliation(s)
- Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Bok Yeon Jo
- Nakdonggang National Institute of Biological Resources, Sangju, South Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju, South Korea
| | - Yeong Du Yoo
- Department of Marine Biology, College of Ocean Sciences and Technology, Kunsan National University, Kunsan, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - John M. Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| |
Collapse
|
7
|
Liu S, Xu Q, Liu K, Zhao Y, Chen N. Chloroplast Genomes for Five Skeletonema Species: Comparative and Phylogenetic Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:774617. [PMID: 34966403 PMCID: PMC8710728 DOI: 10.3389/fpls.2021.774617] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Skeletonema species are cosmopolitan coastal diatoms that exhibit important roles in ecological system. The chloroplast genomes (cpDNAs) have been proven to be important in the study of molecular evolution and genetic diversity. However, cpDNA of only a single Skeletonema species (S. pseudocostatum) has been constructed, hindering in-depth investigation on Skeletonema species. In this study, complete cpDNAs of five Skeletonema species were constructed with cpDNAs of four species S. marinoi, S. tropicum, S. costatum, and S. grevillea constructed for the first time. These cpDNAs had similar sizes and same numbers of genes. These cpDNAs were highly syntenic with no substantial expansions, contractions, or inversions. Interestingly, two copies of petF, which encodes ferredoxin with critical role in iron dependency, were found in all five Skeletonema species, with one copy in the cpDNA and another copy in the nuclear genome of each species. Selection analysis revealed that all PCGs of cpDNAs were undergoing purifying selection. Despite the high conservation of these cpDNAs, nine genomic regions with high sequence divergence were identified, which illustrated substantial variations that could be used as markers for phylogenetic inference and for tracking Skeletonema species in the field. Additionally, the numbers of simple sequence repeats varied among different cpDNAs, which were useful for detecting genetic polymorphisms. The divergence times estimated using PCGs of cpDNAs revealed that most of these species were established within ∼33 Mya, consistent with that estimated using mtDNAs. Overall, the current study deepened our understanding about the molecular evolution of Skeletonema cpDNAs.
Collapse
Affiliation(s)
- Shuya Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Functional 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
| | - Qing Xu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Functional 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
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kuiyan Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Functional 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
- College of Marine Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yongfang Zhao
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Jiaozhou Bay National Marine Ecosystem Research Station, Institute of Oceanology, 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
- Functional 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
| |
Collapse
|
8
|
Górecka E, Gastineau R, Davidovich NA, Davidovich OI, Ashworth MP, Sabir JSM, Lemieux C, Turmel M, Witkowski A. Mitochondrial and Plastid Genomes of the Monoraphid Diatom Schizostauron trachyderma. Int J Mol Sci 2021; 22:ijms222011139. [PMID: 34681800 PMCID: PMC8541233 DOI: 10.3390/ijms222011139] [Citation(s) in RCA: 3] [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: 09/01/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
We provide for the first time the complete plastid and mitochondrial genomes of a monoraphid diatom: Schizostauron trachyderma. The mitogenome is 41,957 bp in size and displays two group II introns in the cox1 gene. The 187,029 bp plastid genome features the typical quadripartite architecture of diatom genomes. It contains a group II intron in the petB gene that overlaps the large single-copy and the inverted repeat region. There is also a group IB4 intron encoding a putative LAGLIDADG homing endonuclease in the rnl gene. The multigene phylogenies conducted provide more evidence of the proximity between S. trachyderma and fistula-bearing species of biraphid diatoms.
Collapse
Affiliation(s)
- Ewa Górecka
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland;
- Correspondence: (E.G.); (R.G.)
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland;
- Correspondence: (E.G.); (R.G.)
| | - Nikolai A. Davidovich
- Karadag Scientific Station—Natural Reserve of the Russian Academy of Sciences, p/o Kurortnoe, Feodosiya, 98188 Crimea, Russia; (N.A.D.); (O.I.D.)
| | - Olga I. Davidovich
- Karadag Scientific Station—Natural Reserve of the Russian Academy of Sciences, p/o Kurortnoe, Feodosiya, 98188 Crimea, Russia; (N.A.D.); (O.I.D.)
| | - Matt P. Ashworth
- Department of Molecular Biosciences, NHB, University of Texas at Austin, Austin, TX 78712, USA;
| | - Jamal S. M. Sabir
- Genomics and Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Claude Lemieux
- Département de Biochimie, Microbiologie et Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada; (C.L.); (M.T.)
| | - Monique Turmel
- Département de Biochimie, Microbiologie et Bio-Informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC G1V 0A6, Canada; (C.L.); (M.T.)
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland;
| |
Collapse
|
9
|
Wu CS, Sudianto E, Hung YM, Wang BC, Huang CJ, Chen CT, Chaw SM. Genome skimming and exploration of DNA barcodes for Taiwan endemic cypresses. Sci Rep 2020; 10:20650. [PMID: 33244113 PMCID: PMC7693304 DOI: 10.1038/s41598-020-77492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 09/16/2020] [Indexed: 11/23/2022] Open
Abstract
Cypresses are characterized by their longevity and valuable timber. In Taiwan, two endemic cypress species, Chamaecyparis formosensis and C. obtusa var. formosana, are threatened by prevalent illegal logging. A DNA barcode system is urgently needed for reforestation and conservation of these two cypresses. In this study, both plastomes and 35S rDNAs from 16, 10, and 6 individuals of C. formosensis, C. obtusa var. formosana, and C. obtusa var. obtusa were sequenced, respectively. We show that the loss of plastid trnT-GGU readily distinguishes C. formosensis from its congeneric species. We demonstrate that entire sequences of plastomes or 35S rDNAs are capable of correctly identifying cypress species and varieties, suggesting that they are effective super-barcodes. We also discover three short hypervariable loci (i.e., 3′ETS, ITS1, and trnH-psbA) that are promising barcodes for identifying cypress species and varieties. Moreover, nine species-specific indels of > 100 bp were detected in the cypress plastomes. These indels, together with the three aforementioned short barcodes, constitute an alternative and powerful barcode system crucial for identifying specimens that are fragmentary or contain degraded/poor DNA. Our sequenced data and barcode systems not only enrich the genetic reference for cypresses, but also contribute to future reforestation, conservation, and forensic investigations.
Collapse
Affiliation(s)
- Chung-Shien Wu
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Edi Sudianto
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Mei Hung
- Department of Forensic Science Investigation Bureau, Ministry of Justice, New Taipei City, 231209, Taiwan
| | - Bo-Cyun Wang
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chiun-Jr Huang
- School of Forestry and Resource Conservation, National Taiwan University, Taipei, 10617, Taiwan
| | - Chi-Tsong Chen
- Department of Forensic Science Investigation Bureau, Ministry of Justice, New Taipei City, 231209, Taiwan.
| | - Shu-Miaw Chaw
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| |
Collapse
|
10
|
Young JN, Schmidt K. It's what's inside that matters: physiological adaptations of high-latitude marine microalgae to environmental change. THE NEW PHYTOLOGIST 2020; 227:1307-1318. [PMID: 32391569 DOI: 10.1111/nph.16648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/23/2020] [Indexed: 05/13/2023]
Abstract
Marine microalgae within seawater and sea ice fuel high-latitude ecosystems and drive biogeochemical cycles through the fixation and export of carbon, uptake of nutrients, and production and release of oxygen and organic compounds. High-latitude marine environments are characterized by cold temperatures, dark winters and a strong seasonal cycle. Within this environment a number of diverse and dynamic habitats exist, particularly in association with the formation and melt of sea ice, with distinct microalgal communities that transition with the season. Algal physiology is a crucial component, both responding to the dynamic environment and in turn influencing its immediate physicochemical environment. As high-latitude oceans shift into new climate regimes the analysis of seasonal responses may provide insights into how microalgae will respond to long-term environmental change. This review discusses recent developments in our understanding of how the physiology of high-latitude marine microalgae is regulated over a polar seasonal cycle, with a focus on ice-associated (sympagic) algae. In particular, physiologies that impact larger scale processes will be explored, with an aim to improve our understanding of current and future ecosystems and biogeochemical cycles.
Collapse
Affiliation(s)
- Jodi N Young
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Katrin Schmidt
- School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| |
Collapse
|
11
|
Li C, Gastineau R, Turmel M, Witkowski A, Otis C, Car A, Lemieux C. Complete chloroplast genome of the tiny marine diatom Nanofrustulum shiloi (Bacillariophyta) from the Adriatic Sea. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3374-3376. [PMID: 33366000 PMCID: PMC7707228 DOI: 10.1080/23802359.2019.1673245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report the chloroplast genome sequence of Nanofrustulum shiloi, a tiny araphid pennate diatom collected from the Adriatic Sea. The 160,994-bp N. shiloi genome displays a quadripartite structure and its gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located in the inverted repeat, psbY is duplicated. A gene-poor region in the large single-copy region contains multiple ORFs sharing sequence similarities with plasmids and chloroplast ORFs found in other diatom species. The genome features a single intron, a group II intron in petB. Phylogenomic analysis identified N. shiloi at a basal position within the araphid 2 clade.
Collapse
Affiliation(s)
- Chunlian Li
- Ecological Institute, South China Normal University, Guangzhou, Guangdong, China.,Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Monique Turmel
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Christian Otis
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Ana Car
- Institute for Marine and Coastal Research, University of Dubrovnik, Dubrovnik, Croatia
| | - Claude Lemieux
- Département de biochimie, de microbiologie et de bio-informatique, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| |
Collapse
|