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Remias D, Procházková L, Nedbalová L, Benning LG, Lutz S. Novel insights in cryptic diversity of snow and glacier ice algae communities combining 18S rRNA gene and ITS2 amplicon sequencing. FEMS Microbiol Ecol 2023; 99:fiad134. [PMID: 37880981 PMCID: PMC10659120 DOI: 10.1093/femsec/fiad134] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/13/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023] Open
Abstract
Melting snow and glacier surfaces host microalgal blooms in polar and mountainous regions. The aim of this study was to determine the dominant taxa at the species level in the European Arctic and the Alps. A standardized protocol for amplicon metabarcoding using the 18S rRNA gene and ITS2 markers was developed. This is important because previous biodiversity studies have been hampered by the dominance of closely related algal taxa in snow and ice. Due to the limited resolution of partial 18S rRNA Illumina sequences, the hypervariable ITS2 region was used to further discriminate between the genotypes. Our results show that red snow was caused by the cosmopolitan Sanguina nivaloides (Chlamydomonadales, Chlorophyta) and two as of yet undescribed Sanguina species. Arctic orange snow was dominated by S. aurantia, which was not found in the Alps. On glaciers, at least three Ancylonema species (Zygnematales, Streptophyta) dominated. Golden-brown blooms consisted of Hydrurus spp. (Hydrurales, Stramenophiles) and these were mainly an Arctic phenomenon. For chrysophytes, only the 18S rRNA gene but not ITS2 sequences were amplified, showcasing how delicate the selection of eukaryotic 'universal' primers for community studies is and that primer specificity will affect diversity results dramatically. We propose our approach as a 'best practice'.
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Affiliation(s)
- Daniel Remias
- Paris Lodron University of Salzburg, Department of Ecology and Biodiversity, Hellbrunnerstr. 34, 5020 Salzburg, Austria
- University of Applied Sciences Upper Austria, Stelzhamerstr. 23, 4600 Wels, Austria
| | - Lenka Procházková
- Charles University, Faculty of Science, Department of Ecology, Viničná 7, 128 44 Praha, Czech Republic
| | - Linda Nedbalová
- Charles University, Faculty of Science, Department of Ecology, Viničná 7, 128 44 Praha, Czech Republic
| | - Liane G Benning
- German Research Centre for Geoscience, GFZ, 14473 Potsdam, Germany
- Department of Earth Sciences, Freie Universität Berlin, 12249 Berlin, Germany
| | - Stefanie Lutz
- German Research Centre for Geoscience, GFZ, 14473 Potsdam, Germany
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Devi MP, Dasgupta M, Mohanty S, Sharma SK, Hegde V, Roy SS, Renadevan R, Kumar KB, Patel HK, Sahoo MR. DNA Barcoding and ITS2 Secondary Structure Predictions in Taro ( Colocasia esculenta L. Schott) from the North Eastern Hill Region of India. Genes (Basel) 2022; 13:genes13122294. [PMID: 36553561 PMCID: PMC9778394 DOI: 10.3390/genes13122294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022] Open
Abstract
Taro (Colocasia esculenta L. Schott, Araceae), an ancient root and tuber crop, is highly polygenic, polyphyletic, and polygeographic in nature, which leads to its rapid genetic erosion. To prevent the perceived loss of taro diversity, species discrimination and genetic conservation of promising taro genotypes need special attention. Reports on genetic discrimination of taro at its center of origin are still untapped. We performed DNA barcoding of twenty promising genotypes of taro indigenous to the northeastern hill region of India, deploying two chloroplast-plastid genes, matK and rbcL, and the ribosomal nuclear gene ITS2. The secondary structure of ITS2 was determined and molecular phylogeny was performed to assess genetic discrimination among the taro genotypes. The matK and rbcL genes were highly efficient (>90%) in amplification and sequencing. However, the ITS2 barcode region achieved significant discrimination among the tested taro genotypes. All the taro genotypes displayed most similar sequences at the conserved matK and rbcL loci. However, distinct sequence lengths were observed in the ITS2 barcode region, revealing accurate discriminations among the genotypes. Multiple barcode markers are unrelated to one another and change independently, providing different estimations of heritable traits and genetic lineages; thus, they are advantageous over a single locus in genetic discrimination studies. A dynamic programming algorithm that used base-pairing interactions within a single nucleic acid polymer or between two polymers transformed the secondary structures into the symbol code data to predict seven different minimum free energy secondary structures. Our analysis strengthens the potential of the ITS2 gene as a potent DNA barcode candidate in the prediction of a valuable secondary structure that would help in genetic discrimination between the genotypes while augmenting future breeding strategies in taro.
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Affiliation(s)
- Mayengbam Premi Devi
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- College of Agriculture, Central Agricultural University (CAU-Imphal), Kyrdemkulai 793105, India
| | - Madhumita Dasgupta
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
| | - Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, India
| | - Susheel Kumar Sharma
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- ICAR—Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Vivek Hegde
- ICAR—Central Tuber Crops Research Institute, Thiruvananthapuram 695017, India
- ICAR—Indian Institute of Horticultural Research, Bengaluru 560089, India
| | - Subhra Saikat Roy
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
| | - Rennya Renadevan
- Centre for Cellular and Molecular Biology, Hyderabad 570007, India
| | | | - Hitendra Kumar Patel
- Centre for Cellular and Molecular Biology, Hyderabad 570007, India
- Correspondence: (H.K.P.); (M.R.S.); Tel.: +91-674-247-1867 (M.R.S.); Fax: +91-674-247-1712 (M.R.S.)
| | - Manas Ranjan Sahoo
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, India
- Correspondence: (H.K.P.); (M.R.S.); Tel.: +91-674-247-1867 (M.R.S.); Fax: +91-674-247-1712 (M.R.S.)
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Acharya GC, Mohanty S, Dasgupta M, Sahu S, Singh S, Koundinya AVV, Kumari M, Naresh P, Sahoo MR. Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India. Genes (Basel) 2022; 13:genes13091678. [PMID: 36140845 PMCID: PMC9498504 DOI: 10.3390/genes13091678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Commercial interest in the culinary herb, Eryngium foetidum L., has increased worldwide due to its typical pungency, similar to coriander or cilantro, with immense pharmaceutical components. The molecular delimitation and taxonomic classification of this lesser-known medicinal plant are restricted to conventional phenotyping and DNA-based marker evaluation, which hinders accurate identification, genetic conservation, and safe utilization. This study focused on species discrimination using DNA sequencing with chloroplast–plastid genes (matK, Kim matK, and rbcL) and the nuclear ITS2 gene in two Eryngium genotypes collected from the east coast region of India. The results revealed that matK discriminated between two genotypes, however, Kim matK, rbcL, and ITS2 identified these genotypes as E. foetidum. The ribosomal nuclear ITS2 region exhibited significant inter- and intra-specific divergence, depicted in the DNA barcodes and the secondary structures derived based on the minimum free energy. Although the efficiency of matK genes is better in species discrimination, ITS2 demonstrated polyphyletic phylogeny, and could be used as a reliable marker for genetic divergence studies understanding the mechanisms of RNA molecules. The results of this study provide insights into the scientific basis of species identification, genetic conservation, and safe utilization of this important medicinal plant species.
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Affiliation(s)
- Gobinda Chandra Acharya
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Madhumita Dasgupta
- ICAR Research Complex for Northeastern Hill Region, Manipur Centre, Imphal 795004, Manipur, India
| | - Supriya Sahu
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
- All India Institute of Medical Sciences, Bhubaneswar 751019, Odisha, India
| | - Satyapriya Singh
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Ayyagari V. V. Koundinya
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Meenu Kumari
- ICAR Research Complex for Eastern Region, Research Centre, Ranchi 834010, Jharkhand, India
| | - Ponnam Naresh
- ICAR–Indian Institute of Horticultural Research, Bengaluru 560089, Karnataka, India
| | - Manas Ranjan Sahoo
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
- Correspondence: ; Tel.: +91-674-2471867; Fax: +91-674-2471712
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Yan Q, Zhu H, Fang J, Liu B, Liu G. Taxonomic study of a novel terrestrial alga, Spongiosarcinopsisqinghaiensis sp. nov. (Protosiphonaceae, Chlorophyta), from the Qinghai-Tibet Plateau. PhytoKeys 2022; 204:83-95. [PMID: 36760612 PMCID: PMC9848930 DOI: 10.3897/phytokeys.204.84886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/29/2022] [Indexed: 06/18/2023]
Abstract
There is only one species of Spongiosarcinopsis in the literature currently. It was found in gray soil in Russia for the first time. According to molecular data analysis results, the isolated algal strain is most closely related to Spongiosarcinopsisterrestris. Unlike Spongiosarcinopsisterrestris, the isolated strain was found on soil surfaces at high altitudes, the young vegetative cell is spherical, vegetative cells are relatively large, and pyrenoids are generally fewer. In view of such morphological differences, phylogenetic analysis results, and comparison of ITS2 secondary structure and ultrastructure, the strain isolated in the present study was proposed to be a novel species.
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Affiliation(s)
- Qiufeng Yan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
| | - Jiao Fang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, ChinaInstitute of Hydrobiology, Chinese Academy of SciencesWuhanChina
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Zhang T, Shao C, Zhang T, Song W, Vd’ačný P, Al-Farraj SA, Wang Y. Multi-Gene Phylogeny of the Ciliate Genus Trachelostyla (Ciliophora, Hypotrichia), With Integrative Description of Two Species, Trachelostyla multinucleata Spec. nov. and T. pediculiformis (Cohn, 1866). Front Microbiol 2022; 12:775570. [PMID: 35178037 PMCID: PMC8844511 DOI: 10.3389/fmicb.2021.775570] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
Many hypotrich genera, including Trachelostyla, are taxonomically challenging and in a need of integrative revision. Using morphological data, molecular phylogenetic analyses, and internal transcribed spacer 2 (ITS2) secondary structures, we attempt to cast more light on species relationships within the genus Trachelostyla. The present multifaceted approach reveals that (1) a large-sized species with numerous macronuclear nodules, isolated from sandy littoral sediments in southern China, is new to science and is endowed here with a name, T. multinucleata spec. nov.; (2) two other Chinese populations previously identified as T. pediculiformis represent undescribed species; and (3) multigene phylogeny is more robust than single-gene trees, recovering the monophyly of the genus Trachelostyla with high bootstrap frequency. Additionally, ITS2 secondary structures and the presence of compensatory base changes in helices A and B indicate the presence of four distinct taxa within the molecularly studied members of the genus Trachelostyla. Molecular data are more suitable for delimitation of Trachelostyla species than morphological characters as interspecific pairwise genetic distances of small subunit (18S) rDNA, ITS1-5.8S-ITS2, and large subunit (28S) rDNA sequences do not overlap, whereas ranges of multiple morphometric features might transcend species boundaries.
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Affiliation(s)
- Tengyue Zhang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Tengteng Zhang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Weibo Song
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Peter Vd’ačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Saleh A. Al-Farraj
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, China
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Singh V, Lakshman DK, Roberts DP, Ismaiel A, Hooda KS, Gogoi R. Morphopathological and Molecular Morphometric Characterization of Waitea circinata var. prodigus Causing a Novel Sheath Spot Disease of Maize in India. Plant Dis 2022; 106:526-534. [PMID: 34261356 DOI: 10.1094/pdis-05-21-0951-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Maize brown sheath spot (MBSS), a new disease of maize, was discovered while surveying for maize leaf and sheath blight diseases in the Indian states of Assam, Jharkhand, Meghalaya, Manipur, and Odisha. Maize is the third most important cereal after rice and wheat in India. Unlike banded leaf and sheath blight disease caused by Rhizoctonia solani, MBSS symptoms on maize were discrete and limited to sheaths only. Symptoms of MBSS in the field were initially water-soaked necrotic lesions of 1 to 2 cm in diameter on the lowermost leaf sheaths, which then progressed to the upper sheaths. Lesions coalesced and covered approximately 2 to 5% of the sheath area. Infected dried lower leaves were shed, whereas infected upper leaves remained on the stem. The pathogen was isolated, characterized morphologically, pathologically, and molecularly, and identified as Waitea circinata var. prodigus, a basidiomycete known to cause basal leaf blight of seashore paspalum. The internal transcribed spacer (ITS) sequence 2 (ITS2) of rDNA from MBSS isolates formed a well supported clade with known W. circinata var. prodigus isolates. Molecular morphometric analysis of the ITS2 regions of the five known varieties of W. circinata detected distinguishing variations in GC content, compensatory base changes (CBCs), hemi- CBCs, indels, and altered base-pairing of helices. Variation in these characteristics may indicate that varieties are distinct biological species within W. circinata sensu lato. The geographical distribution and potential impacts of MBSS on the maize crop in India necessitate further investigations of pathogen identification and disease management.
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Affiliation(s)
- Vimla Singh
- Department of Botany and Plant Physiology, Chaudhary Charan Singh Haryana Agricultural University, Regional Research Station, Karnal 132001, India
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Adnan Ismaiel
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - K S Hooda
- Germplasm Evaluation Division, Indian Council of Agricultural Research, National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Robin Gogoi
- Division of Plant Pathology, Indian Council of Agricultural Research, Indian Agricultural Research Institute, New Delhi 110012, India
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Zhu H, Sun H, Zhao Z, Liu X, Liu B, Hu Z, Leliaert F, Liu G. Chlorocladiella gen. nov. (Pithophoraceae, Cladophorales, Chlorophyta), Including Four New Species From Various Freshwater Habitats in China. J Phycol 2020; 56:895-907. [PMID: 32180225 DOI: 10.1111/jpy.12991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Samples of Pithophoraceae, collected in diverse freshwater and damp terrestrial habitats from tropical and subtropical China, were characterized morphologically and ultrastructurally, and their phylogenetic position was determined based on nuclear ribosomal DNA sequences. Our phylogenetic analysis resolved a novel lineage of Pithophoraceae, sister to Aegagropilopsis. Based on our phylogenetic results, morphological observations and comparative rDNA ITS2 secondary structure analysis, we propose Chlorocladiella gen. nov., characterized by a well-developed system of prostrate filaments, and describe four new species, C. cochlea sp. nov., C. erecta sp. nov., C. medogensis sp. nov., and C. pisformis sp. nov. Two species were found growing on damp soil, which is an unusual habitat for cladophoralean green algae, indicating that the diversity of Cladophorales in terrestrial habitats may be greater than currently recognized.
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Affiliation(s)
- Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Hui Sun
- Qingdao Branch of Shandong Water Diversion Project Operation and Maintenance Center, Qingdao, 266100, China
| | - Zhijuan Zhao
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning, 530001, China
| | - Xudong Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Frederik Leliaert
- Meise Botanic Garden, Meise, 1860, Belgium
- Biology Department, Ghent University, 9000, Ghent, Belgium
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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Obert T, Vďačný P. Delimitation of five astome ciliate species isolated from the digestive tube of three ecologically different groups of lumbricid earthworms, using the internal transcribed spacer region and the hypervariable D1/D2 region of the 28S rRNA gene. BMC Evol Biol 2020; 20:37. [PMID: 32171235 PMCID: PMC7071660 DOI: 10.1186/s12862-020-1601-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/03/2020] [Indexed: 01/19/2023] Open
Abstract
Background Various ecological groups of earthworms very likely constitute sharply isolated niches that might permit speciation of their symbiotic ciliates, even though no distinct morphological features appear to be recognizable among ciliates originating from different host groups. The nuclear highly variable ITS1–5.8S-ITS2 region and the hypervariable D1/D2 region of the 28S rRNA gene have proven to be useful tools for the delimitation of species boundaries in closely related free-living ciliate taxa. In the present study, the power of these molecular markers as well as of the secondary structure of the ITS2 molecule were tested for the first time in order to discriminate the species of endosymbiotic ciliates that were isolated from the gastrointestinal tract of three ecologically different groups of lumbricid earthworms. Results Nineteen new ITS1–5.8S-ITS2 region and D1/D2-28S rRNA gene sequences were obtained from five astome species (Anoplophrya lumbrici, A. vulgaris, Metaradiophrya lumbrici, M. varians, and Subanoplophrya nodulata comb. n.), which were living in the digestive tube of three ecological groups of earthworms. Phylogenetic analyses of the rRNA locus and secondary structure analyses of the ITS2 molecule robustly resolved their phylogenetic relationships and supported the distinctness of all five species, although previous multivariate morphometric analyses were not able to separate congeners in the genera Anoplophrya and Metaradiophrya. The occurrence of all five taxa, as delimited by molecular analyses, was perfectly correlated with the ecological groups of their host earthworms. Conclusions The present study indicates that morphology-based taxonomy of astome ciliates needs to be tested in the light of molecular and ecological data as well. The use of morphological identification alone is likely to miss species that are well delimited based on molecular markers and ecological traits and can lead to the underestimation of diversity and overestimation of host range. An integrative approach along with distinctly increased taxon sampling would be helpful to assess the consistency of the eco-evolutionary trend in astome ciliates.
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Affiliation(s)
- Tomáš Obert
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovak Republic
| | - Peter Vďačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 842 15, Slovak Republic.
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Chen FR, Guo QS, Yang F, Zhu ZB, Wang T. [Application of ITS2 secondary structure phylogenetic information in DNA barcode identification of Chrysanthemum indicum and its related plants]. Zhongguo Zhong Yao Za Zhi 2019; 44:4813-4819. [PMID: 31872587 DOI: 10.19540/j.cnki.cjcmm.20190829.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
By exploring additional phylogenetic information hidden in ITS2 secondary structure,the possibility of identifying Chrysanthemum indicum and its related species with DNA barcode of ITS2 nucleic acid sequence and its structure information were discussed.The genomic DNA was extracted from 12 samples. The ITS2 fragments were amplified by PCR and sequenced bidirectionally to obtain ITS2 sequence information. 28 sequences of related species for Ch. indicum were downloaded from Gen Bank. Until all 40 ITS2 sequences were aligned,ITS2 secondary structure prediction and structure comparison were finished. Then ITS2 secondary structure information was coded. After comparing ITS2 structure information and nucleic acid information,MP phylogenetic trees were built. The results showed that the secondary structures of ITS2 shared the same structure model--a four-fingered hand. They not only have the common characteristics of ITS2 secondary structures in plants,but also have many other conservative sequences,and their overall conservativeness is high. Among all species used in this study,their ITS2 secondary structures had obvious difference. In addition,the number of mutation sites in the joint matrix compared with the nucleic acid sequences increased by nearly 90%,which greatly enriched the number of mutation sites. This method of information analysis distinguished Ch. indicum from its related species. At the same time,the support rate of the branches of evolutionary trees and the identification rate of species were significantly improved. Although there was no distinction between Ch. zawadskii and Ch. morifolium,it effectively distinguished the three species,namely,Ch. hypargyrum,Ch.oreastrum,and Ch. dichrum. Therefore,the authors suggest that the ITS2 sequence combined with its structural data information should be applied to the identification of Ch. indicum and its related species,and be widely applied to DNA barcode research.
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Affiliation(s)
- Fu-Rong Chen
- Institute of Chinese Medicinal Materials,Nanjing Agricultural University Nanjing 210095,China
| | - Qiao-Sheng Guo
- Institute of Chinese Medicinal Materials,Nanjing Agricultural University Nanjing 210095,China
| | - Feng Yang
- Institute of Chinese Medicinal Materials,Nanjing Agricultural University Nanjing 210095,China
| | - Zai-Biao Zhu
- Institute of Chinese Medicinal Materials,Nanjing Agricultural University Nanjing 210095,China
| | - Tao Wang
- Institute of Chinese Medicinal Materials,Nanjing Agricultural University Nanjing 210095,China
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Wang Q, Song H, Liu X, Liu B, Hu Z, Liu G. Morphology and molecular phylogeny of coccoid green algae Coelastrella sensu lato (Scenedesmaceae, Sphaeropeales), including the description of three new species and two new varieties. J Phycol 2019; 55:1290-1305. [PMID: 31411734 DOI: 10.1111/jpy.12915] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/01/2019] [Indexed: 05/16/2023]
Abstract
The genus Coelastrella was established by Chodat (Bull. Soc. Bot. Geneve, 13 [1922] 66), and was characterized as being unicellular or in few-celled aggregations with many longitudinal ribs on the cell wall. Many species of this genus showed strong ability to accumulate carotenoids and oils, so they have recently attracted much attention from researchers due to its potential applicability in the energy and food industries. In this study, a total of 23 strains of Coelastrella were sampled from China, and three new species and two new varieties were described: C. thermophila sp. nov., C. yingshanensis sp. nov., C. tenuitheca sp. nov., C. thermophila var. globulina var. nov., C. rubescens var. oocystiformis var. nov. Besides 18S rDNA and ITS2 sequences, we have newly sequenced the tufA gene marker for this taxon. Phylogenetic analysis combined with morphological studies revealed four morphotypes within the Coelastrella sensu lato clade, which contained the morphotype of original Coelastrella, original Scotiellopsis, Asterarcys, and morphotype of C. vacuolata and C. tenuitheca sp. nov. The relationships between morphological differences and phylogenic diversity based on different markers were discussed. Our results support that 18S rDNA was too conserved to be used a species-specific or even a genus-specific marker in this clade. The topology of tufA gene-based phylogenetic tree had a better match with the morphological findings.
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Affiliation(s)
- Qinghua Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | - Huiyin Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
| | - Xudong Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, P. R. China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, P. R. China
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Obert T, Vďačný P. Evolutionary Origin and Host Range of Plagiotoma lumbrici (Ciliophora, Hypotrichia), an Obligate Gut Symbiont of Lumbricid Earthworms. J Eukaryot Microbiol 2019; 67:176-189. [PMID: 31603571 DOI: 10.1111/jeu.12768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/29/2019] [Accepted: 10/04/2019] [Indexed: 11/28/2022]
Abstract
Four common earthworm species, the anecic Lumbricus terrestris, the endogeic Octolasion tyrteum as well as the epigeic Eisenia fetida and Dendrobaena veneta, were examined for the presence of the microbial gut symbiont Plagiotoma lumbrici. The evolutionary origin of this endobiotic microbe was reconstructed, using the 18S rRNA gene, the ITS1-5.8S-ITS2 region, and the first two domains of the 28S rRNA gene. Plagiotoma lumbrici was exclusively detected in the anecic Lumbricus terrestris. Multigene analyses and the ITS2 secondary structure robustly determined the phylogenetic home of Plagiotoma lumbrici populations within the oxytrichid Dorsomarginalia (Spirotrichea: Hypotrichia) as a sister taxon of the free-living Hemiurosomoida longa. This indicates that earthworms obtained their gut endosymbiont by ingesting soil/leaf litter containing oxytrichine ciliates that became adapted to the intestinal tract of earthworms. Interestingly, according to the literature data, Plagiotoma lumbrici was detected in multiple anecic and some epigeic but never in endogeic earthworms. These observations suggest that Plagiotoma lumbrici might be adapted to certain gut conditions and the lifestyle of anecic Lumbricidae, such as Lumbricus, Aporrectodea, and Scherotheca, as well as of some co-occurring epigeic Lumbricus species.
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Affiliation(s)
- Tomáš Obert
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Peter Vďačný
- Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
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Jirapatrasilp P, Backeljau T, Prasankok P, Chanabun R, Panha S. Untangling a mess of worms: Species delimitations reveal morphological crypsis and variability in Southeast Asian semi-aquatic earthworms (Almidae, Glyphidrilus). Mol Phylogenet Evol 2019; 139:106531. [PMID: 31185298 DOI: 10.1016/j.ympev.2019.106531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/19/2019] [Accepted: 06/07/2019] [Indexed: 11/26/2022]
Abstract
Semi-aquatic freshwater earthworms in the genus Glyphidrilus from Southeast Asia are characterized by both an extreme morphological crypsis among divergent phylogenetic lineages and a high morphological variability within the same phylogenetic lineages. The present study provides a new taxonomic framework for this problematic genus in SE Asia by integrating DNA sequence and morphological data. When single-locus and multilocus multispecies coalescent-based (MSC) species delimitation methods were applied to DNA sequence data, they usually yielded highly incongruent results compared to morphology-based species identifications. This suggested the presence of several cryptic species and high levels of intraspecific morphological variation. Applying reciprocal monophyly to the cytochrome c oxidase subunit 1 (COI) gene tree allowed us to propose the existence of 33 monophyletic species. Yet, often substantially more molecular operational taxonomic units (MOTUs) were obtained when species delimitation was based on COI and 16S rRNA sequences. In contrast, the ITS1 and ITS2 sequences suggested fewer MOTUs and did not recover most of the monophyletic species from the Mekong basin. However, several of these latter taxa were better supported when MSC species delimitation methods were applied to the combined mtDNA and ITS datasets. The ITS2 secondary structure retrieved one unnamed Mekong basin species that was not uncovered by the other methods when applied to ITS2 sequences. In conclusion, based on an integrative taxonomic workflow, 26 Glyphidrilus candidate species were retained and two remained to be confirmed. As such, this study provides evidence to suggest nine species new to science and to synonymize 12 nominal morphospecies. It also illustrates that the uncritical use of COI as a universal DNA barcode may overestimate species diversity because COI may be unable to distinguish between divergent conspecific lineages and different candidate species.
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Affiliation(s)
- Parin Jirapatrasilp
- Biological Sciences Program, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000 Brussels, Belgium; Evolutionary Ecology Group, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Pongpun Prasankok
- School of Biology, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Ratmanee Chanabun
- Program in Animal Science, Faculty of Agriculture Technology, Sakon Nakhon Rajabhat University, Sakon Nakhon 47000, Thailand
| | - Somsak Panha
- Animal Systematics Research Unit, Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Lim ZF, Luo Z, Lee LK, Hii KS, Teng ST, Chan LL, Chomérat N, Krock B, Gu H, Lim PT, Leaw CP. Taxonomy and toxicity of Prorocentrum from Perhentian Islands (Malaysia), with a description of a non-toxigenic species Prorocentrum malayense sp. nov. (Dinophyceae). Harmful Algae 2019; 83:95-108. [PMID: 31097256 DOI: 10.1016/j.hal.2019.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/16/2019] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Thirteen isolates of Prorocentrum species were established from the coral reefs of Perhentian Islands Marine Park, Malaysia and underwent morphological observations and molecular characterization. Six species were found: P. caipirignum, P. concavum, P. cf. emarginatum, P. lima, P. mexicanum and a new morphotype, herein designated as P. malayense sp. nov. Prorocentrum malayense, a species closely related to P. leve, P. cf. foraminosum, P. sp. aff. foraminossum, and P. concavum (Clade A sensu Chomérat et al. 2018), is distinguished from its congeners as having larger thecal pore size and a more deeply excavated V-shaped periflagellar area. Platelet arrangement in the periflagellar area of P. malayense is unique, with the presence of platelet 1a and 1b, platelet 2 being the most anterior platelet, and a broad calabash-shaped platelet 3. The species exhibits consistent genetic sequence divergences for the nuclear-encoded large subunit ribosomal RNA gene (LSU rDNA) and the second internal transcribed spacer (ITS2). The phylogenetic inferences further confirmed that it represents an independent lineage, closely related to species in Clade A sensu Chomérat et al. Pairwise comparison of ITS2 transcripts with its closest relatives revealed the presence of compensatory base changes (CBCs). Toxicity analysis showed detectable levels of okadaic acid in P. lima (1.0-1.6 pg cell-1) and P. caipirignum (3.1 pg cell-1); this is the first report of toxigenic P. caipirignum in the Southeast Asian region. Other Prorocentrum species tested, including the new species, however, were below the detection limit.
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Affiliation(s)
- Zhen Fei Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Zhaohe Luo
- Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Li Keat Lee
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Kieng Soon Hii
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Leo Lai Chan
- State Key Laboratory in Marine Pollution, Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, 999077, China
| | - Nicolas Chomérat
- IFREMER, Department ODE, Laboratory Environment and Resources Bretagne Occidentale, Station de Biologie Marine, Place de la Croix, 29900, Concarneau, France
| | - Bernd Krock
- Alfred Wegener Institut-Helmholtz Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, D-27570, Bremerhaven, Germany
| | - Haifeng Gu
- Third Institute of Oceanography, SOA, Xiamen, 361005, China
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia.
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Yang S, Xue YY, Li MH, Zhao FX, Zhao H, Zhang W. [Application of phylogenetic information of ITS2 secondary structure in DNA barcoding of Solanum medicinal plant]. Zhongguo Zhong Yao Za Zhi 2017; 42:456-464. [PMID: 28952249 DOI: 10.19540/j.cnki.cjcmm.20170103.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Indexed: 11/18/2022]
Abstract
Internal transcript spacer 2 (ITS2) is one of the broadly used standard core barcodes and also the only nuclear barcode in identification of Chinese traditional medicine. Although the DNA barcode method based on ITS2 is popular and has been used in Chinese Pharmacopoeia, its low discriminatory efficiency is still a problem to its extensive application. Therefore, further study is still necessary to explore its phylogenetic information for medicinal plants identification. In cells, ITS2 activity is based on its secondary structure. The secondary structures are particularly useful in phylogenetic analysis because they include information not found in the primary sequence. In this study ITS2 secondary structure of 40 samples from 26 species were predicted and used to explore their utility in addressing the identification problems of Chinese traditional medicine in Solanum. The secondary structures were predicted and aligned, and their consensus models were generated using the three different software of LocARNA, MASTR and PicXAA-R. RNAstat software was used to transform the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the phylogenetic information increased 88.57% after ITS2 secondary structure information has been added, and then the support values above 50%, 75% and 90% in the tree increased 19.05%, 66.67% and 66.67%, respectively, indicating that the identification of Solanum medical plants has been well resolved. Thus, our analysis suggests that ITS2 secondary structure information should be incorporated into the current DNA barcoding analysis as a beneficial supplement of phylogenetic information.
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Affiliation(s)
- Shuo Yang
- Marine College, Shandong University at Weihai, Weihai 264209, China
| | - Yuan-Yuan Xue
- Marine College, Shandong University at Weihai, Weihai 264209, China
| | - Mei-Hui Li
- Marine College, Shandong University at Weihai, Weihai 264209, China
| | - Feng-Xi Zhao
- Marine College, Shandong University at Weihai, Weihai 264209, China
| | - Hong Zhao
- Marine College, Shandong University at Weihai, Weihai 264209, China
| | - Wei Zhang
- Marine College, Shandong University at Weihai, Weihai 264209, China.,Xinjiang Education Ministry Key Laboratory of City Inteligenlizing and Environment Modeling, Urumqi 830046, China
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15
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Balzano S, Percopo I, Siano R, Gourvil P, Chanoine M, Marie D, Vaulot D, Sarno D. Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex. J Phycol 2017; 53:161-187. [PMID: 27809344 DOI: 10.1111/jpy.12489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 07/19/2016] [Indexed: 06/06/2023]
Abstract
Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.
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Affiliation(s)
- Sergio Balzano
- CNRS, UMR7144, Station Biologique De Roscoff, Sorbonne Universités, UPMC Univ Paris 06, 29680, Roscoff, France
| | - Isabella Percopo
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | | | - Priscillia Gourvil
- CNRS, UMR7144, Station Biologique De Roscoff, Sorbonne Universités, UPMC Univ Paris 06, 29680, Roscoff, France
| | - Mélanie Chanoine
- CNRS, UMR7144, Station Biologique De Roscoff, Sorbonne Universités, UPMC Univ Paris 06, 29680, Roscoff, France
| | - Dominique Marie
- CNRS, UMR7144, Station Biologique De Roscoff, Sorbonne Universités, UPMC Univ Paris 06, 29680, Roscoff, France
| | - Daniel Vaulot
- CNRS, UMR7144, Station Biologique De Roscoff, Sorbonne Universités, UPMC Univ Paris 06, 29680, Roscoff, France
| | - Diana Sarno
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
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Percopo I, Ruggiero MV, Balzano S, Gourvil P, Lundholm N, Siano R, Tammilehto A, Vaulot D, Sarno D. Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex. J Phycol 2016; 52:184-199. [PMID: 27037584 DOI: 10.1111/jpy.12395] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
A new nontoxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P. arctica is phylogenetically most closely related to P. granii and P. subcurvata, from which the species is, however, morphologically different. P. granii and P. subcurvata lack the central larger interspace which is one of the defining features of the P. pseudodelicatissima complex. The close genetic relationship between P. arctica and the two species P. granii and P. subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P. arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species.
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Affiliation(s)
- Isabella Percopo
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Maria Valeria Ruggiero
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
| | - Sergio Balzano
- Station Biologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Place Georges Teissier, Roscoff, 29680, France
| | - Priscillia Gourvil
- Station Biologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Place Georges Teissier, Roscoff, 29680, France
| | - Nina Lundholm
- The Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, Copenhagen K, 1307, Denmark
| | - Raffaele Siano
- DYNECO/Pelagos, IFREMER, Centre de Brest, BP 70, Plouzané, 29280, France
| | - Anna Tammilehto
- The Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, Copenhagen K, 1307, Denmark
| | - Daniel Vaulot
- Station Biologique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7144, Place Georges Teissier, Roscoff, 29680, France
| | - Diana Sarno
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, 80121, Italy
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Ramos V, Salvi D, Machado JP, Vale M, Azevedo J, Vasconcelos V. Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization. Toxins (Basel) 2015; 7:2514-33. [PMID: 26134259 PMCID: PMC4516926 DOI: 10.3390/toxins7072514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/06/2015] [Accepted: 06/24/2015] [Indexed: 02/03/2023] Open
Abstract
Available genomic data for the toxic, bloom-forming, benthic Ostreopsis spp. are traditionally obtained from isolates rather than from individuals originally present in environmental samples. Samples from the final phase of the first reported Ostreopsis bloom in European North Atlantic waters (Algarve, south coast of Portugal) were studied and characterized, using a culture-independent approach. In the first instance, a microscopy-based analysis revealed the intricate complexity of the samples. Then, we evaluated the adequacy of commonly used molecular tools (i.e., primers and nuclear ribosomal markers) for the study of Ostreopsis diversity in natural samples. A PCR-based methodology previously developed to identify/detect common Ostreopsis species was tested, including one new combination of existing PCR primers. Two sets of environmental rRNA sequences were obtained, one of them (1052 bp) with the newly tested primer set. These latter sequences encompass both the ITS1-5.8S-ITS2 region and the D1/D2 domain of the LSU rRNA gene, leading us to an accurate identification of ITS2. In turn, this allowed us to predict and show for the first time the ITS2 secondary structure of Ostreopsis. With 92 bp in length and a two-helix structure, the ITS2 of this genus revealed to be unique among the dinoflagellates. Both the PCR approach as the phylogenetic analyses allowed to place the Ostreopsis cells observed in the samples within the O. cf. ovata phylospecies’ complex, discarding the presence of O. cf. siamensis. The (phylo)genetic results point out a certain level of nucleotide sequence divergence, but were inconclusive in relation to a possible geographic origin of the O. cf. ovata population from the Algarve’s bloom.
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Affiliation(s)
- Vitor Ramos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Daniele Salvi
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - João Paulo Machado
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Micaela Vale
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Joana Azevedo
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Vitor Vasconcelos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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MacGillivary ML, Kaczmarska I. Paralia (Bacillariophyta) stowaways in ship ballast: implications for biogeography and diversity of the genus. ACTA ACUST UNITED AC 2015; 22:2. [PMID: 25984507 PMCID: PMC4389653 DOI: 10.1186/s40709-015-0024-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/20/2015] [Indexed: 11/17/2022]
Abstract
Background The genus Paralia Heiberg is one of the most recognizable, widely distributed and commonly reported diatoms from contemporary coastal marine environments and ship ballast. Species discovery has historically been made in diatoms through the recognition of morphological discontinuities between specimens, first using light and later electron microscopy. However, recently, morphologically semi-cryptic species of Paralia were delineated using genetic analyses, among mostly tropical and subtropical sites. Results Ten morphological characters of the frustules and sequence fragments from the nuclear genome (conserved 18S regions of ribosomal RNA and the variable internal transcribed spacer [ITS]), and from the RuBisCo large subunit (rbcL) gene of the chloroplast genome were examined. Frustule morphology did not segregate species, however, comparisons of sequence fragments and ITS2 secondary structures yielded a new species from North American waters, P. guyana (with four genodemes), and another widely-distributed species, P. marina. The latter was lecto- and epitypified here because it is most similar to specimens in the type preparation BM1021 representing Smith’s concept of the species. Paralia marina and certain genodemes of P. guyana were morphologically cryptic. Only those genodemes of P. guyana that possess prickly separation valves could be morphologically distinguished from P. marina with relative confidence in SEM preparations. All clones established from chains isolated from the ballast sediment of the ships sailing along the Atlantic coast of North America belonged to P. guyana. All DNA sequences of preserved Paralia chains recovered from the three trans-Atlantic voyages (TAVs) samples arriving to eastern Canada from Europe shared 100% identity with P. marina. Conclusion First, if the \documentclass[12pt]{minimal}
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\begin{document}$$ \overline{x} $$\end{document}x¯ = 130592 P. marina cells per ballast tank at the end of the TAVs represents their abundance in ballast tanks of similar crossings and following mid-ocean ballast water exchange, then this diatom, if de-ballasted, exerts a strong and continued propagule pressure on Eastern Canadian coasts. Despite this, as of 2009, P. marina was found only in Cheticamp, Nova Scotia, Canada. Second, genetic analysis readily segregated cryptic and semi-cryptic taxa of Paralia, highlighting the usefulness of the molecular approach to species recognition, e.g., in programs monitoring alien introductions. Electronic supplementary material The online version of this article (doi:10.1186/s40709-015-0024-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael L MacGillivary
- Department of Biology, Mount Allison University, 63B York Street, Sackville, NB E4L 1G7 Canada
| | - Irena Kaczmarska
- Department of Biology, Mount Allison University, 63B York Street, Sackville, NB E4L 1G7 Canada
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Majaneva M, Remonen I, Rintala JM, Belevich I, Kremp A, Setälä O, Jokitalo E, Blomster J. Rhinomonas nottbecki n. sp. (cryptomonadales) and molecular phylogeny of the family Pyrenomonadaceae. J Eukaryot Microbiol 2014; 61:480-92. [PMID: 24913840 DOI: 10.1111/jeu.12128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 03/09/2014] [Accepted: 03/14/2014] [Indexed: 11/30/2022]
Abstract
The cryptomonad Rhinomonas nottbecki n. sp., isolated from the Baltic Sea, is described from live and fixed cells studied by light, scanning, and transmission electron microscopy together with sequences of the partial nucleus- and nucleomorph-encoded 18S rRNA genes as well as the nucleus-encoded ITS1, 5.8S, ITS2, and the 5'-end of the 28S rRNA gene regions. The sequence analyses include comparison with 43 strains from the family Pyrenomonadaceae. Rhinomonas nottbecki cells are dorsoventrally flattened, obloid in shape; 10.0-17.2 μm long, 5.5-8.1 μm thick, and 4.4-8.8 μm wide. The inner periplast has roughly hexagonal plates. Rhinomonas nottbecki cells resemble those of Rhinomonas reticulata, but the nucleomorph 18S rRNA gene of R. nottbecki differs by 2% from that of R. reticulata, while the ITS region by 11%. The intraspecific variability in the ITS region of R. nottbecki is 5%. In addition, the predicted ITS2 secondary structures are different in R. nottbecki and R. reticulata. The family Pyrenomonadaceae includes three clades: Clade A, Clade B, and Clade C. All Rhinomonas sequences branched within the Clade C, while the genus Rhodomonas is paraphyletic. The analyses suggest that the genus Storeatula is an alternating morphotype of the genera Rhinomonas and Rhodomonas and that the family Pyrenomonadaceae includes some species that were described multiple times, as well as novel species.
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Affiliation(s)
- Markus Majaneva
- Tvärminne Zoological Station, University of Helsinki, Hanko, 10900, Finland; Marine Centre, Finnish Environment Institute, Helsinki, 00560, Finland; Department of Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland
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Kaczmarska I, Mather L, Luddington IA, Muise F, Ehrman JM. Cryptic diversity in a cosmopolitan diatom known as Asterionellopsis glacialis (Fragilariaceae): Implications for ecology, biogeography, and taxonomy. Am J Bot 2014; 101:267-286. [PMID: 24509794 DOI: 10.3732/ajb.1300306] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Diatoms have long been known as the most species-rich of algal groups, with a wide range of estimates for species number (20-200 k) due to differing species concepts. The fine valve structure in Asterionellopsis glacialis, a diatom believed cosmopolitan and eurytopic, has never been systematically examined using modern microscopy and is an excellent candidate to genetically test morphology-based conspecificity among its geographically distant culture isolates. METHODS Isolates from the Atlantic and Pacific Oceans that were morphologically delineated as A. glacialis were genetically characterized using three nuclear DNA regions (two 18S rDNA fragments and ITS region) and one plastidal (rbcL) and one mitochondrial gene (cox1) and related to SEM-based morphometrics. KEY RESULTS Five genetically distinct groupings were found, four of which are new to science. ITS2 RNA transcript secondary structure was species specific as were plastidal and mitochondrial genes, while the 18S gene fragments did not diverge sufficiently to segregate new species efficiently. We genetically circumscribed the A. glacialis epitype. CONCLUSIONS The morphological diversification of the species examined in this study lags behind their genetic divergence. The currently accepted 2% cutoff level of operational taxonomic unit (OTU) clustering in 18S rDNA environmental sequencing is too high to recognize genetic diversity in Asterionellopsis and very likely in many other species. Our results support the notion that a considerable number of species and diversity remain to be discovered among diatoms and that species number may be more in line with higher estimates. Molecular signatures of the species discovered here will aid in their globally consistent identification and ultimate understanding of their ecology.
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Affiliation(s)
- Irena Kaczmarska
- Biology Department, Mount Allison University, Sackville, New Brunswick E4L 1G7 Canada
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