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Liu B, Lan Q, Dai Q, Zhu H, Liu G. Morphology and Molecular Phylogeny of the Genus Stigeoclonium (Chaetophorales, Chlorophyta) from China, Including Descriptions of the Pseudostigeoclonium gen. nov. PLANTS (BASEL, SWITZERLAND) 2024; 13:748. [PMID: 38475594 DOI: 10.3390/plants13050748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024]
Abstract
Stigeoclonium is a genus of green algae that is widely distributed in freshwater habitats around the world. The genus comprises species with variously developed prostrates and erect systems of uniseriate branched filaments and grows attached to a wide range of different surfaces. It holds significant promise for applications in water quality indicators, sewage treatment, and the development of high-value-added products. Nevertheless, our comprehension of Stigeoclonium remains unclear and perplexing, particularly regarding its fundamental systematic taxonomy. Recent molecular analyses have revealed that the morphologically well-defined genus Stigeoclonium is polyphyletic and requires taxonomic revision. Phylogenetic analysis based on a single molecular marker and limited samples is insufficient to address the polyphyletic nature of Stigeoclonium. In the present study, 34 out of 45 strains of Stigeoclonium were newly acquired from China. Alongside the morphological data, a concatenated dataset of three markers (18S rDNA + ITS2 + tufA) was utilized to determine their molecular phylogeny. The phylogenetic analysis successfully resolved the broadly defined Stigeoclonium into three robustly supported clades (Stigeoclonim tenue clade, S. farctum clade, and S. helveticum clade). The morphological characteristics assessment results showed that the cell type of the main axis-producing branch, considered a crucial morphological characteristic of the Stigeoclonium taxonomy, did not accurately reflect the real phylogeny of the genus. A new taxonomical classification of the genus Stigeoclonium was proposed based on zoospores' germination types, which aligned well with the phylogenetic topologies. Species where zoospores showed erect germination (S. helveticum clade) formed a distinct monophyletic clade, clearly separated from the other two clades, with zoospores showing prostrate germination or pseudo-erect germination. Consequently, a new genus, Pseudostigeoclonium gen. nov., is suggested to include all species in the broadly defined Stigeoclonium with zoospores with erect germination. The taxonomic diversity is supported by distinctive morphological differences and phylogenetic divergence within the broadly defined Stigeoclonium identified in this study. Further evaluation of the genus Stigeoclonium is necessary, especially via examining additional specimens and re-evaluating morphological characters under precisely defined laboratory conditions.
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Affiliation(s)
- Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Qiumei Lan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Qingyu Dai
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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Jiménez-Gaona Y, Vivanco-Galván O, Cruz D, Armijos-Carrión A, Suárez JP. Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota). J Fungi (Basel) 2023; 9:894. [PMID: 37755002 PMCID: PMC10532482 DOI: 10.3390/jof9090894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella. OBJECTIVES The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella. METHODOLOGY Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale. RESULTS AND CONCLUSIONS The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.
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Affiliation(s)
- Yuliana Jiménez-Gaona
- Departamento de Química, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Oscar Vivanco-Galván
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Darío Cruz
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Angelo Armijos-Carrión
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada;
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
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Krivina ES, Bobrovnikova LA, Temraleeva AD, Markelova AG, Gabrielyan DA, Sinetova MA. Description of Neochlorella semenenkoi gen. et. sp. nov. (Chlorophyta, Trebouxiophyceae), a Novel Chlorella-like Alga with High Biotechnological Potential. DIVERSITY 2023. [DOI: 10.3390/d15040513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Despite many publications about Chlorella-like algae, their reliable and accurate identification is still difficult due to their simplicity and high phenotypic plasticity. The molecular approach has revolutionized our understanding of the diversity of ’small green balls’, and a natural classification of this group is currently being developed. This work is aimed at providing a detailed study of the phylogenetic position, morphology, ultrastructure, and physiology of the biotechnologically remarkable Chlorella-like strain IPPAS C-1210. Based on the SSU–ITS1–5.8S–ITS2 phylogeny, genetic distances, and the presence of compensatory base changes (CBCs) in ITS1 and conserved regions of ITS2 secondary structures, we describe a new genus, Neochlorella, with IPPAS C-1210 as the authentic strain of the type species, N. semenenkoi gen. and sp. nov. In addition, we justify the reassignment of the strain C. thermophila ITBB HTA 1–65 into N. thermophila comb. nov. The distinctive ultrastructural and physiological traits of the new species are discussed.
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Affiliation(s)
- Elena S. Krivina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Prosp. Nauki, 3, Pushchino 142290, Russia
| | - Lidia A. Bobrovnikova
- K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Botanicheskaya Str. 35, Moscow 127276, Russia
- Department of Agricultural Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100 Godollo, Hungary
| | - Anna D. Temraleeva
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Prosp. Nauki, 3, Pushchino 142290, Russia
| | - Alexandra G. Markelova
- K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Botanicheskaya Str. 35, Moscow 127276, Russia
| | - David A. Gabrielyan
- K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Botanicheskaya Str. 35, Moscow 127276, Russia
| | - Maria A. Sinetova
- K.A. Timiryazev Institute of Plant Physiology of the Russian Academy of Sciences, Botanicheskaya Str. 35, Moscow 127276, Russia
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Novis PM, Dhami M, Podolyan A, Matsumoto M, Kodner R. The austral biflagellate Chloromonas rubroleosa (Chlorophyceae) is the closest relative of the unusual quadriflagellate genus Chlainomonas, both found in snow. JOURNAL OF PHYCOLOGY 2023; 59:342-355. [PMID: 36680562 DOI: 10.1111/jpy.13318] [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: 09/14/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 05/28/2023]
Abstract
The quadriflagellate genus Chlainomonas frequently dominates red snow globally. It is unusual in several respects, with two separated pairs of flagella, apparent cell division via extrusion of cytoplasmic threads, and being nested phylogenetically within the biflagellate genus Chloromonas. Here, we showed that the austral species Chloromonas (Cr.) rubroleosa, originally described from Antarctic red snow, is a close biflagellate relative of Chlainomonas, challenging the monophyly of Chlainomonas as currently conceived. Sequences of the 18S rRNA gene robustly linked Cr. rubroleosa with near-identical environmental sequences from Antarctic red snow and Chlainomonas from North America, Japan, and Europe. Furthermore, the 18S rRNA and rbcL gene sequences of Cr. rubroleosa were almost identical to New Zealand and North American collections of Chlainomonas. Cr. rubroleosa and New Zealand Chlainomonas are separated by only a single-base substitution across the ITS1-5.8S-ITS2 rRNA loci (and according to ITS2, the North American collection is the next closest relative). This again raises the possibility that Chlainomonas is a life-cycle stage of vegetatively biflagellate organisms, although this remains confounded by the scarcity of biflagellates in field populations, the apparent cell division by quadriflagellates, and the absence of Chlainomonas-type cells in cultures of Cr. rubroleosa. The latter species is broadly similar to Chlainomonas, being poor at swimming, with similar pigment, chloroplast arrangement and ultrastructure, and is relatively large. Increased size is a feature of the wider clade of "Group D" snow algae. A synthesis of field and laboratory investigations may be needed to unravel the life cycle and correct the systematics of this group.
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Affiliation(s)
- Phil M Novis
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
| | - Manpreet Dhami
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
| | | | - Maya Matsumoto
- Department of Biology and Environmental Science, Western Washington University, Washington, USA
| | - Robin Kodner
- Department of Biology and Environmental Science, Western Washington University, Washington, USA
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Krivina E, Sinetova M, Savchenko T, Degtyaryov E, Tebina E, Temraleeva A. Micractinium lacustre and M. thermotolerans spp. nov. (Trebouxiophyceae, Chlorophyta): Taxonomy, temperature-dependent growth, photosynthetic characteristics and fatty acid composition. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
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Arteaga-Sogamoso E, Rodríguez F, Amato A, Ben-Gigirey B, Fraga S, Mafra LL, Fernandes LF, de Azevedo Tibiriçá CEJ, Chomérat N, Nishimura T, Homma C, Adachi M, Mancera-Pineda JE. Morphology and phylogeny of Prorocentrum porosum sp. nov. (Dinophyceae): A new benthic toxic dinoflagellate from the Atlantic and Pacific Oceans. HARMFUL ALGAE 2023; 121:102356. [PMID: 36639183 DOI: 10.1016/j.hal.2022.102356] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/04/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
A new marine benthic toxic Prorocentrum species is described from the tropical/subtropical regions of the Atlantic (Colombian Caribbean Sea and Northeast Brazil) and Pacific (Southern Japan) oceans. Morphological cell structures were examined using light (LM) and scanning electron (SEM) microscopy. Prorocentrum porosum sp. nov. was characterized by 35.9-50.2 μm long and 25.4-45.7 μm deep cells, covered by broadly ovoid symmetric thecal plates. The surface of both thecal plates is smooth and covered by randomly scattered kidney-shaped pores (n = 102-149), rounder towards the center, absent in the central part, and surrounded by a conspicuous marginal ring of about 69-92 evenly spaced pores. Broad V-shaped periflagellar area exhibiting flagellar and accessory pores. The molecular phylogenetic position of P. porosum sp. nov. was inferred using partial LSU rRNA gene (rDNA) and rDNA ITS sequences. This new species branched with high support in a Prorocentrum clade including P. caipirignum, P. hoffmannianum and P. cf. lima (P. lima morphotype 5 sensuZhang et al., 2015). Pairwise comparison of ITS1 and ITS2 transcripts with these closest relatives revealed the presence of compensatory base changes (CBCs), with the exception of P. cf. lima (P. lima morphotype 5), which only showed in ITS2 a hemi-CBC (HCBC) and two base changes that possibly induce a structural modification. Toxin analyses performed in two Colombian and Brazilian strains in the present study detected the presence of low amounts of okadaic acid.
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Affiliation(s)
- Edgar Arteaga-Sogamoso
- Instituto de Investigaciones Marinas y Costeras José Benito Vives de Andréis, INVEMAR, Santa Marta, Colombia. Calle 25 No. 2-55, Playa Salguero, Rodadero, Santa Marta, Colombia; Universidad Nacional de Colombia, sede Caribe, Santa Marta, Colombia. Calle 25 No. 2-55, Playa Salguero, Rodadero, Santa Marta, Colombia.
| | - Francisco Rodríguez
- Centro Nacional Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de Vigo. Subida a Radio Faro 50, 36390 Vigo, Spain; European Union Reference Laboratory for Monitoring of Marine Biotoxins, Citexvi Campus Universitario de Vigo, 36310, Vigo, Spain
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes CEA CNRS INRA IRIG-CEA Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France
| | - Begoña Ben-Gigirey
- European Union Reference Laboratory for Monitoring of Marine Biotoxins, Citexvi Campus Universitario de Vigo, 36310, Vigo, Spain
| | | | - Luiz Laureno Mafra
- Centro de Estudos do Mar, Universidade Federal do Paraná, P.O. Box 61, 83255-976, Pontal do Paraná, PR, Brazil
| | - Luciano Felício Fernandes
- Departamento de Botânica, SCB, Centro Politécnico, Universidade Federal do Paraná, P.O. Box 19031, 81531-990, Curitiba, Paraná CEP Brazil
| | | | - Nicolas Chomérat
- Station de Biologie Marine, IFREMER, Littoral, LER BO, Place de la Croix, F-29900, Concarneau, France
| | - Tomohiro Nishimura
- Cawthron Institute, 98 Halifax Street East, 7010 Nelson, New Zealand; Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, 783-8502, Kochi Japan
| | - Chiho Homma
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, 783-8502, Kochi Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, 783-8502, Kochi Japan
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Martynenko N, Gusev E, Kapustin D, Kulikovskiy M. A New Cryptic Species of the Genus Mychonastes (Chlorophyceae, Sphaeropleales). PLANTS (BASEL, SWITZERLAND) 2022; 11:3363. [PMID: 36501404 PMCID: PMC9741059 DOI: 10.3390/plants11233363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
A new species of green coccoid algae, Mychonastes hindakii sp. nov., was isolated from the River Moscow (Russia, Moscow). The taxon is described using morphological and molecular methods. Mychonastes hindakii sp. nov. belongs to the group of species of the genus Mychonastes with spherical single cells joined with mucilaginous, irregularly shaped stalks. A comparison of ITS2 rDNA sequences and its secondary structures combined with the compensatory base changes approach confirms the separation between Mychonastes hindakii and other species of the genus. Mychonastes hindakii sp. nov. represents a cryptic species that can only be reliably identified using molecular data.
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Affiliation(s)
- Nikita Martynenko
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Evgeniy Gusev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Dmitry Kapustin
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanical Street 35, 127276 Moscow, Russia
| | - Maxim Kulikovskiy
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanical Street 35, 127276 Moscow, Russia
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Species delimitation polyphasic approach reveals Meyerella similis sp. nov.: a new species of “small green balls” within the Chlorella-clade (Trebouxiophyceae, Chlorophyta). ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00590-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Liu B, Chen Y, Zhu H, Liu G. Phylotranscriptomic and Evolutionary Analyses of the Green Algal Order Chaetophorales (Chlorophyceae, Chlorophyta). Genes (Basel) 2022; 13:genes13081389. [PMID: 36011300 PMCID: PMC9407426 DOI: 10.3390/genes13081389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Considering the phylogenetic differences in the taxonomic framework of the Chaetophorales as determined by the use of nuclear molecular markers or chloroplast genes, the current study was the first to use phylotranscriptomic analyses comparing the transcriptomes of 12 Chaetophorales algal species. The results showed that a total of 240,133 gene families and 143 single-copy orthogroups were identified. Based on the single-copy orthogroups, supergene analysis and the coalescent-based approach were adopted to perform phylotranscriptomic analysis of the Chaetophorales. The phylogenetic relationships of most species were consistent with those of phylogenetic analyses based on the chloroplast genome data rather than nuclear molecular markers. The Schizomeriaceae and the Aphanochaetaceae clustered into a well-resolved basal clade in the Chaetophorales by either strategy. Evolutionary analyses of divergence time and substitution rate also revealed that the closest relationships existed between the Schizomeriaceae and Aphanochaetaceae. All species in the Chaetophorales exhibited a large number of expanded and contracted gene families, in particular the common ancestor of the Schizomeriaceae and Aphanochaetaceae. The only terrestrial alga, Fritschiella tuberosa, had the greatest number of expanded gene families, which were associated with increased fatty acid biosynthesis. Phylotranscriptomic and evolutionary analyses all robustly identified the unique taxonomic relationship of Chaetophorales consistent with chloroplast genome data, proving the advantages of high-throughput data in phylogeny.
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Affiliation(s)
- Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yangliang Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence: ; Tel.: +86-027-6878-0576
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Pánek T, Barcytė D, Treitli SC, Záhonová K, Sokol M, Ševčíková T, Zadrobílková E, Jaške K, Yubuki N, Čepička I, Eliáš M. A new lineage of non-photosynthetic green algae with extreme organellar genomes. BMC Biol 2022; 20:66. [PMID: 35296310 PMCID: PMC8928634 DOI: 10.1186/s12915-022-01263-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 12/27/2022] Open
Abstract
Background The plastid genomes of the green algal order Chlamydomonadales tend to expand their non-coding regions, but this phenomenon is poorly understood. Here we shed new light on organellar genome evolution in Chlamydomonadales by studying a previously unknown non-photosynthetic lineage. We established cultures of two new Polytoma-like flagellates, defined their basic characteristics and phylogenetic position, and obtained complete organellar genome sequences and a transcriptome assembly for one of them. Results We discovered a novel deeply diverged chlamydomonadalean lineage that has no close photosynthetic relatives and represents an independent case of photosynthesis loss. To accommodate these organisms, we establish the new genus Leontynka, with two species (L. pallida and L. elongata) distinguishable through both their morphological and molecular characteristics. Notable features of the colourless plastid of L. pallida deduced from the plastid genome (plastome) sequence and transcriptome assembly include the retention of ATP synthase, thylakoid-associated proteins, the carotenoid biosynthesis pathway, and a plastoquinone-based electron transport chain, the latter two modules having an obvious functional link to the eyespot present in Leontynka. Most strikingly, the ~362 kbp plastome of L. pallida is by far the largest among the non-photosynthetic eukaryotes investigated to date due to an extreme proliferation of sequence repeats. These repeats are also present in coding sequences, with one repeat type found in the exons of 11 out of 34 protein-coding genes, with up to 36 copies per gene, thus affecting the encoded proteins. The mitochondrial genome of L. pallida is likewise exceptionally large, with its >104 kbp surpassed only by the mitogenome of Haematococcus lacustris among all members of Chlamydomonadales hitherto studied. It is also bloated with repeats, though entirely different from those in the L. pallida plastome, which contrasts with the situation in H. lacustris where both the organellar genomes have accumulated related repeats. Furthermore, the L. pallida mitogenome exhibits an extremely high GC content in both coding and non-coding regions and, strikingly, a high number of predicted G-quadruplexes. Conclusions With its unprecedented combination of plastid and mitochondrial genome characteristics, Leontynka pushes the frontiers of organellar genome diversity and is an interesting model for studying organellar genome evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01263-w.
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Affiliation(s)
- Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Dovilė Barcytė
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 42, Vestec, Czech Republic
| | - Kristína Záhonová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Martin Sokol
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Tereza Ševčíková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Eliška Zadrobílková
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Karin Jaške
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic
| | - Naoji Yubuki
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic.,Bioimaging Facility, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, 128 43, Prague, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 00, Ostrava, Czech Republic.
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Krivina ES, Temraleeva AD, Bukin YS. Species delimitation and microalgal cryptic diversity analysis of the genus Micractinium (Chlorophyta). Vavilovskii Zhurnal Genet Selektsii 2022; 26:74-85. [PMID: 35342860 PMCID: PMC8894098 DOI: 10.18699/vjgb-22-11] [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: 04/23/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022] Open
Abstract
In this article, the system of the green microalgal genus Micractinium, based on morphological, physiological, ecological and molecular data, is considered. The main diagnostic species characteristics and the taxonomic placement of some taxa are also discussed. Phylogenetic analysis showed that the genus Micractinium is characterized by high cryptic diversity. The algorithms used for species delimitation had different results on the number of potentially species-level clusters allocated. The ABGD method was less “sensitive”. The tree-based approaches GMYC and PTP showed a more feasible taxonomy of the genus Micractinium, being an effective additional tool for distinguishing species. The clustering obtained by the latter two methods is in good congruence with morphological (cell size and shape, ability to form colonies, production of bristles, chloroplast type), physiological (vitamin requirements, reaction to high and low temperatures), molecular (presence of introns, level of genetic differences, presence of CBCs or special features of the secondary structure in ITS1 and ITS2) and ecological characteristics (habitat). The polyphyly
of the holotype of the genus M. pusillum as well as M. belenophorum is shown. The intron was effective as an additional
tool for distinguishing species, and the results of the intron analysis should be taken into account together
with other characteristics. The CBC approach, based on the search for compensatory base changes in conservative
ITS2 regions, was successful only for distinguishing cryptic species from “true” members of M. pusillum. Therefore, to
distinguish species, it is more effective to take into account all the CBC in ITS1 and ITS2 and analyze characteristic
structural differences (molecular signatures) in the secondary structure of internal transcribed spacers. The genetic
distances analysis of 18S–ITS1–5.8S–ITS2 nucleotide sequences showed that intraspecific differences in the genus
ranged from 0 to 0.5 % and interspecific differences, from 0.6 to 4.7 %. Due to the polyphasic approach, it was possible
to characterize 29 clusters and phylogenetic lines at the species level within the genus Micractinium and to
make assumptions about the species.
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Affiliation(s)
- E. S. Krivina
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”
| | - A. D. Temraleeva
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”
| | - Yu. S. Bukin
- Limnological Institute of the Siberian Branch of the Russian Academy of Sciences
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12
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Phylotranscriptomic and Evolutionary Analyses of Oedogoniales (Chlorophyceae, Chlorophyta). DIVERSITY 2022. [DOI: 10.3390/d14030157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study determined the transcriptomes of eight Oedogoniales species, including six species from Oedogonium and two species from Oedocladium to conduct phylotranscriptomic and evolutionary analyses. 155,952 gene families and 192 single-copy orthogroups were detected. Phylotranscriptomic analyses based on single-copy orthogroups were conducted using supermatrix and coalescent-based approaches. The phylotranscriptomic analysis results revealed that Oedogonium is polyphyletic, and Oedocladium clustered with Oedogonium. Together with the transcriptomes of the OCC clade in the public database, the phylogenetic relationship of the three orders (Oedogoniales, Chaetophorales, Chaetopeltidales) is discussed. The non-synonymous (dN) to synonymous substitution (dS) ratios of single-copy orthogroups of the terrestrial Oedogoniales species using a branch model of phylogenetic analysis by maximum likelihood were estimated, which showed that 92 single-copy orthogroups were putative rapidly evolving genes. Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses results revealed that some of the rapidly evolving genes were associated with photosynthesis, implying that terrestrial Oedogoniales species experienced rapid evolution to adapt to terrestrial habitats. The phylogenetic results combined with evolutionary analyses suggest that the terrestrialization process of Oedogoniales may have occured more than once.
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Lipid accumulation by Coelastrella multistriata (Scenedesmaceae, Sphaeropleales) during nitrogen and phosphorus starvation. Sci Rep 2021; 11:19818. [PMID: 34615938 PMCID: PMC8494790 DOI: 10.1038/s41598-021-99376-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023] Open
Abstract
A novel freshwater strain of Coelastrella multistriata MZ-Ch23 was discovered in Tula region, Russia. The identification is based on morphological features, phylogenetic analysis of SSU rDNA gene and ITS1-5.8S rDNA-ITS2 region and predicted secondary structure of the ITS2. Phylogenetic analysis places the novel strain in the "core" Coelastrella clade within the Chlorophyceae. This is the first record of Coelastrella multistriata in the algal flora of Russia. Cultivation experiments were carried out to evaluate growth dynamics of the newly identified strain and the impact of nitrogen and/or phosphorus depletion on the fatty acid profiles and lipid productivity. On the fully supplemented Bold's basal medium and under phosphorus-depleted conditions as well, the fatty acid profiles were dominated by α-linolenic acid (29.4-38.1% of total fatty acids). Depletion of either nitrogen or both nitrogen and phosphorus was associated with increased content of oleic acid (32.9-33.7%) and linoleic acid (11.9%). Prolongation of the growth to two months (instead of 25 days) resulted in increased content and diversity of very long-chain fatty acids including saturated species. The total very long-chain fatty acid content of 9.99% achieved in these experiments was 1.9-12.3-fold higher than in stress experiments. The highest variation was observed for oleic acid (3.4-33.7%). The novel strain showed the ability to accumulate lipids in amounts up to 639.8 mg L-1 under nitrogen and phosphorus starvation, which exceeds the previously obtained values for most Coelastrella strains. Thus, the newly identified MZ-Ch23 strain can be considered as a potential producer of omega-3 fatty acids on fully supplemented Bold's basal medium or as a source of biomass with high content of saturated and monounsaturated fatty acids after nitrogen and phosphorus starvation.
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14
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Krivina ES, Temraleeva AD, Bukin YS. Species Delimitation and Cryptic Diversity Analysis of Parachlorella-Сlade Microalgae (Chlorophyta). Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721040081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Kumar N, Banerjee C, Jagadevan S. Identification, characterization, and lipid profiling of microalgae Scenedesmus sp. NC1, isolated from coal mine effluent with potential for biofuel production. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00621. [PMID: 34026574 PMCID: PMC8120858 DOI: 10.1016/j.btre.2021.e00621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 01/25/2021] [Accepted: 04/16/2021] [Indexed: 11/29/2022]
Abstract
An autoflocculating microalgal strain was isolated from coal mine effluent wastewater which was named as Scenedesmus sp. NC1 after morphological and molecularly characterization. Further analysis of internal transcribed spacer 2 (ITS2) and compensatory base changes (CBCs) showed it does not belong to the clade comprising Scenedesmus sensu stricto. In stationary phase of growth, Scenedesmus sp. NC1 exhibited excellent autoflocculation efficiency (> 88 %) within 150 min of setting. Temperature, pH, and inorganic metals exhibited minor influence on the autoflocculation activity of Scenedesmus sp. NC1. The fatty acid profiling of Scenedesmus sp.NC1 showed that palmitic acid (C16:0), oleic acid (C18:1), and stearic acid (18:0) accounted for more than 68 % of total fatty acids. Moreover, Scenedesmus sp. NC1 demonstrated significant bioflocculation potential over non-flocculating freshwater microalgae, Chlorella sp. NCQ and Micractinium sp. NCS2. Hence, Scenedesmus sp. NC1 could be effective for economical harvesting of other non-flocculating microalgae for productions of biodiesel and other metabolites.
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Affiliation(s)
- Niwas Kumar
- Department of Environmental Science & Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, India
| | - Chiranjib Banerjee
- Department of Botany & Microbiology (Deemed to be University), Haridwar, 249404, Uttarakhand, India
| | - Sheeja Jagadevan
- Department of Environmental Science & Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, 826004, India
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16
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Liu B, Zhu H, Dong X, Yan Q, Liu G, Hu Z. Reassessment of suitable markers for taxonomy of Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes. J Eukaryot Microbiol 2021; 68:e12858. [PMID: 34022092 DOI: 10.1111/jeu.12858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Filamentous green algae Chaetophorales present numerous taxonomic problems as many other green algae. Phylogenetic analyses based on nuclear genes have limited solutions. Studies with appropriate chloroplast molecular markers may solve this problems; however, suitable molecular markers for the order Chaetophorales are still unknown. In this study, 50 chloroplast genomes of Chlorophyceae, including 15 of Chaetophorales, were subjected to single protein-coding gene phylogenetic analyses, and substitution rate and evolutionary rate assays, and PCR amplification verification was conducted to screen the suitable molecular markers. Phylogenetic analyses of three chloroplast representative genes (psaB, tufA, and rbcL) amplified from 124 strains of Chaetophorales showed that phylogenetic relationships were not improved by increasing the number of samples, implying that the genes themselves, rather than limited samples, were the reason for the unsupported Topology I. Seven genes (atpF, atpI, ccsA, cemA, chlB, psbB, and rpl2) with robust support were selected to be the most suitable molecular markers for phylogenetic analyses of Chaetophorales, and the concatenated seven genes could replace the time-consuming and labor-intensive phylogenetic analyses based on chloroplast genome to some extent. To further solve the taxonomic problems of Chaetophorales, suitable chloroplast markers combined with more taxon-rich approach could be helpful and efficient.
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Affiliation(s)
- Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaoqi Dong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qiufeng Yan
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhengyu Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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17
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Maltsev Y, Maltseva I, Maltseva S, Kociolek JP, Kulikovskiy M. A New Species of Freshwater Algae Nephrochlamys yushanlensis sp. nov. (Selenastraceae, Sphaeropleales) and Its Lipid Accumulation during Nitrogen and Phosphorus Starvation. JOURNAL OF PHYCOLOGY 2021; 57:606-618. [PMID: 33296071 DOI: 10.1111/jpy.13116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 10/17/2020] [Accepted: 10/28/2020] [Indexed: 06/12/2023]
Abstract
The new species Nephrochlamys yushanlensis sp. nov. is described from a freshwater plankton sample. A comparison of morphology, 18S rDNA gene and ITS2 sequences, and fatty acid profiles showed that the novel strain represents a new lineage within the genus Nephrochlamys. For the first time with a member of the Selenastraceae, experiments with phosphate and nitrate deprivation were conducted to evaluate changes in biomass, lipid and triacylglycerol (TAGs) accumulation, and composition of fatty acids. Biomass dry weight under simultaneous nitrogen and phosphorus depletion was 1.73 g · L-1 , which is significantly lower than the 2.41 g · L-1 observed in the control. All conditions of nutrient restriction significantly increased the lipid content in comparison with the control. The largest increase in the total lipid content, reaching 58.64% DW per cell at the end of cultivation, occurred with nitrogen deficiency. Significant increases in TAGs content (to 23.69% and 21.74%, respectively) occurred in phosphorus- and nitrogen-depleted conditions in comparison to the control (16.90%). Oleic (49.8-64.1%), palmitic (21.1-22.7%), and linoleic (8.6-10.3%) acids were the dominant fatty acids when cultured on standard BBM medium, as well as with the shortage of nutrients. Phosphorus deprivation as well as absence of both nitrogen and phosphorus led to the appearance of FAMEs α-linolenic (1.5-4.1%) and stearidonic (1.0-1.8%) acids. In general, FAME profiles revealed that the relative percentage of saturated and monounsaturated fatty acids increased (88.9% of total fatty acids) in nitrogen-depletion conditions, suggesting this strain may be suitable for biodiesel production.
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Affiliation(s)
- Yevhen Maltsev
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Irina Maltseva
- Bohdan Khmelnytskyi Melitopol State Pedagogical University, 72312, Melitopol, Ukraine
| | - Svetlana Maltseva
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - John Patrick Kociolek
- Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Maxim Kulikovskiy
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
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18
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Greczek-Stachura M, Leśnicka PZ, Tarcz S, Rautian M, Możdżeń K. Genetic Diversity of Symbiotic Green Algae of Paramecium bursaria Syngens Originating from Distant Geographical Locations. PLANTS (BASEL, SWITZERLAND) 2021; 10:609. [PMID: 33806926 PMCID: PMC8005025 DOI: 10.3390/plants10030609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/16/2021] [Accepted: 03/21/2021] [Indexed: 11/16/2022]
Abstract
Paramecium bursaria (Ehrenberg 1831) is a ciliate species living in a symbiotic relationship with green algae. The aim of the study was to identify green algal symbionts of P. bursaria originating from distant geographical locations and to answer the question of whether the occurrence of endosymbiont taxa was correlated with a specific ciliate syngen (sexually separated sibling group). In a comparative analysis, we investigated 43 P. bursaria symbiont strains based on molecular features. Three DNA fragments were sequenced: two from the nuclear genomes-a fragment of the ITS1-5.8S rDNA-ITS2 region and a fragment of the gene encoding large subunit ribosomal RNA (28S rDNA), as well as a fragment of the plastid genome comprising the 3'rpl36-5'infA genes. The analysis of two ribosomal sequences showed the presence of 29 haplotypes (haplotype diversity Hd = 0.98736 for ITS1-5.8S rDNA-ITS2 and Hd = 0.908 for 28S rDNA) in the former two regions, and 36 haplotypes in the 3'rpl36-5'infA gene fragment (Hd = 0.984). The following symbiotic strains were identified: Chlorella vulgaris, Chlorella variabilis, Chlorella sorokiniana and Micractinium conductrix. We rejected the hypotheses concerning (i) the correlation between P. bursaria syngen and symbiotic species, and (ii) the relationship between symbiotic species and geographic distribution.
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Affiliation(s)
- Magdalena Greczek-Stachura
- Institute of Biology, Pedagogical University of Krakow, Podchorążych 2, 30-084 Kraków, Poland; (M.G.-S.); (P.Z.L.)
| | - Patrycja Zagata Leśnicka
- Institute of Biology, Pedagogical University of Krakow, Podchorążych 2, 30-084 Kraków, Poland; (M.G.-S.); (P.Z.L.)
| | - Sebastian Tarcz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Sławkowska 17, 31-016 Krakow, Poland;
| | - Maria Rautian
- Laboratory of Protistology and Experimental Zoology, Faculty of Biology and Soil Science, St. Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia;
| | - Katarzyna Możdżeń
- Institute of Biology, Pedagogical University of Krakow, Podchorążych 2, 30-084 Kraków, Poland; (M.G.-S.); (P.Z.L.)
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19
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Gálvez FE, Saldarriaga-Córdoba M, Huovinen P, Silva AX, Gómez I. Revealing the Characteristics of the Antarctic Snow Alga Chlorominima collina gen. et sp. nov. Through Taxonomy, Physiology, and Transcriptomics. FRONTIERS IN PLANT SCIENCE 2021; 12:662298. [PMID: 34163502 PMCID: PMC8215615 DOI: 10.3389/fpls.2021.662298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/10/2021] [Indexed: 05/13/2023]
Abstract
Snow algae play crucial roles in cold ecosystems, however, many aspects related to their biology, adaptations and especially their diversity are not well known. To improve the identification of snow algae from colored snow, in the present study we used a polyphasic approach to describe a new Antarctic genus, Chlorominima with the species type Chlorominima collina. This new taxon was isolated of colored snow collected from the Collins Glacier (King George Island) in the Maritime Antarctic region. Microscopy revealed biflagellated ellipsoidal cells with a rounded posterior end, a C-shaped parietal chloroplast without a pyrenoid, eyespot, and discrete papillae. Several of these characteristics are typical of the genus Chloromonas, but the new isolate differs from the described species of this genus by the unusual small size of the cells, the presence of several vacuoles, the position of the nucleus and the shape of the chloroplast. Molecular analyzes confirm that the isolated alga does not belong to Chloromonas and therefore forms an independent lineage, which is closely related to other unidentified Antarctic and Arctic strains, forming a polar subclade in the Stephanosphaerinia phylogroup within the Chlamydomonadales. Secondary structure comparisons of the ITS2 rDNA marker support the idea that new strain is a distinct taxon within of Caudivolvoxa. Physiological experiments revealed psychrophilic characteristics, which are typical of true snow algae. This status was confirmed by the partial transcriptome obtained at 2°C, in which various cold-responsive and cryoprotective genes were identified. This study explores the systematics, cold acclimatization strategies and their implications for the Antarctic snow flora.
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Affiliation(s)
- Francisca E. Gálvez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
- *Correspondence: Francisca E. Gálvez,
| | - Mónica Saldarriaga-Córdoba
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Pirjo Huovinen
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Andrea X. Silva
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- AUSTRAL-omics, Vicerrectoría de Investigación, Desarrollo y Creación Artística, Universidad Austral de Chile, Valdivia, Chile
| | - Iván Gómez
- Instituto de Ciencias Marinas y Limnológicas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- Centro FONDAP de Investigación en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
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20
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Namba N, Nakayama T. Taxonomic study of a new green alga, Annulotesta cochlephila gen. et sp. nov. (Kornmanniaceae, Ulvales, Ulvophyceae), growing on the shells of door snails. JOURNAL OF PLANT RESEARCH 2021; 134:77-89. [PMID: 33387091 PMCID: PMC8938341 DOI: 10.1007/s10265-020-01239-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/09/2020] [Indexed: 06/12/2023]
Abstract
Some algae are known to grow on shellfish shells. Most of these have been reported in aquatic environments. The species specificity for substrate shells varies, and some algae grow only on the shells of a certain species of shellfish, such as Pseudocladophora conchopheria (Cladophorales, Ulvophyceae) on Lunella coreensis (Trochida, Gastropoda). There are very few reports of algae that grow on land snails. In this study, we discovered green algae growing on the shells of six species of door snails (Clausiliidae) from nine localities in Japan. These green algae formed a green mat composed of thalli embedded in the extracellular matrix. The thallus was composed of aggregated oval cells and peripheral branched filaments. The cells possessed a single parietal chloroplast with a pyrenoid surrounded by two starch sheaths and transversed by a thylakoid. Oil droplets in the cell and ring-like structures on the cell wall surface were frequently observed. The 18S rDNA sequences of all shell-attached algae on different clausiliid species from different localities were almost identical and formed a new clade in the family Kornmanniaceae (Ulvales, Ulvophyceae). No other algae forming visible colonies on the clausiliid shell were found. These findings indicate the presence of specificity between the alga and clausiliid shells. Based on the results of morphological observation and molecular phylogenetic analysis, we propose a new genus and new species of shell-attached green alga, Annulotesta cochlephila.
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Affiliation(s)
- Noriaki Namba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takeshi Nakayama
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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21
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Krivina ES, Temraleeva AD. Identification Problems and Cryptic Diversity of Chlorella-Clade Microalgae (Chlorophyta). Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720060107] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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Martignier A, De Respinis S, Filella M, Segovia-Campos I, Marin B, Günther G, Barja F, Tonolla M, Jaquet JM, Melkonian M, Ariztegui D. Biomineralization Capacities of Chlorodendrophyceae: Correlation Between Chloroplast Morphology and the Distribution of Micropearls in the Cell. Protist 2020; 171:125760. [DOI: 10.1016/j.protis.2020.125760] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/17/2020] [Accepted: 08/22/2020] [Indexed: 11/30/2022]
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23
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Zhang W, Tian W, Gao Z, Wang G, Zhao H. Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint. Int J Mol Sci 2020; 21:ijms21176395. [PMID: 32899108 PMCID: PMC7504139 DOI: 10.3390/ijms21176395] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 is under evolutionary constraints to maintain the specific secondary structures that provide functionality. A link between function, structure and evolution could contribute an understanding to each other and recently has created a growing point of sequence-structure phylogeny of ITS2. Here we briefly review the current knowledge of ITS2 processing in ribosome biogenesis, focusing on the conservative characteristics of ITS2 secondary structure, including structure form, structural motifs, cleavage sites, and base-pair interactions. We then review the phylogenetic implications and applications of this structure information, including structure-guiding sequence alignment, base-pair mutation model, and species distinguishing. We give the rationale for why incorporating structure information into tree construction could improve reliability and accuracy, and some perspectives of bioinformatics coding that allow for a meaningful evolutionary character to be extracted. In sum, this review of the integration of function, structure and evolution of ITS2 will expand the traditional sequence-based ITS2 phylogeny and thus contributes to the tree of life. The generality of ITS2 characteristics may also inspire phylogenetic use of other similar structural regions.
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Affiliation(s)
- Wei Zhang
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
- Correspondence: ; Tel.: +86-631-5688-303
| | - Wen Tian
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214440, China;
| | - Zhipeng Gao
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
| | - Guoli Wang
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
| | - Hong Zhao
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
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Liu B, Hu Y, Hu Z, Liu G, Zhu H. Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes. BMC Genomics 2020; 21:442. [PMID: 32590931 PMCID: PMC7320567 DOI: 10.1186/s12864-020-06845-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/17/2020] [Indexed: 11/11/2022] Open
Abstract
Background Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily based on short and less informative rDNA sequences. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme, and to further understand the evolution of order Chaetophorales. Results In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships. Conclusions chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.
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Affiliation(s)
- Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuxin Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhengyu Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Huan Zhu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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25
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Procházková L, Leya T, Křížková H, Nedbalová L. Sanguina nivaloides and Sanguina aurantia gen. et spp. nov. (Chlorophyta): the taxonomy, phylogeny, biogeography and ecology of two newly recognised algae causing red and orange snow. FEMS Microbiol Ecol 2020; 95:5487888. [PMID: 31074825 PMCID: PMC6545352 DOI: 10.1093/femsec/fiz064] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/09/2019] [Indexed: 12/15/2022] Open
Abstract
Melting snowfields in polar and alpine regions often exhibit a red and orange colouration caused by microalgae. The diversity of these organisms is still poorly understood. We applied a polyphasic approach using three molecular markers and light and electron microscopy to investigate spherical cysts sampled from alpine mountains in Europe, North America and South America as well as from both polar regions. Molecular analyses revealed the presence of a single independent lineage within the Chlamydomonadales. The genus Sanguina is described, with Sanguina nivaloides as its type. It is distinguishable from other red cysts forming alga by the number of cell wall layers, cell size, cell surface morphology and habitat preference. Sanguina nivaloides is a diverse species containing a total of 18 haplotypes according to nuclear ribosomal DNA internal transcribed spacer 2, with low nucleotide divergence (≤3.5%). Based on molecular data we demonstrate that it has a cosmopolitan distribution with an absence of geographical structuring, indicating an effective dispersal strategy with the cysts being transported all around the globe, including trans-equatorially. Additionally, Sanguina aurantia is described, with small spherical orange cysts often clustered by means of mucilaginous sheaths, and causing orange blooms in snow in subarctic and Arctic regions.
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Affiliation(s)
- Lenka Procházková
- Charles University, Faculty of Science, Department of Ecology, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Thomas Leya
- Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses IZI-BB, Extremophile Research & Biobank CCCryo, Am Muehlenberg 13, 14476 Potsdam-Golm, Germany
| | - Heda Křížková
- Charles University, Faculty of Science, Department of Ecology, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Linda Nedbalová
- Charles University, Faculty of Science, Department of Ecology, Viničná 7, 128 44 Prague 2, Czech Republic.,The Czech Academy of Sciences, Institute of Botany, Dukelská 135, Třeboň, 379 82, Czech Republic
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Lutz S, Procházková L, Benning LG, Nedbalová L, Remias D. Evaluating High-Throughput Sequencing Data of Microalgae Living in Melting Snow: Improvements and Limitations 1. FOTTEA (PRAHA) 2019; 19:115-131. [PMID: 33414851 PMCID: PMC7116558 DOI: 10.5507/fot.2019.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Melting snow fields are an extremophilic habitat dominated by closely related Chlamydomonadaceae (Chlorophyta). Microscopy-based classification of these cryophilic microalgae is challenging and may not reveal the true diversity. High-throughput sequencing (HTS) allows for a more comprehensive evaluation of the community. However, HTS approaches have been rarely used in such ecosystems and the output of their application has not been evaluated. Furthermore, there is no consensus on the choice for a suitable DNA marker or data processing workflow. We found that the correct placement of taxonomic strings onto OTUs strongly depends on the quality of the reference databases. We improved the assignments of the HST data by generating additional reference sequences of the locally abundant taxa, guided by light microscopy. Furthermore, a manual inspection of all automated OTU assignments, oligotyping of the most abundant 18S OTUs, as well as ITS2 secondary structure analyses were necessary for accurate species assignments. Moreover, the sole use of one marker can cause misleading results, either because of insufficient variability within the locus (18S) or the scarcity of reference sequences (ITS2). Our evaluation reveals that HTS output needs to be thoroughly checked when the studied habitats or organisms are poorly represented in publicly available databases. We recommend an optimized workflow for an improved biodiversity evaluation of not only snow algal communities, but generally 'exotic' ecosystems where similar problems arise. A consistent sampling strategy, two- molecular marker approach, light microscopy-based guidance, generation of appropriate reference sequences and final manual verification of all taxonomic assignments are highly recommended.
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Affiliation(s)
| | | | - Liane G. Benning
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany School of Earth & Environment, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany
| | - Linda Nedbalová
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44 Prague 2, Czech Republic
- The Czech Academy of Sciences, Institute of Botany, Dukelská 135, 379 82 Třeboň, Czech Republic
| | - Daniel Remias
- University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria
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Maltsev Y, Maltseva I, Maltseva S, Kociolek JP, Kulikovskiy M. Fatty Acid Content and Profile of the Novel Strain of Coccomyxa elongata (Trebouxiophyceae, Chlorophyta) Cultivated at Reduced Nitrogen and Phosphorus Concentrations. JOURNAL OF PHYCOLOGY 2019; 55:1154-1165. [PMID: 31318981 DOI: 10.1111/jpy.12903] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
A novel freshwater strain of Coccomyxa elongata (MZ-Ch64) was isolated from the Zaporizhia region, Ukraine. The identification was based on the phylogenetic analysis of SSU rDNA gene and ITS1-5.8S rDNA-ITS2 region and predicted secondary structure of the ITS2. Phylogenetic analysis placed this strain in the Coccomyxa group, within the class Trebouxiophyceae. The novel strain MZ-Ch64 formed a strongly supported lineage closest with C. elongata. The MZ-Ch64 strain differed from the morphological description of the species by the size of vegetative cells and absence of small mucilaginous caps at one end of the cell. A number of experiments with different concentrations of phosphate and nitrate were conducted to evaluate changes in the resulting fatty acid profiles and biomass productivity. The fatty acid profile and total fatty acids varied significantly under different nutrient deficiencies. The dominant fatty acid during cultivation on standard BBM medium, as well as in phosphorus-depleted conditions, was oleic acid (to 48.0%-54.6% of total fatty acids). Absence of nitrogen alone, and absence of both nitrogen and phosphorus, led to an increase of palmitic acid (to 24.7%-25.6%), cis-7-hexadecenoic acid (to 14.8%) and α-linolenic acid (to 9.1%-10.1%) in comparison with the control sample. The greatest variation was found for oleic acid (31.9%-54.6%). Thus, this strain can be considered as a potential producer of oleic acid or cis-7-hexadecenoic and α-linolenic acids for biotechnological applications.
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Affiliation(s)
- Yevhen Maltsev
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Irina Maltseva
- Bohdan Khmelnytskyi Melitopol State Pedagogical University, 72312, Melitopol, Ukraine
| | - Svetlana Maltseva
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - John Patrick Kociolek
- Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, 80309, Boulder, Colorado, USA
| | - Maxim Kulikovskiy
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
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Li M, Zhao H, Zhao F, Jiang L, Peng H, Zhang W, Simmons MP. Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae). ANNALS OF BOTANY 2019; 124:233-243. [PMID: 31152554 PMCID: PMC6758584 DOI: 10.1093/aob/mcz062] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 04/03/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND AND AIMS Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models. METHODS We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing. KEY RESULTS Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models. CONCLUSIONS Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.
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Affiliation(s)
- Meihui Li
- Marine College, Shandong University, Weihai, China
| | - Hong Zhao
- Marine College, Shandong University, Weihai, China
| | - Fengxi Zhao
- Marine College, Shandong University, Weihai, China
| | - Lu Jiang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Wei Zhang
- Marine College, Shandong University, Weihai, China
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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Sundaresan N, Sahu AK, Jagan EG, Pandi M. Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study. Fungal Biol 2019; 123:517-527. [PMID: 31196521 DOI: 10.1016/j.funbio.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 04/01/2019] [Accepted: 05/02/2019] [Indexed: 01/19/2023]
Abstract
Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Amit Kumar Sahu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
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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] [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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Temraleeva AD, Moslalenko SV. Application of Morphological and Molecular Systematics for Identification of Green Microalgae of the Genus Chlorococcum and Some Closely Related Taxa. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719010077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Sundaresan N, Jagan EG, Kathamuthu G, Pandi M. Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia. PLoS One 2019; 14:e0215024. [PMID: 30964914 PMCID: PMC6456209 DOI: 10.1371/journal.pone.0215024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/25/2019] [Indexed: 11/19/2022] Open
Abstract
Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence-secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea, Flacourtia inermis, and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P. serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A. elaeagnoidea, F. inermis, and P. serratifolia respectively. Diversity indices were higher in A. elaeagnoidea, despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A. elaeagnoidea (39%) and P. serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F. inermis. Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - GokulRaj Kathamuthu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
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Liu B, Xiong Q, Liu X, Liu G, Hu Z. Molecular phylogeny and taxonomy of the genus Chaetophora (Chlorophyceae, Chlorophyta), including descriptions of Chaetophoropsis aershanensis gen. et sp. nov. JOURNAL OF PHYCOLOGY 2019; 55:74-83. [PMID: 30347440 DOI: 10.1111/jpy.12803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 08/08/2018] [Indexed: 06/08/2023]
Abstract
The broadly defined genus Chaetophora consisted of species with minute, uniseriate branching filaments enveloped in soft or firm mucilage forming macroscopic growths that are spherical, hemispherical, and tubercular or arbuscular, growing epiphytically on freshwater aquatic plants and other submerged surfaces in standing or fast-flowing water. Recent molecular analyses clearly showed that this genus was polyphyletic. In this study, eight strains of Chaetophora and three strains of Stigeoclonium were identified and successfully cultured. In combination with the morphological data, a concatenated data set of four markers (18S + 5.8S + ITS2+ partial 28S rDNA) was also used to determine their taxonomic relationships and phylogenetic positions. The molecular analysis resolved the broadly defined Chaetophora to at least two genera. Species with a globose thallus of genus Chaetophora formed a separate monophyletic clade, which clearly separated from, a type of lobe-form Chaetophora species. Therefore, we propose to erect a new genus, Chaetophoropsis, which includes all globose species of the Chaetophora. Chaetophoropsis aershanensis was determined to be a new species, based on its special characteristic of profuse long rhizoids. Stigeoclonium polyrhizum, as the closest relative to Chaetophoropsis, revealed its distant relationships to other species of Stigeoclonium. A globose thallus with a thick, soft mucilage matrix, and special rhizoidal branches lent further support to the placement of S. polyrhizum in the genus Chaetophoropsis and had the closest relationship to C. aershanensis. Taxonomic diversity was proven by distinctive morphological differences and by phylogenetic divergence in the broadly defined Chaetophora identified herein.
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Affiliation(s)
- Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xudong Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Guoxiang 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
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Usual alga from unusual habitats: Biodiversity of Klebsormidium (Klebsormidiophyceae, Streptophyta) from the phylogenetic superclade G isolated from biological soil crusts. Mol Phylogenet Evol 2018; 133:236-255. [PMID: 30576758 DOI: 10.1016/j.ympev.2018.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 01/13/2023]
Abstract
Seven new species and two varieties of Klebsormidium were described using an integrative approach on the base of 28 strains from the poorly studied phylogenetic superclade G. These strains originated from the unusual and exotic habitats (semi-deserts, semi-arid shrublands, Mediterranean shrub and deciduous vegetation, temperate Araucaria forests, peat bogs, dumps after coal mining, maritime sand dunes etc.) of four continents (Africa, South and North America, and Europe). Molecular phylogenies based on ITS-1,2, rbcL gene and concatenated dataset of ITS-1,2-rbcL, secondary structure of ITS-2, morphology, ecology and biogeography, micrographs and drawings of the investigated strains were assessed. Additionally, phylogeny and morphology of 18 Klebsormidium strains from other lineages isolated from the same localities (different vegetation types of Chile and maritime sand dunes of Germany) were investigated for the comparison with representatives of clade G. Clade G Klebsormidium is characterized by distant phylogenetic position from the other Klebsormidium lineages and prominent morphology: four-lobed chloroplasts and mostly short swollen cells in young culture, compact small pyrenoids, curved or disintegrated filaments, unusual elongation of cells in old culture, formation of specific cluster- and knot-like colonies on agar surface, especially prominent in strains isolated from desert regions, from which the group probably originated. Comparison of Klebsormidium diversity from different biogeographic regions showed that the representatives of clade G are common algae in regions of the southern hemisphere (South Africa and Chile) and rare representatives in terrestrial ecosystems of the northern hemisphere. Further investigation of mostly unstudied territories of the southern hemisphere could bring many surprises and discoveries, leading to a change of the present concept that Klebsormidium is cosmopolitan in distribution.
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Samanta B, Ehrman JM, Kaczmarska I. A consensus secondary structure of ITS2 for the diatom Order Cymatosirales (Mediophyceae, Bacillariophyta) and reappraisal of the order based on DNA, morphology, and reproduction. Mol Phylogenet Evol 2018; 129:117-129. [DOI: 10.1016/j.ympev.2018.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/18/2018] [Accepted: 08/23/2018] [Indexed: 01/24/2023]
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Zhu S, Li Q, Chen S, Wang Y, Zhou L, Zeng C, Dong J. Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure. PHARMACEUTICAL BIOLOGY 2018; 56:548-558. [PMID: 30392423 PMCID: PMC6225500 DOI: 10.1080/13880209.2018.1499780] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/22/2018] [Accepted: 07/06/2018] [Indexed: 05/31/2023]
Abstract
CONTEXT The plant genus Uncaria (Rubiaceae), also known as Gouteng, is the source of an important traditional Chinese medicine. Misidentification and adulteration of Gouteng affect the safety and efficacy of the medication. Phylogenetic relationships among the species of this genus are unknown. OBJECTIVE The present study sought to detect the phylogenetic relationships based on internal transcribed spacer (ITS) region of all 12 species of Uncaria recorded in the Flora of China. MATERIALS AND METHODS Accession of seven species of Uncaria served as reference samples. ITS region was used for polymerase chain reaction (PCR) amplification of the reference samples representing 39 specimens. Distance analysis, species discrimination, and secondary structure of ITS2 were used to assess the ability of ITS sequence in authenticating. The phylogenetic relationships were detected using three methods: Bayesian inference (BI), maximum likelihood (ML), and neighbor joining (NJ). RESULTS Five species of traditional Chinese medicine Gouteng were well resolved in molecular phylogenetic tree. Besides, Uncaria lancifolia Hutch. was closer to U. rhynchophylloides F.C. How and U. sessilifructus Roxb. was closer to U. laevigata Wall. within the tree. Further, we also found that ITS2 secondary structure can be a candidate tool in distinguishing two closely related species U. yunnanensis K.C.Hsia and U. lanosa Wall. For accurate identification of different species of Uncaria based on species-specific nucleotide sites, a consensus sequences database with all 12 species is established. DISCUSSIONS AND CONCLUSIONS The results are able to discriminate Uncaria species and illustrate the phylogenetic relationships, which are essential for the investigation of adulterants and misidentifications of Uncaria.
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Affiliation(s)
- Shuang Zhu
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Qiwei Li
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Shanchong Chen
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Yesheng Wang
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Lin Zhou
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Changqing Zeng
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Jun Dong
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
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Hoef-Emden K. Revision of the Genus Chroomonas HANSGIRG: The Benefits of DNA-containing Specimens. Protist 2018; 169:662-681. [DOI: 10.1016/j.protis.2018.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/29/2022]
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Martyniuk V, Karpenko N, Tarieiev A, Kostikov I. Differences of Atocion lithuanicum from A. armeria (Sileneae, Caryophyllaceae) and their hybrid by ITS1-ITS2 sequences and secondary structure of their transcripts. UKRAINIAN BOTANICAL JOURNAL 2018. [DOI: 10.15407/ukrbotj75.04.322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Maltsev Y, Gusev E, Maltseva I, Kulikovskiy M, Namsaraev Z, Petrushkina M, Filimonova A, Sorokin B, Golubeva A, Butaeva G, Khrushchev A, Zotko N, Kuzmin D. Description of a new species of soil algae, Parietochloris grandis sp. nov., and study of its fatty acid profiles under different culturing conditions. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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He L, Wang Z, Lou S, Lin X, Hu F. The complete chloroplast genome of the green algae Hariotina reticulata (Scenedesmaceae, Sphaeropleales, Chlorophyta). Genes Genomics 2018; 40:543-552. [DOI: 10.1007/s13258-018-0652-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/26/2017] [Indexed: 10/18/2022]
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Lo YT, Shaw PC. DNA barcoding in concentrated Chinese medicine granules using adaptor ligation-mediated polymerase chain reaction. J Pharm Biomed Anal 2017; 149:512-516. [PMID: 29175746 DOI: 10.1016/j.jpba.2017.11.048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/18/2017] [Accepted: 11/20/2017] [Indexed: 10/18/2022]
Abstract
The use of DNA barcodes for species identification is a common laboratory practice. However, PCR amplification of full-length DNA barcode in processed material is difficult because of severe DNA fragmentation. In this study, an adaptor ligation-mediated PCR protocol was derived to amplify sets of target DNA fragments isolated from two CCMG products. The specially designed adaptor with asymmetric strands and terminal modification avoids amplification of non-target DNA sequences. DNA extracted from Angelica sinensis and Panax notoginseng CCMG were ligated with the adaptors and amplified by an adaptor primer and a single universal barcode primer to obtain partial ITS2 sequence. Results showed that various length of DNA fragments within the ITS2 region were amplified and could be used to identify the concerned species. The adaptor ligation-mediated PCR is therefore a promising universal method for species identification in highly processed herbal products.
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Affiliation(s)
- Yat-Tung Lo
- Li Dak Sum Yip Yio Chin R & D Center for Chinese Medicine, State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK) and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T. Hong Kong, China.
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Center for Chinese Medicine, State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK) and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T. Hong Kong, China.
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Chloropicophyceae, a new class of picophytoplanktonic prasinophytes. Sci Rep 2017; 7:14019. [PMID: 29070840 PMCID: PMC5656628 DOI: 10.1038/s41598-017-12412-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/04/2017] [Indexed: 11/08/2022] Open
Abstract
Prasinophytes are a paraphyletic group of nine lineages of green microalgae that are currently classified either at the class or order level or as clades without formal taxonomic description. Prasinophyte clade VII comprises picoplanktonic algae that are important components of marine phytoplankton communities, particularly in moderately oligotrophic waters. Despite first being cultured in the 1960s, this clade has yet to be formally described. Previous phylogenetic analyses using the 18S rRNA gene divided prasinophyte clade VII into three lineages, termed A, B and C, the latter formed by a single species, Picocystis salinarum, that to date has only been found in saline lakes. Strains from lineages A and B cannot be distinguished by light microscopy and have very similar photosynthetic pigment profiles corresponding to the prasino-2A pigment group. We obtained phenotypic and genetic data on a large set of prasinophyte clade VII culture strains that allowed us to clarify the taxonomy of this important marine group. We describe two novel classes, the Picocystophyceae and the Chloropicophyceae, the latter containing two novel genera, Chloropicon and Chloroparvula, and eight new species of marine picoplanktonic green algae.
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Zahradníková M, Andersen HL, Tønsberg T, Beck A. Molecular Evidence of Apatococcus, including A. fuscideae sp. nov., as Photobiont in the Genus Fuscidea. Protist 2017; 168:425-438. [PMID: 28803921 DOI: 10.1016/j.protis.2017.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/14/2017] [Accepted: 06/19/2017] [Indexed: 01/05/2023]
Abstract
The knowledge of the taxonomy and classification of algae (including lichenized) has recently increased rapidly, but there are still many gaps. We aimed to 1) identify the Fuscidea photobionts by locating their taxonomic positions in the green algal classification, and 2) to resolve their interspecific relationships. The lichenized algae were examined based on morphological observations of axenic isolates as well as molecular studies of 18S and ITS nrDNA sequences. Analysis of the secondary structure of the ITS2 operon complemented these investigations. We found that the Fuscidea photobionts were placed within the Trebouxiophyceae, related to Apatococcus lobatus (Chodat) J.B.Petersen. Phylogenetic analyses revealed one clade nesting free-living and lichenized Apatococcus F.Brand which comprised six different lineages in the ITS phylogeny. The lichenized alga associated with the investigated Fuscidea species, except for F. lightfootii (Sm.) Coppins & James, represents a hitherto unknown lineage within Apatococcus. Fuscidea lightfootii was lichenized with a separate lineage within Apatococcus, together with free-living members, which were already known from Genbank sequences. All retrieved groups within Apatococcus were rather different in their ITS sequences, thus most likely corresponding to different species. The most common photobiont of Fuscidea species, Apatococcus fuscideae A.Beck & Zahradn., was described as new to science.
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Affiliation(s)
- Martina Zahradníková
- Department of Natural History, University Museum, University of Bergen, Allégaten 41, P.O. Box 7800, N-5020 Bergen, Norway.
| | - Heidi L Andersen
- The Arboretum and Botanical Gardens, Department of Natural History, University Museum, University of Bergen, Allégaten 41, P.O. Box 7800, N-5020 Bergen, Norway
| | - Tor Tønsberg
- Department of Natural History, University Museum, University of Bergen, Allégaten 41, P.O. Box 7800, N-5020 Bergen, Norway
| | - Andreas Beck
- Department of Lichenology and Bryology, Botanische Staatssammlung München, 80638 München, Germany
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Identity, ecology and ecophysiology of planktic green algae dominating in ice-covered lakes on James Ross Island (northeastern Antarctic Peninsula). Extremophiles 2016; 21:187-200. [PMID: 27888351 DOI: 10.1007/s00792-016-0894-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/18/2016] [Indexed: 10/20/2022]
Abstract
The aim of this study was to assess the phylogenetic relationships, ecology and ecophysiological characteristics of the dominant planktic algae in ice-covered lakes on James Ross Island (northeastern Antarctic Peninsula). Phylogenetic analyses of 18S rDNA together with analysis of ITS2 rDNA secondary structure and cell morphology revealed that the two strains belong to one species of the genus Monoraphidium (Chlorophyta, Sphaeropleales, Selenastraceae) that should be described as new in future. Immotile green algae are thus apparently capable to become the dominant primary producer in the extreme environment of Antarctic lakes with extensive ice-cover. The strains grew in a wide temperature range, but the growth was inhibited at temperatures above 20 °C, indicating their adaptation to low temperature. Preferences for low irradiances reflected the light conditions in their original habitat. Together with relatively high growth rates (0.4-0.5 day-1) and unprecedently high content of polyunsaturated fatty acids (PUFA, more than 70% of total fatty acids), it makes these isolates interesting candidates for biotechnological applications.
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Molecular phylogeny and species delimitation within the ciliate genus Spirostomum (Ciliophora, Postciliodesmatophora, Heterotrichea), using the internal transcribed spacer region. Mol Phylogenet Evol 2016; 102:128-44. [DOI: 10.1016/j.ympev.2016.05.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/23/2016] [Accepted: 05/31/2016] [Indexed: 11/23/2022]
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Nozaki H, Matsuzaki R, Yamamoto K, Kawachi M, Takahashi F. Delineating a New Heterothallic Species of Volvox (Volvocaceae, Chlorophyceae) Using New Strains of "Volvox africanus". PLoS One 2015; 10:e0142632. [PMID: 26562165 PMCID: PMC4643018 DOI: 10.1371/journal.pone.0142632] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
The volvocine algae represent an excellent model lineage in which to study evolution of female and male genders based on comparative analyses of related species. Among these species, Volvox carteri has been extensively studied as a model of an oogamous and complex organism. However, it may have unique derived features that are not present in other species of Volvox. Therefore, information regarding the characteristics of sexual reproduction of other species of Volvox is also important. In 1971, Starr studied four types of sexuality in several global strains identified as Volvox africanus; however, further taxonomic studies of these strains have been lacking, and strains of three of the four sexual types are not available. Here, we studied the morphology, sexual reproduction, and taxonomy of two V. africanus-like species isolated recently from Lake Biwa, Japan. These two species were very similar to two sexual types described by Starr in 1971: one producing dioecious sexual spheroids in heterothallic strains and the other forming both male spheroids and monoecious spheroids in a single strain. The former species produced zygotes with a reticulate cell wall, whereas a smooth zygote wall was observed in the latter species as in V. africanus previously reported from various localities around the world. Our multigene phylogenetic analysis demonstrated that these are sister species to each other. However, the presence of a compensatory base change in the most conserved region of the secondary structure of nuclear ribosomal DNA internal transcribed spacer-2, hybrid inviability demonstrated by intercrossing experiments, and morphological differences in the density of abutment between the gelatinous material of adjacent cells (individual sheaths) in the spheroid supported the recognition of the two species, V. africanus having a smooth zygote wall and V. reticuliferus Nozaki sp. nov. having a reticulate zygote wall.
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Affiliation(s)
- Hisayoshi Nozaki
- Department of Biological Sciences, Graduate school of Science, University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Ryo Matsuzaki
- Department of Biological Sciences, Graduate school of Science, University of Tokyo, Tokyo, Japan
| | - Kayoko Yamamoto
- Department of Biological Sciences, Graduate school of Science, University of Tokyo, Tokyo, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Fumio Takahashi
- Ritsumeikan University, College of Life Sciences, Kusatsu, Shiga, Japan
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Caisová L, Reyes CP, Álamo VC, Quintana AM, Surek B, Melkonian M. Barrancaceae: A new green algal lineage with structural and behavioral adaptations to a fluctuating environment. AMERICAN JOURNAL OF BOTANY 2015; 102:1482-92. [PMID: 26391710 DOI: 10.3732/ajb.1500199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/21/2015] [Indexed: 05/15/2023]
Abstract
PREMISE OF THE STUDY To enhance our knowledge of the diversity of microalgae, a phycological survey of the Canary Islands (Spain) was undertaken. Here we report the discovery of a (semi)terrestrial green filamentous alga isolated from a steep volcanic canyon on La Palma. This alga is continually exposed to changing weather conditions (floods vs. droughts) and thus provides a good opportunity to investigate possible adaptations to a semiterrestrial habitat with large fluctuations of environmental parameters. METHODS We used axenic cultures, simulated flood and drought stresses and studied their effect on the life history of the alga using light, confocal laser scanning and scanning electron microscopy including fluorescent staining. Furthermore, phylogenetic analyses using rDNA sequence comparisons were performed. KEY RESULTS Three specific life-history traits that likely represent adaptations to the fluctuating environment of the canyon were observed: (1) fragmentation through "filament splitting", a unique branching mechanism not reported before in algae and initiated by formation of oblique cross walls, (2) aplanospore formation, and (3) reproduction by multiflagellate zoospores with 4-24 flagella arranged in groups of four. Phylogenetic analyses identified the alga as Barranca multiflagellata gen. et sp. nov. (Barrancaceae fam. nov., Chaetophorales, Chlorophyceae). Moreover, the Chaetophoraceae Greville, 1824 was emended and a new family, Uronemataceae (fam. nov.) erected. CONCLUSIONS The discovery of Barrancaceae fam. nov. highlights the importance of investigating nonconventional habitats to explore microalgal diversity. The reproductive versatility demonstrated by Barranca suggests adaptation to a semiterrestrial habitat with large fluctuations in water availability.
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Affiliation(s)
- Lenka Caisová
- Universität zu Köln, Biozentrum Köln, Botanisches Institut, Zülpicher Str. 47b 50674 Köln, Germany
| | - Carolina Pérez Reyes
- Spanish Bank of Algae (BEA), University of Las Palmas de Gran Canaria, Muelle de Taliarte s/n 35214 Telde, Las Palmas, Gran Canaria, Spain
| | - Virginia Cruz Álamo
- Spanish Bank of Algae (BEA), University of Las Palmas de Gran Canaria, Muelle de Taliarte s/n 35214 Telde, Las Palmas, Gran Canaria, Spain
| | - Antera Martel Quintana
- Spanish Bank of Algae (BEA), University of Las Palmas de Gran Canaria, Muelle de Taliarte s/n 35214 Telde, Las Palmas, Gran Canaria, Spain
| | - Barbara Surek
- Universität zu Köln, Biozentrum Köln, Botanisches Institut, Zülpicher Str. 47b 50674 Köln, Germany
| | - Michael Melkonian
- Universität zu Köln, Biozentrum Köln, Botanisches Institut, Zülpicher Str. 47b 50674 Köln, Germany
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Darienko T, Gustavs L, Eggert A, Wolf W, Pröschold T. Evaluating the Species Boundaries of Green Microalgae (Coccomyxa, Trebouxiophyceae, Chlorophyta) Using Integrative Taxonomy and DNA Barcoding with Further Implications for the Species Identification in Environmental Samples. PLoS One 2015; 10:e0127838. [PMID: 26080086 PMCID: PMC4469705 DOI: 10.1371/journal.pone.0127838] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/16/2015] [Indexed: 11/19/2022] Open
Abstract
Integrative taxonomy is an approach for defining species and genera by taking phylogenetic, morphological, physiological, and ecological data into account. This approach is appropriate for microalgae, where morphological convergence and high levels of morphological plasticity complicate the application of the traditional classification. Although DNA barcode markers are well-established for animals, fungi, and higher plants, there is an ongoing discussion about suitable markers for microalgae and protists because these organisms are genetically more diverse compared to the former groups. To solve these problems, we assess the usage of a polyphasic approach combining phenotypic and genetic parameters for species and generic characterization. The application of barcode markers for database queries further allows conclusions about the ‘coverage’ of culture-based approaches in biodiversity studies and integrates additional aspects into modern taxonomic concepts. Although the culture-dependent approach revealed three new lineages, which are described as new species in this paper, the culture-independent analyses discovered additional putative new species. We evaluated three barcode markers (V4, V9 and ITS-2 regions, nuclear ribosomal operon) and studied the morphological and physiological plasticity of Coccomyxa, which became a model organism because its whole genome sequence has been published. In addition, several biotechnological patents have been registered for Coccomyxa. Coccomyxa representatives are distributed worldwide, are free-living or in symbioses, and colonize terrestrial and aquatic habitats. We investigated more than 40 strains and reviewed the biodiversity and biogeographical distribution of Coccomyxa species using DNA barcoding. The genus Coccomyxa formed a monophyletic group within the Trebouxiophyceae separated into seven independent phylogenetic lineages representing species. Summarizing, the combination of different characteristics in an integrative approach helps to evaluate environmental data and clearly identifies microalgae at generic and species levels.
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Affiliation(s)
- Tatyana Darienko
- M. G. Kholodny Institute of Botany, National Academy Science of Ukraine, Kyiv 01601, Ukraine
| | - Lydia Gustavs
- University of Rostock, Institute of Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
| | - Anja Eggert
- Leibniz Institute for Baltic Sea Research Warnemünde, Physical Oceanography, D-18119 Rostock, Germany
| | - Wiebke Wolf
- University of Rostock, Institute of Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
| | - Thomas Pröschold
- University of Rostock, Institute of Biological Sciences, Applied Ecology and Phycology, Albert-Einstein-Strasse 3, D-18059 Rostock, Germany
- University of Vienna, Department of Limnology and Biooceanography, A-1090 Vienna, Austria
- * E-mail:
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Škaloud P, Steinová J, Řídká T, Vančurová L, Peksa O. Assembling the challenging puzzle of algal biodiversity: species delimitation within the genus Asterochloris (Trebouxiophyceae, Chlorophyta). JOURNAL OF PHYCOLOGY 2015; 51:507-527. [PMID: 26986666 DOI: 10.1111/jpy.12295] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 01/19/2015] [Indexed: 06/05/2023]
Abstract
The genus Asterochloris represents one of the most common, widespread, and diverse taxa of lichen photobionts. In this report, we describe and characterize six new species (A. echinata, A. friedlii, A. gaertneri, A. leprarii, A. lobophora, and A. woessiae) that were identified during our recent investigation of photobiont diversity. We found that the species differed genetically, morphologically, ecologically, and with respect to their mycobiont partners. Statistical analyses revealed significant morphological differentiation of all six newly described species, as well as their separation from previously described Asterochloris species. Chloroplast morphology represented the best morphological marker for species delineation. In fact, each species can be recognized by the dominance and unique assemblage of particular chloroplast types. Although genetically well recognized by rapidly evolving internal transcribed spacer rDNA and actin intron markers, all 13 investigated Asterochloris species shared identical small subunit rDNA sequences. We therefore demonstrated that morphologically and ecologically diverse species can frequently be grouped into a single taxonomic unit in whole-transcriptome sequencing studies, considerably affecting the resulting estimates of species diversity. Finally, we demonstrated the presence of isogamous sexual reproduction in Asterochloris, disputing the current symbiotic dogma of the loss of sexual reproduction in algal symbionts.
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Affiliation(s)
- Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Jana Steinová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Tereza Řídká
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Lucie Vančurová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 2, 128 01, Czech Republic
| | - Ondřej Peksa
- The West Bohemian Museum in Pilsen, Kopeckého sady 2, Plzeň, 30 100, Czech Republic
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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] [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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