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von Dassow P, Mikhno M, Percopo I, Orellana VR, Aguilera V, Álvarez G, Araya M, Cornejo-Guzmán S, Llona T, Mardones JI, Norambuena L, Salas-Rojas V, Kooistra WHCF, Montresor M, Sarno D. Diversity and toxicity of the planktonic diatom genus Pseudo-nitzschia from coastal and offshore waters of the Southeast Pacific, including Pseudo-nitzschia dampieri sp. nov. HARMFUL ALGAE 2023; 130:102520. [PMID: 38061816 DOI: 10.1016/j.hal.2023.102520] [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: 06/06/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 12/18/2023]
Abstract
To expand knowledge of Pseudo-nitzschia species in the Southeast Pacific, we isolated specimens from coastal waters of central Chile (36°S-30°S), the Gulf of Corcovado, and the oceanic Robinson Crusoe Island (700 km offshore) and grew them into monoclonal strains. A total of 123 Pseudo-nitzschia strains were identified to 11 species based on sequencing of the ITS region of the nuclear rDNA and on ultrastructural and morphometric analyses of the frustule in selected representatives of each clade: P. australis, P. bucculenta, P. cf. chiniana, P. cf. decipiens, P. fraudulenta, P. hasleana, P. multistriata, P. plurisecta, P. cf. sabit, the new species P. dampieri sp. nov., and one undescribed species. Partial 18S and 28S rDNA sequences, including the hypervariable V4 and D1-D3 regions used for barcoding, were gathered from representative strains of each species to facilitate future metabarcoding studies. Results showed different levels of genetic, and at times ultrastructural, diversity among the above-mentioned entities, suggesting morphological variants (P. bucculenta), rapidly radiating complexes with ill-defined species boundaries (P. cf. decipiens and P. cf. sabit), and the presence of new species (P. dampieri sp. nov., Pseudo-nitzschia sp. 1, and probably P. cf. chiniana). Domoic acid (DA) was detected in 18 out of 82 strains tested, including those of P. australis, P. plurisecta, and P. multistriata. Toxicity varied among species mostly corresponding to expectations from previous reports, with the prominent exception of P. fraudulenta; DA was not detected in any of its 10 strains tested. In conclusion, a high diversity of Pseudo-nitzschia exists in Chilean waters, particularly offshore.
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Affiliation(s)
- Peter von Dassow
- Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile; Instituto Milenio de Oceanografía, Universidad de Concepción, Barrio Universitario S/N, Concepción, 4070112, Chile; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - Marta Mikhno
- Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Isabella Percopo
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Valentina Rubio Orellana
- Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile; Instituto Milenio de Oceanografía, Universidad de Concepción, Barrio Universitario S/N, Concepción, 4070112, Chile
| | - Víctor Aguilera
- Instituto Milenio de Oceanografía, Universidad de Concepción, Barrio Universitario S/N, Concepción, 4070112, Chile; Laboratorio de Oceanografía Desértico Costera (LODEC), Centro de Estudios Avanzados en Zonas Áridas, Larrondo 1281, Coquimbo, 1781421, Chile
| | - Gonzalo Álvarez
- Facultad de Ciencias del Mar, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo, 1781421, Chile; Centro de Investigación y Desarrollo Tecnológico en Algas (CIDTA), Universidad Católica del Norte, Larrondo 1281, Coquimbo, 1781421, Chile
| | - Michael Araya
- Centro de Investigación y Desarrollo Tecnológico en Algas (CIDTA), Universidad Católica del Norte, Larrondo 1281, Coquimbo, 1781421, Chile
| | - Sebastián Cornejo-Guzmán
- Departamento de Geofísica, Universidad de Concepción, Barrio Universitario S/N, Concepción, 4070112 Chile
| | - Tomás Llona
- Instituto Milenio de Oceanografía, Universidad de Concepción, Barrio Universitario S/N, Concepción, 4070112, Chile
| | - Jorge I Mardones
- Centro de Estudio de Algas Nocivas (CREAN), Instituto de Fomento Pesquero, Padre Harter 574, Puerto Montt, 5501679, Chile; Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O´Higgins, Santiago 8370993, Chile
| | - Luis Norambuena
- Centro de Estudio de Algas Nocivas (CREAN), Instituto de Fomento Pesquero, Padre Harter 574, Puerto Montt, 5501679, Chile
| | - Victoria Salas-Rojas
- Departamento de Ecología, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Avenida Libertador Bernardo O'Higgins 340, Santiago, 8331150, Chile; Instituto Milenio de Oceanografía, Universidad de Concepción, Barrio Universitario S/N, Concepción, 4070112, Chile
| | | | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Diana Sarno
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
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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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Gontcharov AA, Nikulin AY, Nikulin VY, Allaguvatova RZ, Bagmet VB, Abdullin SR. Ulosarcina terrestrica gen. nov., sp. nov., a New Ulvophycean Sarcinoid Alga from the Russian Far East. PLANTS (BASEL, SWITZERLAND) 2022; 11:3228. [PMID: 36501268 PMCID: PMC9737678 DOI: 10.3390/plants11233228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
Many filamentous and sarcinoid terrestrial or freshwater green algae that were previously assigned to the Chlorophyceae are members of lineages belonging to the class Ulvophyceae. One of these lineages is the Planophila-clade (Ulotrichales). Some genera in this clade share similar morphology: cell packages forming branched pseudofilaments, uniseriate or sometimes biseriate filaments, often embedded in common mucilage. During a study on soil algal diversity in the temperate monsoon climate zone in Russia (Primorsky Territory, Vladivostok), we isolated a strain of sarcinoid green alga and examined it using an integrative approach. SSU and ITS rDNA sequence data, morphological characteristics, and life cycle features differentiated this strain from closely related genera of the order Ulotrichales and led us to describe it as Ulosarcina terrestrica gen. et sp. nov.
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Réblová M, Kolařík M, Nekvindová J, Réblová K, Sklenář F, Miller AN, Hernández-Restrepo M. Phylogenetic Reassessment, Taxonomy, and Biogeography of Codinaea and Similar Fungi. J Fungi (Basel) 2021; 7:1097. [PMID: 34947079 PMCID: PMC8704094 DOI: 10.3390/jof7121097] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
The genus Codinaea is a phialidic, dematiaceous hyphomycete known for its intriguing morphology and turbulent taxonomic history. This polyphasic study represents a new, comprehensive view on the taxonomy, systematics, and biogeography of Codinaea and its relatives. Phylogenetic analyses of three nuclear loci confirmed that Codinaea is polyphyletic. The generic concept was emended; it includes four morphotypes that contribute to its morphological complexity. Ancestral inference showed that the evolution of some traits is correlated and that these traits previously used to delimit taxa at the generic level occur in species that were shown to be congeneric. Five lineages of Codinaea-like fungi were recognized and introduced as new genera: Codinaeella, Nimesporella, Stilbochaeta, Tainosphaeriella, and Xyladelphia. Dual DNA barcoding facilitated identification at the species level. Codinaea and its segregates thrive on decaying plants, rarely occurring as endophytes or plant pathogens. Environmental ITS sequences indicate that they are common in bulk soil. The geographic distribution found using GlobalFungi database was consistent with known data. Most species are distributed in either the Holarctic realm or tropical geographic regions. The ancestral climatic zone was temperate, followed by transitions to the tropics; these fungi evolved primarily in Eurasia and Americas, with subsequent transitions to Africa and Australasia.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
| | - Miroslav Kolařík
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Jana Nekvindová
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Králové, 500 05 Hradec Králové, Czech Republic;
| | - Kamila Réblová
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- CEITEC—Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - František Sklenář
- Department of Taxonomy, Institute of Botany, The Czech Academy of Sciences, 252 43 Průhonice, Czech Republic; (K.R.); (F.S.)
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology, The Czech Academy of Sciences, 142 20 Prague, Czech Republic;
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA;
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Belevich TA, Milyutina IA, Abyzova GA, Troitsky AV. The pico-sized Mamiellophyceae and a novel Bathycoccus clade from the summer plankton of Russian Arctic Seas and adjacent waters. FEMS Microbiol Ecol 2021; 97:6031321. [PMID: 33307552 DOI: 10.1093/femsec/fiaa251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Global climate changes and anthropogenic activity greatly impact Arctic marine biodiversity including phytoplankton which contribute greatly to atmospheric oxygen production. Thus the study of microalgae has rising topicality. Class Mamiellophyceae is an important component of phototrophic picoplankton. To gain more knowledge about Mamiellophyceae distribution and diversity special studies were performed in such remote areas as the Russian Arctic seas. A metabarcoding of pico-sized Mamiellophyceae was undertaken by high-throughput sequencing of the 18S rRNA gene sequence V4 region from samples collected in July-September 2017 in the Barents, Kara and Laptev seas, and in the adjacent waters of the Norwegian Sea. Our study is the first to show that Mamiellophyceae among the summer picoplankton of Russian Arctic seas are diverse and represented by 16 algae species/phylotypes. We discovered a new candidate species of Bathycoccus assigned to a new Bathycoccus clade A-uncultured Bathycoccus Kara 2017. It was found that several Micromonas species can co-exist, with Micromonas polaris dominating north of 72°N. The presence of Ostreococcus tauri, Ostreococcus lucimarinus and Ostreococcus mediterraneus at high latitudes beyond 65°N was documented for the first time, similar to findings for some other taxa. Our results will be important for obtaining a global view of Mamiellophyceae community dynamics.
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Affiliation(s)
- Tatiana A Belevich
- Lomonosov Moscow State University, Biological Faculty, Moscow, Russia.,Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Irina A Milyutina
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
| | - Galina A Abyzova
- Shirshov Institute of Oceanology, Russian Academy of Science, Moscow, Russia
| | - Aleksey V Troitsky
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, Russia
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An integrative approach sheds new light onto the systematics and ecology of the widespread ciliate genus Coleps (Ciliophora, Prostomatea). Sci Rep 2021; 11:5916. [PMID: 33723272 PMCID: PMC7960993 DOI: 10.1038/s41598-021-84265-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 01/07/2021] [Indexed: 01/05/2023] Open
Abstract
Species of the genus Coleps are one of the most common planktonic ciliates in lake ecosystems. The study aimed to identify the phenotypic plasticity and genetic variability of different Coleps isolates from various water bodies and from culture collections. We used an integrative approach to study the strains by (i) cultivation in a suitable culture medium, (ii) screening of the morphological variability including the presence/absence of algal endosymbionts of living cells by light microscopy, (iii) sequencing of the SSU and ITS rDNA including secondary structures, (iv) assessment of their seasonal and spatial occurrence in two lakes over a one-year cycle both from morphospecies counts and high-throughput sequencing (HTS), and, (v) proof of the co-occurrence of Coleps and their endosymbiotic algae from HTS-based network analyses in the two lakes. The Coleps strains showed a high phenotypic plasticity and low genetic variability. The algal endosymbiont in all studied strains was Micractinium conductrix and the mutualistic relationship turned out as facultative. Coleps is common in both lakes over the whole year in different depths and HTS has revealed that only one genotype respectively one species, C. viridis, was present in both lakes despite the different lifestyles (mixotrophic with green algal endosymbionts or heterotrophic without algae). Our results suggest a future revision of the species concept of the genus Coleps.
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Jayatunga DPW, Harischandra IN, Chandrasekharan NV, de Silva BGDNK. Compensatory Base Changes Reveal Sexual Incompatibility among Members of the Anopheles subpictus Sensu Lato (Diptera: Culicidae) Species Complex in Sri Lanka. Life (Basel) 2021; 11:life11030211. [PMID: 33800295 PMCID: PMC7998985 DOI: 10.3390/life11030211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
The mosquito Anopheles (Cellia) subpictus sensu lato (s.l.) is a major secondary vector of malaria in Sri Lanka. The sibling species composition in this species complex in Sri Lanka remains debatable. Compensatory base changes (CBCs) in the secondary structures of internal transcribed spacer 2 (ITS2) are reliable sources to predict sexual incompatibility among closely related species. The objective of the present study was to investigate the An. subpictus s.l. populations in Sri Lanka using the CBC analysis. Mosquito DNA was amplified and sequenced for the ITS2 region. The sequences were annotated using ITS2 Database. ITS2 secondary structures were constructed and analyzed for CBCs using various bioinformatics tools. The ITS2 regions consisted of two different lengths, 575 bp and 480 bp. The two CBCs and three hemi CBCs identified in the present study suggest that there may be at least two sexually incompatible sibling species. In conclusion, it is likely that there may be only two reproductively isolated sibling species in the An. subpictus species complex in Sri Lanka. However, due to high divergence of ITS2 in these species, it is reasonable to assume that they may be undergoing a speciation event to separate as a distinct species.
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Affiliation(s)
- D. P. W. Jayatunga
- Center for Biotechnology, Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
| | - I. N. Harischandra
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
| | - N. V. Chandrasekharan
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo 00300, Sri Lanka;
| | - B. G. D. N. K. de Silva
- Center for Biotechnology, Department of Zoology, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
- Genetics and Molecular Biology Unit, Faculty of Applied Sciences, University of Sri Jayewardenepura, Gangodawila, Nugegoda 10250, Sri Lanka;
- Correspondence: ; Tel.: +94-112804515 or +94-774467277
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Cultivation and characterization of snowbound microorganisms from the South Pole. Extremophiles 2021; 25:159-172. [PMID: 33590336 DOI: 10.1007/s00792-021-01218-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/28/2021] [Indexed: 02/03/2023]
Abstract
Little is known about microbial ecosystems of interior Antarctica, if indeed such ecosystems exist. Although considerable research has assessed microorganisms indigenous to coastal regions of Antarctica, particularly their lakes, ponds, and soils, to our knowledge only one characterized bacterium, a strain of Pseudomonas, has been isolated from South Pole ice or snow. Metagenomic community analyses described in this work and elsewhere reveal that a diversity of bacteria exists in inland polar snows, yet attempts to culture and characterize these microbes from this extreme environment have been few to date. In this molecular and culture-dependent investigation of the microbiology of inland Antarctica, we enriched and isolated two new strains of bacteria and one strain of yeast (Fungi) from South Pole snow samples. The bacteria were of the genera Methylobacterium and Sphingomonas, and the yeast grouped with species of Naganishia (class Tremellocytes). In addition to phylogenetic analyses, characterization of these isolates included determinations of cell morphology, growth as a function of temperature, salinity tolerance, and carbon and energy source versatility. All organisms were found to be cold-adapted, and the yeast strain additionally showed considerable halotolerance. These descriptions expand our understanding of the diversity and metabolic activities of snowbound microorganisms of interior Antarctica.
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Anaz K M, N S, A R, M V D. ITS 2 and RNA secondary structure-based analysis reveals a clear picture on phylogeny of South Indian Salacia spp. Comput Biol Chem 2021; 91:107438. [PMID: 33524844 DOI: 10.1016/j.compbiolchem.2021.107438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/02/2020] [Accepted: 01/17/2021] [Indexed: 10/22/2022]
Abstract
The genus Salacia (Celastraceae) consists of many important medicinal plants used mainly against type II diabetes. Segregation and delimitation of species is difficult based on morphological features alone. DNA barcoding is the most effective and emerging method of molecular identification. It was reported that ITS2 has better discriminating power in the genus Salacia in comparison to other barcode loci. This paper describe the analysis of sequence and structural information of ITS2 to discriminate the species of Salacia. A total of 8 species of Salacia in South India and the available sequences in NCBI database were taken for the present study. NJ method based phylogenetic trees were constructed using MEGAX with primary sequence as well as using sequence and secondary structural information. Primary structure based phylogeny did not give much information whereas the dendrogram based on sequence and structural information was more informative to decipher the phylogeny of South Asian species of Salacia. The present study revealed some interesting facts regarding the genus. Secondary structure of the ITS2 sequence of S. chinensis reported from Kerala differs consistently from that of S. chinensis reported from other parts of India and of South Asia. Probably the S. chinensis in Kerala, India has diverged a lot from the original S. chinensis. ITS2 sequence of S. reticulata reported from Sri Lanka was identical to S. chinensis reported by other groups from Thailand and Udupi, India. The molecular level identity of ITS2 sequence of S. chinensis with S. reticulata suggest merger of the two species. ITS2 sequence of S. beddomei is only reported from Kerala, India showed it to be identical to S. macrosperma. This observation points to a mistaken identity of S. beddomei which could be elusive from Kerala. Phylogenetic trees constructed based on sequence and structural features of ITS2 suggest that the ancestor species of S.chinensis diversified in two evolutionary lines. One line leads to the present day S. chinensis and the other line further diversified and lead to the rest of the present day Salacia species.
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Affiliation(s)
- Muhammad Anaz K
- Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India.
| | - Sasidharan N
- Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
| | - Remakanthan A
- Department of Botany, University College, Thiruvananthapuram, Kerala, India
| | - Dilsha M V
- Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
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Micractinium tetrahymenae (Trebouxiophyceae, Chlorophyta), a New Endosymbiont Isolated from Ciliates. DIVERSITY-BASEL 2020. [DOI: 10.3390/d12050200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Endosymbiosis between coccoid green algae and ciliates are widely distributed and occur in various phylogenetic lineages among the Ciliophora. Most mixotrophic ciliates live in symbiosis with different species and genera of the so-called Chlorella clade (Trebouxiophyceae). The mixotrophic ciliates can be differentiated into two groups: (i) obligate, which always live in symbiosis with such green algae and are rarely algae-free and (ii) facultative, which formed under certain circumstances such as in anoxic environments an association with algae. A case of the facultative endosymbiosis is found in the recently described species of Tetrahymena, T. utriculariae, which lives in the bladder traps of the carnivorous aquatic plant Utricularia reflexa. The green endosymbiont of this ciliate belonged to the genus Micractinium. We characterized the isolated algal strain using an integrative approach and compared it to all described species of this genus. The phylogenetic analyses using complex evolutionary secondary structure-based models revealed that this endosymbiont represents a new species of Micractinium, M. tetrahymenae sp. nov., which was further confirmed by the ITS2/CBC approach.
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Liu ZW, Gao YZ, Zhou J. Molecular Authentication of the Medicinal Species of Ligusticum (Ligustici Rhizoma et Radix, "Gao-ben") by Integrating Non-coding Internal Transcribed Spacer 2 (ITS2) and Its Secondary Structure. FRONTIERS IN PLANT SCIENCE 2019; 10:429. [PMID: 31024595 PMCID: PMC6465525 DOI: 10.3389/fpls.2019.00429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 03/21/2019] [Indexed: 05/16/2023]
Abstract
Ligustici Rhizoma et Radix (LReR), an important Chinese medicine known as "Gao-ben," refers to Ligusticum sinense Oliv. or Ligusticum jeholense Nakai et Kitag. However, a number of other species are commonly sold as "Gao-ben" in the herbal medicine market, which may result in a series of quality control problems and inconsistent therapeutic effects. The "Gao-ben" is commonly sold sliced and dried, making traditional identification methods difficult. Here, the mini barcode ITS2 region was examined on 68 samples representing LReR and 7 potential adulterant or substitute species. The results showed 100% success rates of PCR and sequencing and the existence of a barcoding gap. The neighbor-joining (NJ) tree indicated that all the tested samples could be exactly identified. The ITS2 secondary structure revealed a clear difference between true "Gao-ben" and three adulterant species. We therefore recommend the use of ITS2 as a mini barcode for distinguishing between closely or distantly related plant species that may be used in Chinese medicine.
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Affiliation(s)
- Zhen-wen Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yu-zhen Gao
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
| | - Jing Zhou
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, China
- *Correspondence: Jing Zhou,
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Li CY, Sun Y, Xie Y, Zhou X, Gu XB, Lai WM, Peng XR, Yang G. Genetic variability of wildlife-derived Sarcoptes scabiei determined by the ribosomal ITS-2 and mitochondrial 16S genes. EXPERIMENTAL & APPLIED ACAROLOGY 2018; 76:53-70. [PMID: 30238307 DOI: 10.1007/s10493-018-0290-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
Infestation by the ectoparasitic mite Sarcoptes scabiei (Acari: Sarcoptidae) has important implications for global wildlife conservation and both animal and human health. Ribosomal and mitochondrial DNA sequences of parasites are useful to determine genetic diversity and to describe their likely dynamic evolution. In this study, we described the genetic diversity of S. scabiei individuals collected from wild animals in China by sequencing the ribosomal ITS-2 and mitochondrial 16S rRNA genes. A total of 13 Sarcoptes isolates of wildlife, coupled with one of rabbit origin, were subjected to genetic characteristics. After cloning and sequencing, 14 ITS-2 sequences and 12 16S rRNA sequences were obtained and analyzed. Further analysis of haplotype network and population genetic structure revealed that there were 79 haplotypes in ITS-2 (main haplotype H2) and 31 haplotypes in 16S rRNA (main haplotype C10). The phylogenetic trees showed some partial clustering by location and host, and the analysis of gene polymorphism may prompt that all isolates of S. scabiei have a similar origin. We speculate that the genetic evolution of S. scabiei may be related with that of the hosts, but more research is necessary to better understand the host-parasite co-evolutionary relationship in S. scabiei. These results provide new insights into understanding the population genetics and evolutionary biology of S. scabiei and therefore a better understanding of controlling its infestation pathways worldwide.
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Affiliation(s)
- Chun-Yan Li
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan Province, China
| | - Yin Sun
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan Province, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan Province, China
| | - Xuan Zhou
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Bin Gu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan Province, China
| | - Wei-Ming Lai
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan Province, China
| | - Xue-Rong Peng
- Department of Chemistry, College of Life and Basic Science, Sichuan Agricultural University, Wenjiang, China
| | - Guangyou Yang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 211 Huimin Road, Wenjiang, Chengdu, 611130, Sichuan Province, China.
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13
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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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14
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Landis FC, Gargas A. Using ITS2 secondary structure to create species-specific oligonucleotide probes for fungi. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Frank C. Landis
- Botany Department, University of Wisconsin-Madison, Madison, Wisconsin 53706
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15
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Réblová M, Hubka V, Thureborn O, Lundberg J, Sallstedt T, Wedin M, Ivarsson M. From the Tunnels into the Treetops: New Lineages of Black Yeasts from Biofilm in the Stockholm Metro System and Their Relatives among Ant-Associated Fungi in the Chaetothyriales. PLoS One 2016; 11:e0163396. [PMID: 27732675 PMCID: PMC5061356 DOI: 10.1371/journal.pone.0163396] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/14/2016] [Indexed: 11/25/2022] Open
Abstract
Rock-inhabiting fungi harbour species-rich, poorly differentiated, extremophilic taxa of polyphyletic origin. Their closest relatives are often well-known species from various biotopes with significant pathogenic potential. Speleothems represent a unique rock-dwelling habitat, whose mycobiota are largely unexplored. Isolation of fungi from speleothem biofilm covering bare granite walls in the Kungsträdgården metro station in Stockholm yielded axenic cultures of two distinct black yeast morphotypes. Phylogenetic analyses of DNA sequences from six nuclear loci, ITS, nuc18S and nuc28S rDNA, rpb1, rpb2 and β-tubulin, support their placement in the Chaetothyriales (Ascomycota). They are described as a new genus Bacillicladium with the type species B. lobatum, and a new species Bradymyces graniticola. Bacillicladium is distantly related to the known five chaetothyrialean families and is unique in the Chaetothyriales by variable morphology showing hyphal, meristematic and yeast-like growth in vitro. The nearest relatives of Bacillicladium are recruited among fungi isolated from cardboard-like construction material produced by arboricolous non-attine ants. Their sister relationship is weakly supported by the Maximum likelihood analysis, but strongly supported by Bayesian inference. The genus Bradymyces is placed amidst members of the Trichomeriaceae and is ecologically undefined; it includes an opportunistic animal pathogen while two other species inhabit rock surfaces. ITS rDNA sequences of three species accepted in Bradymyces and other undescribed species and environmental samples were subjected to phylogenetic analysis and in-depth comparative analysis of ITS1 and ITS2 secondary structures in order to study their intraspecific variability. Compensatory base change criterion in the ITS2 secondary structure supported delimitation of species in Bradymyces, which manifest a limited number of phenotypic features useful for species recognition. The role of fungi in the speleothem biofilm and relationships of Bacillicladium and Bradymyces with other members of the Chaetothyriales are discussed.
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Affiliation(s)
- Martina Réblová
- Department of Taxonomy, Institute of Botany of the Czech Academy of Sciences, 252 43, Průhonice, Czech Republic
- * E-mail:
| | - Vit Hubka
- Department of Botany, Faculty of Science, Charles University in Prague, 128 01, Prague, 2, Czech Republic
- Laboratory of Fungal Genetics and Metabolism, Institute of Microbiology of the Czech Academy of Sciences, 142 20, Prague, 4, Czech Republic
| | - Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91, Stockholm, Sweden
| | - Johannes Lundberg
- Department of Botany, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
| | - Therese Sallstedt
- Department of Biology, University of Southern Denmark, 5230, Odense, Denmark
- Department of Palaeobiology, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
| | - Mats Wedin
- Department of Botany, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
| | - Magnus Ivarsson
- Department of Palaeobiology, Swedish Museum of Natural History, 104 05, Stockholm, Sweden
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MacDonald SM, Lee RW. A survey of Polytomella (Chlorophyceae, Chlorophyta) strains in public culture collections. JOURNAL OF PHYCOLOGY 2016; 52:656-663. [PMID: 27168310 DOI: 10.1111/jpy.12430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 03/28/2016] [Indexed: 06/05/2023]
Abstract
Polytomella is a genus of colorless green algae in the Reinhardtinia clade of the Chlamydomonadales, which has proven useful for a broad range of studies particularly those exploring the evolutionary loss of photosynthesis and mitochondrial genomics/biochemistry. Although 13 Polytomella strain accessions are currently available from public culture collections, the taxonomic status and redundancy of many of these strains is not clear because of possible mix-ups, deficient historical records, and incomplete molecular data. This study therefore considers previously available and/or new cox1 and mitochondrial DNA telomere sequences from all 13 Polytomella strain accessions. Among four of these, namely P. parva SAG 63-3, P. piriformis SAG 63-10, P. capuana SAG 63-5, and P. magna SAG 63-9, cox1 and mitochondrial telomere regions are both highly divergent between strains. All of the remaining nine Polytomella strain accessions have cox1 sequences that are identical to that of P. parva SAG 63-3 and although five of these have a mitochondrial telomere haplotype that is identical to that of P. parva SAG 63-3, the remaining four have one of three different haplotypes. Among the 10 strains with identical cox1 sequences, we suggest that three of the telomere haplotypes are associated with distinct geographical isolates of Polytomella and the fourth evolved from one of these isolates during 50 years of active culture.
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Affiliation(s)
- Shelley M MacDonald
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia, Canada, B3H 4R2
| | - Robert W Lee
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, Nova Scotia, Canada, B3H 4R2
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Munakata H, Nakada T, Nakahigashi K, Nozaki H, Tomita M. Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis
(Volvocales, Chlorophyceae), among Unicellular Algae. J Eukaryot Microbiol 2015; 63:340-8. [DOI: 10.1111/jeu.12283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 11/10/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Hidehito Munakata
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Takashi Nakada
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Kenji Nakahigashi
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences; Graduate School of Science; University of Tokyo; 7-3-1 Hongo, Bunkyo Tokyo 113-0033 Japan
| | - Masaru Tomita
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
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Zhang W, Yuan Y, Yang S, Huang J, Huang L. ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding. PLoS One 2015; 10:e0131185. [PMID: 26132382 PMCID: PMC4488503 DOI: 10.1371/journal.pone.0131185] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/30/2015] [Indexed: 01/25/2023] Open
Abstract
DNA barcoding is a promising species identification method, but it has proved difficult to find a standardized DNA marker in plant. Although the ITS/ITS2 RNA transcript has been proposed as the core barcode for seed plants, it has been criticized for being too conserved in some species to provide enough information or too variable in some species to align it within the different taxa ranks. We selected 30 individuals, representing 16 species and four families, to explore whether ITS2 can successfully resolve species in terms of secondary structure. Secondary structure was predicted using Mfold software and sequence-structure was aligned by MARNA. RNAstat software transformed the secondary structures into 28 symbol code data for maximum parsimony (MP) analysis. The results showed that the ITS2 structures in our samples had a common four-helix folding type with some shared motifs. This conserved structure facilitated the alignment of ambiguous sequences from divergent families. The structure alignment yielded a MP tree, in which most topological relationships were congruent with the tree constructed using nucleotide sequence data. When the data was combined, we obtained a well-resolved and highly supported phylogeny, in which individuals of a same species were clustered together into a monophyletic group. As a result, the different species that are often referred to as the herb “Mu tong” were successfully identified using short fragments of 250 bp ITS2 sequences, together with their secondary structure. Thus our analysis strengthens the potential of ITS2 as a promising DNA barcode because it incorporates valuable secondary structure information that will help improve discrimination between species.
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Affiliation(s)
- Wei Zhang
- Marine College, Shandong University at Weihai, Weihai, Shandong, China; State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuan Yuan
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shuo Yang
- Marine College, Shandong University at Weihai, Weihai, Shandong, China
| | - Jianjun Huang
- Marine College, Shandong University at Weihai, Weihai, Shandong, China
| | - Luqi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Marques S, Huss VAR, Pfisterer K, Grosse C, Thompson G. Internal transcribed spacer sequence-based rapid molecular identification of Prototheca zopfii and Prototheca blaschkeae directly from milk of infected cows. J Dairy Sci 2015; 98:3001-9. [PMID: 25726118 DOI: 10.3168/jds.2014-9271] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 01/23/2015] [Indexed: 11/19/2022]
Abstract
The increasing incidence of rare mastitis-causing pathogens has urged the implementation of fast and efficient diagnostic and control measures. Prototheca algae are known to be associated with diseases in humans and animals. In the latter, the most prevalent form of protothecosis is bovine mastitis with Prototheca zopfii and Prototheca blaschkeae representing the most common pathogenic species. These nonphotosynthetic and colorless green algae are ubiquitous in different environments and are widely resistant against harmful conditions and antimicrobials. Hence, the association of Prototheca with bovine mastitis represents a herd problem, requiring fast and easy identification of the infectious agent. The purpose of this study was to develop a reliable and rapid method, based on the internal transcribed spacer (ITS) sequences of ribosomal DNA, for molecular identification and discrimination between P. zopfii and P. blaschkeae in bovine mastitic milk. The complete ITS sequences of 32 Prototheca isolates showed substantial interspecies but moderate intraspecies variability facilitating the design of species-specific PCR amplification primers. The species-specific PCR was successfully applied to the identification of P. zopfii and P. blaschkeae directly from milk samples. The intraspecific ITS phylogeny was compared for each species with the geographical distribution of the respective Prototheca isolates, but no significant correlation was found.
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Affiliation(s)
- S Marques
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO/UP), InBio Laboratório Associado Campus Agrário de Vairão, Rua Padre Armando Quintas, n 7, 4485-661 Vairão, Portugal; Laboratório de Doenças Infecciosas do Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, n 228, 4050-313 Porto, Portugal.
| | - V A R Huss
- Department of Biology, Molecular Plant Physiology, University of Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - K Pfisterer
- Department of Biology, Molecular Plant Physiology, University of Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - C Grosse
- Department of Biology, Molecular Plant Physiology, University of Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - G Thompson
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO/UP), InBio Laboratório Associado Campus Agrário de Vairão, Rua Padre Armando Quintas, n 7, 4485-661 Vairão, Portugal; Laboratório de Doenças Infecciosas do Departamento de Clínicas Veterinárias, Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Rua de Jorge Viterbo Ferreira, n 228, 4050-313 Porto, Portugal
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Kawafune K, Hongoh Y, Hamaji T, Sakamoto T, Kurata T, Hirooka S, Miyagishima SY, Nozaki H. Two different rickettsial bacteria invading Volvox carteri. PLoS One 2015; 10:e0116192. [PMID: 25671568 PMCID: PMC4324946 DOI: 10.1371/journal.pone.0116192] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 12/02/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Bacteria of the family Rickettsiaceae are principally associated with arthropods. Recently, endosymbionts of the Rickettsiaceae have been found in non-phagotrophic cells of the volvocalean green algae Carteria cerasiformis, Pleodorina japonica, and Volvox carteri. Such endosymbionts were present in only C. cerasiformis strain NIES-425 and V. carteri strain UTEX 2180, of various strains of Carteria and V. carteri examined, suggesting that rickettsial endosymbionts may have been transmitted to only a few algal strains very recently. However, in preliminary work, we detected a sequence similar to that of a rickettsial gene in the nuclear genome of V. carteri strain EVE. METHODOLOGY/PRINCIPAL FINDINGS Here we explored the origin of the rickettsial gene-like sequences in the endosymbiont-lacking V. carteri strain EVE, by performing comparative analyses on 13 strains of V. carteri. By reference to our ongoing genomic sequence of rickettsial endosymbionts in C. cerasiformis strain NIES-425 cells, we confirmed that an approximately 9-kbp DNA sequence encompassing a region similar to that of four rickettsial genes was present in the nuclear genome of V. carteri strain EVE. Phylogenetic analyses, and comparisons of the synteny of rickettsial gene-like sequences from various strains of V. carteri, indicated that the rickettsial gene-like sequences in the nuclear genome of V. carteri strain EVE were closely related to rickettsial gene sequences of P. japonica, rather than those of V. carteri strain UTEX 2180. CONCLUSION/SIGNIFICANCE At least two different rickettsial organisms may have invaded the V. carteri lineage, one of which may be the direct ancestor of the endosymbiont of V. carteri strain UTEX 2180, whereas the other may be closely related to the endosymbiont of P. japonica. Endosymbiotic gene transfer from the latter rickettsial organism may have occurred in an ancestor of V. carteri. Thus, the rickettsiae may be widely associated with V. carteri, and likely have often been lost during host evolution.
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Affiliation(s)
- Kaoru Kawafune
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuichi Hongoh
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Takashi Hamaji
- Donald Danforth Plant Science Center, Saint Louis, Missouri, United States of America
| | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Shunsuke Hirooka
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Shin-ya Miyagishima
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Molecular systematics of Barbatosphaeria (Sordariomycetes): multigene phylogeny and secondary ITS structure. Persoonia - Molecular Phylogeny and Evolution of Fungi 2015; 35:21-38. [PMID: 26823626 PMCID: PMC4713105 DOI: 10.3767/003158515x687434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/04/2014] [Indexed: 11/25/2022]
Abstract
Thirteen morphologically similar strains of barbatosphaeria- and tectonidula-like fungi were studied based on the comparison of cultural and morphological features of sexual and asexual morphs and phylogenetic analyses of five nuclear loci, i.e. internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA, β-tubulin, and second largest subunit of RNA polymerase II. Phylogenetic results were supported by in-depth comparative analyses of common core secondary structure of ITS1 and ITS2 in all strains and the identification of non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript. Barbatosphaeria is defined as a well-supported monophyletic clade comprising several lineages and is placed in the Sordariomycetes incertae sedis. The genus is expanded to encompass nine species with both septate and non-septate ascospores in clavate, stipitate asci with a non-amyloid apical annulus and non-stromatic ascomata with a long decumbent neck and carbonised wall often covered by pubescence. The asexual morphs are dematiaceous hyphomycetes with holoblastic conidiogenesis belonging to Ramichloridium and Sporothrix types. The morphologically similar Tectonidula, represented by the type species T. hippocrepida, grouped with members of Barbatosphaeria and is transferred to that genus. Four new species are introduced and three new combinations in Barbatosphaeria are proposed. A dichotomous key to species accepted in the genus is provided.
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Hametner C, Stocker-Wörgötter E, Grube M. New insights into diversity and selectivity of trentepohlialean lichen photobionts from the extratropics. Symbiosis 2014; 63:31-40. [PMID: 25076805 PMCID: PMC4110408 DOI: 10.1007/s13199-014-0285-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/13/2014] [Indexed: 11/03/2022]
Abstract
Aerial green algae of Trentepohliaceae can form conspicuous free-living colonies, be parasites of plants or photobionts of lichen-forming ascomycetes. So far, their diversity in temperate regions is still poorly known as it has been mostly studied by phenotypic approaches only. We present new insights in the phylogenetic relationships of lichenized representatives from temperate and Mediterranean parts of Europe by analysis of 18S rRNA and rbcL gene fragments, and nuclear ITS sequence data. For this purpose we isolated the trentepohlialean photobionts from lichens representing different genera. Algal cultures from lichenized and free-living Trentepohliaceae were used to design new primers for amplification of the marker loci. We constructed a phylogenetic hypothesis to reveal the phylogenetic placements of lichenized lineages with 18S rRNA and rbcL sequences. ITS variation among the clades was substantial and did not allow including them in the general phylogenetic assessment, yet ITS appears to be a promising marker for DNA-barcoding approaches. Specific algae were found in particular lichen but the overall diversity of photobionts was limited. The multilocus tree does not support the current morphological classification of genera in Trentepohliaceae, suggesting that morphology is more variable than previously thought in this group of algae.
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Affiliation(s)
- Christina Hametner
- Department of Organismic Biology, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | | | - Martin Grube
- Department of Plant Science, Karl-Franzens-University of Graz, Holteigasse 6, 8010 Graz, Austria
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A review on bovine besnoitiosis: a disease with economic impact in herd health management, caused by Besnoitia besnoiti (Franco and Borges, ). Parasitology 2014; 141:1406-17. [PMID: 24694568 DOI: 10.1017/s0031182014000262] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Bovine besnoitiosis is caused by the largely unexplored apicomplexan parasite Besnoitia besnoiti. In cows, infection during pregnancy often results in abortion, and chronically infected bulls become infertile. Similar to other apicomplexans B. besnoiti has acquired a largely intracellular lifestyle, but its complete life cycle is still unknown, modes of transmission have not been entirely resolved and the definitive host has not been identified. Outbreaks of bovine besnoitiosis in cattle were described in the 1990s in Portugal and Spain, and later several cases were also detected in France. More cases have been reported recently in hitherto unaffected countries, including Italy, Germany, Switzerland, Hungary and Croatia. To date, there is still no effective pharmaceutical compound available for the treatment of besnoitiosis in cattle, and progress in the identification of novel targets for intervention through pharmacological or immunological means is hampered by the lack of molecular data on the genomic and transcriptomic level. In addition, the lack of an appropriate small animal laboratory model, and wide gaps in our knowledge on the host-parasite interplay during the life cycle of this parasite, renders vaccine and drug development a cost- and labour-intensive undertaking.
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A review of molecular approaches for investigating patterns of coevolution in marine host-parasite relationships. ADVANCES IN PARASITOLOGY 2014; 84:209-52. [PMID: 24480315 DOI: 10.1016/b978-0-12-800099-1.00004-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Parasites and their relationships with hosts play a crucial role in the evolutionary pathways of every living organism. One method of investigating host-parasite systems is using a molecular approach. This is particularly important as analyses based solely on morphology or laboratory studies of parasites and their hosts do not take into account historical evolutionary interactions that can shape the distribution, abundance and population structure of parasites and their hosts. However, the predominant host-parasite coevolution literature has focused on terrestrial hosts and their parasites, and there still is a lack of studies in marine environments. Given that marine systems are generally more open than terrestrial ones, they provide fascinating opportunities for large-scale (as well as small-scale) geographic studies. Further, patterns and processes of genetic structuring and systematics are becoming more available across many different taxa (but especially fishes) in many marine systems, providing an excellent basis for examining whether parasites follow host population/species structure. In this chapter, we first highlight the factors and processes that challenge our ability to interpret evolutionary patterns of coevolution of hosts and their parasites in marine systems at different spatial, temporal and taxonomic scales. We then review the use of the most commonly utilized genetic markers in studying marine host-parasite systems. We give an overview and discuss which molecular methodologies resolve evolutionary relationships best and also discuss the applicability of new approaches, such as next-generation sequencing and studies utilizing functional markers to gain insights into more contemporary processes shaping host-parasite relationships.
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Woo SH, Seo JS, Lee EH. Discrimination and simultaneous detection of two myxozoan parasites belonging to genus Thelohanellus by multiplex polymerase chain reaction. Vet Parasitol 2014; 203:212-6. [PMID: 24582523 DOI: 10.1016/j.vetpar.2014.01.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 01/21/2014] [Accepted: 01/23/2014] [Indexed: 11/26/2022]
Abstract
Thelohanellus kitauei and Thelohanellus hovorkai are myxozoan parasites pathogenic in cyprinid fish especially adult Israel carp and common carp. In the present study, the complete 18S rRNA-ITS1-5.8S rRNA-ITS2 sequences of these two Thelohanellus species were cloned with primers designed from information from Genbank and previous studies. The results revealed that ITS1 and ITS2 sequences of T. kitauei and T. hovorkai were clearly distinguished although the 18S rRNA regions of the two parasites were highly conserved. Based on these sequences, new primer sets were designed for specific identification of these two parasites by multiplex PCR. Both single and multiplex PCR methods using these primers could identify these two myxozoan parasites from mixed DNA samples successfully. Our findings provide a powerful tool for the differentiation of the highly similar pathogenic Thelohanellus species for specific detection for the early diagnosis of diseases.
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Affiliation(s)
- Sung Ho Woo
- Institute of Fisheries Sciences, Pukyong National University, 474, Ilgwang-Ro, Ilgwang-myeon, Gijang-gun, Busan, 619-911, South Korea
| | - Jung Soo Seo
- Pathology Division, National Fisheries Research & Development Institute (NFRDI), 152-1, Haean-Lo, Gijang-Up, Gijang-Gun, Busan 619-705, South Korea.
| | - Eun Hye Lee
- Center for Food and Drug Analysis, Busan Regional Korea Food and Drug Administration, Ministry of Food and Drug Safety, 65, 356-Gil, Shinseon-Ro, Nam-Gu, Busan 608-829, South Korea.
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Novel evolutionary lineages revealed in the Chaetothyriales (fungi) based on multigene phylogenetic analyses and comparison of its secondary structure. PLoS One 2013; 8:e63547. [PMID: 23723988 PMCID: PMC3665825 DOI: 10.1371/journal.pone.0063547] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/01/2013] [Indexed: 11/19/2022] Open
Abstract
Cyphellophora and Phialophora (Chaetothyriales, Pezizomycota) comprise species known from skin infections of humans and animals and from a variety of environmental sources. These fungi were studied based on the comparison of cultural and morphological features and phylogenetic analyses of five nuclear loci, i.e., internal transcribed spacer rDNA operon (ITS), large and small subunit nuclear ribosomal DNA (nuc28S rDNA, nuc18S rDNA), β-tubulin, DNA replication licensing factor (mcm7) and second largest subunit of RNA polymerase II (rpb2). Phylogenetic results were supported by comparative analysis of ITS1 and ITS2 secondary structure of representatives of the Chaetothyriales and the identification of substitutions among the taxa analyzed. Base pairs with non-conserved, co-evolving nucleotides that maintain base pairing in the RNA transcript and unique evolutionary motifs in the ITS2 that characterize whole clades or individual taxa were mapped on predicted secondary structure models. Morphological characteristics, structural data and phylogenetic analyses of three datasets, i.e., ITS, ITS-β-tubulin and 28S-18S-rpb2-mcm7, define a robust clade containing eight species of Cyphellophora (including the type) and six species of Phialophora. These taxa are now accommodated in the Cyphellophoraceae, a novel evolutionary lineage within the Chaetothyriales. Cyphellophora is emended and expanded to encompass species with both septate and nonseptate conidia formed on discrete, intercalary, terminal or lateral phialides. Six new combinations in Cyphellophora are proposed and a dichotomous key to species accepted in the genus is provided. Cyphellophora eugeniae and C. hylomeconis, which grouped in the Chaetothyriaceae, represent another novel lineage and are introduced as the type species of separate genera.
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González MA, Pröschold T, Palacios Y, Aguayo P, Inostroza I, Gómez PI. Taxonomic identification and lipid production of two Chilean Chlorella-like strains isolated from a marine and an estuarine coastal environment. AOB PLANTS 2013; 5:plt020. [PMCID: PMC4104639 DOI: 10.1093/aobpla/plt020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 02/26/2013] [Indexed: 06/06/2023]
Abstract
This paper emphasizes the value of knowing the correct identity of microalgal strains that may have biotechnological potential. Here, two Chilean small green coccoid referred as Chlorella-like strains were identified using a polyphasic approach. Only one of them corresponded to the genus Chlorella (C. vulgaris); the other belonged to the recently amended genus Chloroidium (C. saccharophilum). Lipids characterization of the biomass obtained from these strains showed that Chlorella vulgaris (Baker strain) appeared to be suitable as raw material for biodiesel production, while Chloroidium saccharophilum (Coliumo strain) would be more appropriate for animal nutrition. The genus Chlorella was the first microalga to be massively cultured as food, feed and as a source of nutraceuticals. More recently, some species have been suggested as candidates for biodiesel production. One of the most difficult tasks in studying the systematics of green coccoids is the identification of species assigned to the genus Chlorella. In the context of several projects carried out by our research group we isolated two Chlorella-like strains from a marine and an estuarine coastal environment in Chile (Coliumo strain and Baker strain, respectively). The main objectives of this research were to identify these Chilean strains—at the species level—and determine and compare their lipid production when cultured under identical conditions. Cell size and shape, autospore number and sizes, and chloroplast and pyrenoid ultrastructure were considered as taxonomic descriptors, and 18S rDNA sequences and internal transcribed spacer ITS-1 + ITS-2 sequences and secondary structure were adopted as phylogenetic tools. The combined use of these morphological, ultrastructural and molecular attributes revealed that only the Baker strain belongs to the genus Chlorella (C. vulgaris), while the Coliumo strain corresponds to the recently amended genus Chloroidium (C. saccharophilum). Lipid characterization of the biomass obtained from these strains showed that Chlorella vulgaris (Baker strain) appears to be suitable as a raw material for biodiesel production, while Chloroidium saccharophilum (Coliumo strain) would be more appropriate for animal nutrition.
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Affiliation(s)
- Mariela A. González
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Thomas Pröschold
- Department of Applied Ecology,University of Rostock, Albert-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Yussi Palacios
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Paula Aguayo
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Ingrid Inostroza
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Patricia I. Gómez
- Departamento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
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Preetha K, John L, Subin CS, Vijayan KK. Phenotypic and genetic characterization of Dunaliella (Chlorophyta) from Indian salinas and their diversity. AQUATIC BIOSYSTEMS 2012; 8:27. [PMID: 23114277 PMCID: PMC3598838 DOI: 10.1186/2046-9063-8-27] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 10/16/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND The genus Dunaliella (Class - Chlorophyceae) is widely studied for its tolerance to extreme habitat conditions, physiological aspects and many biotechnological applications, such as a source of carotenoids and many other bioactive compounds. Biochemical and molecular characterization is very much essential to fully explore the properties and possibilities of the new isolates of Dunaliella. In India, hyper saline lakes and salt pans were reported to bloom with Dunaliella spp. However, except for the economically important D. salina, other species are rarely characterized taxonomically from India. Present study was conducted to describe Dunaliella strains from Indian salinas using a combined morphological, physiological and molecular approach with an aim to have a better understanding on the taxonomy and diversity of this genus from India. RESULTS Comparative phenotypic and genetic studies revealed high level of diversity within the Indian Dunaliella isolates. Species level identification using morphological characteristics clearly delineated two strains of D. salina with considerable β-carotene content (>20 pg/cell). The variation in 18S rRNA gene size, amplified with MA1-MA2 primers, ranged between ~1800 and ~2650 base pairs, and together with the phylogeny based on ITS gene sequence provided a pattern, forming five different groups within Indian Dunaliella isolates. Superficial congruency was observed between ITS and rbcL gene phylogenetic trees with consistent formation of major clades separating Indian isolates into two distinct clusters, one with D. salina and allied strains, and another one with D. viridis and allied strains. Further in both the trees, few isolates showed high level of genetic divergence than reported previously for Dunaliella spp. This indicates the scope of more numbers of clearly defined/unidentified species/sub-species within Indian Dunaliella isolates. CONCLUSION Present work illustrates Indian Dunaliella strains phenotypically and genetically, and confirms the presence of not less than five different species (or sub-species) in Indian saline waters, including D. salina and D. viridis. The study emphasizes the need for a combined morphological, physiological and molecular approach in the taxonomic studies of Dunaliella.
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Affiliation(s)
- Krishna Preetha
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
| | - Lijo John
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
| | - Cherampillil Sukumaran Subin
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
| | - Koyadan Kizhakkedath Vijayan
- Genetics and Genomics Section, Marine Biotechnology Division, Central Marine Fisheries Research Institute, Post Box No. 1603, Ernakulam North P.O, Kochi, 682018, India
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Georgianna DR, Mayfield SP. Exploiting diversity and synthetic biology for the production of algal biofuels. Nature 2012; 488:329-35. [PMID: 22895338 DOI: 10.1038/nature11479] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Modern life is intimately linked to the availability of fossil fuels, which continue to meet the world's growing energy needs even though their use drives climate change, exhausts finite reserves and contributes to global political strife. Biofuels made from renewable resources could be a more sustainable alternative, particularly if sourced from organisms, such as algae, that can be farmed without using valuable arable land. Strain development and process engineering are needed to make algal biofuels practical and economically viable.
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Affiliation(s)
- D Ryan Georgianna
- San Diego Center for Algae Biotechnology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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Phylogenetic relationships among the Caribbean members of the Cliona viridis complex (Porifera, Demospongiae, Hadromerida) using nuclear and mitochondrial DNA sequences. Mol Phylogenet Evol 2012; 64:271-84. [DOI: 10.1016/j.ympev.2012.03.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 03/31/2012] [Accepted: 03/31/2012] [Indexed: 11/22/2022]
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Tang HJ, Lan YG, Wen YZ, Zhang XC, Desquesnes M, Yang TB, Hide G, Lun ZR. Detection of Trypanosoma lewisi from wild rats in Southern China and its genetic diversity based on the ITS1 and ITS2 sequences. INFECTION GENETICS AND EVOLUTION 2012; 12:1046-51. [DOI: 10.1016/j.meegid.2012.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/12/2022]
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Degtjareva GV, Valiejo-Roman CM, Samigullin TH, Guara-Requena M, Sokoloff DD. Phylogenetics of Anthyllis (Leguminosae: Papilionoideae: Loteae): Partial incongruence between nuclear and plastid markers, a long branch problem and implications for morphological evolution. Mol Phylogenet Evol 2012; 62:693-707. [DOI: 10.1016/j.ympev.2011.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/14/2011] [Accepted: 11/15/2011] [Indexed: 11/17/2022]
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Assunção P, Jaén-Molina R, Caujapé-Castells J, de la Jara A, Carmona L, Freijanes K, Mendoza H. Molecular taxonomy of Dunaliella (Chlorophyceae), with a special focus on D. salina: ITS2 sequences revisited with an extensive geographical sampling. AQUATIC BIOSYSTEMS 2012; 8:2. [PMID: 22520929 PMCID: PMC3310333 DOI: 10.1186/2046-9063-8-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 01/30/2012] [Indexed: 05/08/2023]
Abstract
We used an ITS2 primary and secondary structure and Compensatory Base Changes (CBCs) analyses on new French and Spanish Dunallela salina strains to investigate their phylogenetic position and taxonomic status within the genus Dunaliella. Our analyses show a great diversity within D. salina (with only some clades not statistically supported) and reveal considerable genetic diversity and structure within Dunaliella, although the CBC analysis did not bolster the existence of different biological groups within this taxon. The ITS2 sequences of the new Spanish and French D. salina strains were very similar except for two of them: ITC5105 "Janubio" from Spain and ITC5119 from France. Although the Spanish one had a unique ITS2 sequence profile and the phylogenetic tree indicates that this strain can represent a new species, this hypothesis was not confirmed by CBCs, and clarification of its taxonomic status requires further investigation with new data. Overall, the use of CBCs to define species boundaries within Dunaliella was not conclusive in some cases, and the ITS2 region does not contain a geographical signal overall.
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Affiliation(s)
- Patrícia Assunção
- Departamento de Biotecnología. División de Investigación y Desarrollo Tecnológico. Instituto Tecnológico de Canarias (ITC). Pozo Izquierdo, 35119 Sta. Lucía, Canary Islands, Spain
| | - Ruth Jaén-Molina
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario "Viera y Clavijo"-Unidad Asociada CSIC, Apartado de correos 14 de Tafira Alta, 35017 Las Palmas de Gran Canaria, Canary Islands, Spain
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario "Viera y Clavijo"-Unidad Asociada CSIC, Apartado de correos 14 de Tafira Alta, 35017 Las Palmas de Gran Canaria, Canary Islands, Spain
| | - Adelina de la Jara
- Departamento de Biotecnología. División de Investigación y Desarrollo Tecnológico. Instituto Tecnológico de Canarias (ITC). Pozo Izquierdo, 35119 Sta. Lucía, Canary Islands, Spain
| | - Laura Carmona
- Departamento de Biotecnología. División de Investigación y Desarrollo Tecnológico. Instituto Tecnológico de Canarias (ITC). Pozo Izquierdo, 35119 Sta. Lucía, Canary Islands, Spain
| | - Karen Freijanes
- Departamento de Biotecnología. División de Investigación y Desarrollo Tecnológico. Instituto Tecnológico de Canarias (ITC). Pozo Izquierdo, 35119 Sta. Lucía, Canary Islands, Spain
| | - Héctor Mendoza
- Departamento de Biotecnología. División de Investigación y Desarrollo Tecnológico. Instituto Tecnológico de Canarias (ITC). Pozo Izquierdo, 35119 Sta. Lucía, Canary Islands, Spain
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Fulnečková J, Hasíková T, Fajkus J, Lukešová A, Eliáš M, Sýkorová E. Dynamic evolution of telomeric sequences in the green algal order Chlamydomonadales. Genome Biol Evol 2012; 4:248-64. [PMID: 22247428 PMCID: PMC3318450 DOI: 10.1093/gbe/evs007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Telomeres, which form the protective ends of eukaryotic chromosomes, are a ubiquitous and conserved structure of eukaryotic genomes but the basic structural unit of most telomeres, a repeated minisatellite motif with the general consensus sequence TnAmGo, may vary between eukaryotic groups. Previous studies on several species of green algae revealed that this group exhibits at least two types of telomeric sequences, a presumably ancestral type shared with land plants (Arabidopsis type, TTTAGGG) and conserved in, for example, Ostreococcus and Chlorella species, and a novel type (Chlamydomonas type, TTTTAGGG) identified in Chlamydomonas reinhardtii. We have employed several methodical approaches to survey the diversity of telomeric sequences in a phylogenetically wide array of green algal species, focusing on the order Chlamydomonadales. Our results support the view that the Arabidopsis-type telomeric sequence is ancestral for green algae and has been conserved in most lineages, including Mamiellophyceae, Chlorodendrophyceae, Trebouxiophyceae, Sphaeropleales, and most Chlamydomonadales. However, within the Chlamydomonadales, at least two independent evolutionary changes to the Chlamydomonas type occurred, specifically in a subgroup of the Reinhardtinia clade (including C. reinhardtii and Volvox carteri) and in the Chloromonadinia clade. Furthermore, a complex structure of telomeric repeats, including a mix of the ancestral Arabidopsis-type motifs and derived motifs identical to the human-type telomeric repeats (TTAGGG), was found in the chlamydomonadalean clades Dunaliellinia and Stephanosphaeria. Our results indicate that telomere evolution in green algae, particularly in the order Chlamydomonadales, is far more dynamic and complex than thought before. General implications of our findings for the mode of telomere evolution are discussed.
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Affiliation(s)
- Jana Fulnečková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Potvin É, Jeong HJ, Kang NS, Tillmann U, Krock B. First Report of the Photosynthetic Dinoflagellate Genus Azadinium in the Pacific Ocean: Morphology and Molecular Characterization of Azadinium cf. poporum. J Eukaryot Microbiol 2011; 59:145-56. [DOI: 10.1111/j.1550-7408.2011.00600.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 10/21/2011] [Indexed: 11/30/2022]
Affiliation(s)
- Éric Potvin
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul; 151-747; Korea
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul; 151-747; Korea
| | - Nam Seon Kang
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul; 151-747; Korea
| | - Urban Tillmann
- Alfred Wegener Institute; Am Handelshafen 12; Bremerhaven; D-27570; Germany
| | - Bernd Krock
- Alfred Wegener Institute; Am Handelshafen 12; Bremerhaven; D-27570; Germany
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Chen X, Li S, Li C, Zhao S, Serap A. Phytogeny of genusGlossina (Diptera:Glossinidae) according to ITS2 sequences. ACTA ACUST UNITED AC 2011; 42:249-58. [PMID: 20229338 DOI: 10.1007/bf03183600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/1998] [Indexed: 10/19/2022]
Abstract
The flies of genusGlossina (Diptera: Glossinidae) are an important vector of African trypanosomiases which cause diseases in humans and animals. The ribosomal DNA Internal Transcribed Spacer-2 (ITS-2) region sequences from differentGlossina species were PCR-amplified and analyzed in order to construct a molecular phylogeny for genusGlossina. Trees generated by parsimony confirmed the monophyletic taxonomic placement of genusGlossina wherefusca group species formed the deepest branch followed bymorsitans andpalpalis groups, respectively. The placement ofGlossina austeni by both the traditional morphological and biochemical criteria has been controversial. Results presented here, based on ITS-2 locus sequence analysis, suggest thatGlossina austeni can be placed into a separate subgenerus which forms a sister-group relationship with themorsitans group species.
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Affiliation(s)
- X Chen
- Institute of Genetics, Fudan University, 200433, Shanghai, China
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Andree KB, Fernández-Tejedor M, Elandaloussi LM, Quijano-Scheggia S, Sampedro N, Garcés E, Camp J, Diogène J. Quantitative PCR coupled with melt curve analysis for detection of selected pseudo-nitzschia spp. (Bacillariophyceae) from the Northwestern Mediterranean sea. Appl Environ Microbiol 2011; 77:1651-9. [PMID: 21193668 PMCID: PMC3067299 DOI: 10.1128/aem.01978-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 12/20/2010] [Indexed: 02/04/2023] Open
Abstract
The frequency and intensity of Pseudo-nitzschia spp. blooms along the coast of Catalonia have been increasing over the past 20 years. As species from this genus that are documented as toxigenic have been found in local waters, with both toxic and nontoxic species cooccurring in the same bloom, there is a need to develop management tools for discriminating the difference. Currently, differentiation of toxic and nontoxic species requires time-consuming electron microscopy to distinguish taxonomic features that would allow identification as to species, and cryptic species can still remain misidentified. In this study, cells of Pseudo-nitzschia from clonal cultures isolated from seawater were characterized to their species identity using scanning electron microscopy, and subsamples of each culture were used to create an internal transcribed spacer 1 (ITS-1), 5.8S, and ITS-2 ribosomal DNA database for development of species-specific quantitative PCR (qPCR) assays. Once developed, these qPCR assays were applied to field samples collected over a 2-year period in Alfaques Bay in the northwestern Mediterranean Sea to evaluate the possibility of a comprehensive surveillance for all Pseudo-nitzschia spp. using molecular methods to supplement optical microscopy, which can discern taxonomy only to the genus level within this taxon. Total Pseudo-nitzschia cell density was determined by optical microscopy from water samples collected weekly and compared to results obtained from the sum of eight Pseudo-nitzschia species-specific qPCR assays using duplicate samples. Species-specific qPCR followed by melt curve analysis allowed differentiation of amplicons and identification of false positives, and results correlated well with the total Pseudo-nitzschia cell counts from optical microscopy.
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MESH Headings
- Cluster Analysis
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/genetics
- Diatoms/classification
- Diatoms/genetics
- Diatoms/isolation & purification
- Diatoms/ultrastructure
- Genes, rRNA
- Mediterranean Sea
- Microscopy, Electron, Scanning
- Phylogeny
- Polymerase Chain Reaction/methods
- RNA, Ribosomal, 5.8S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Karl B Andree
- Institut de Recerca i Tecnologia Agroalimentàries, Crta. de Poble Nou, Km 5.5, E-43540 San Carlos de la Rapita (Tarragona), Spain.
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Buchheim MA, Keller A, Koetschan C, Förster F, Merget B, Wolf M. Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One 2011; 6:e16931. [PMID: 21347329 PMCID: PMC3037400 DOI: 10.1371/journal.pone.0016931] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2010] [Accepted: 01/05/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta. METHODOLOGY/PRINCIPAL FINDINGS Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses. CONCLUSIONS/SIGNIFICANCE Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.
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Affiliation(s)
- Mark A Buchheim
- Department of Biological Science and the Mervin Bovaird Institute for Molecular Biology and Biotechnology, The University of Tulsa, Tulsa, Oklahoma, United States of America.
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Milyutina IA, Goryunov DV, Ignatov MS, Ignatova EA, Troitsky AV. The phylogeny of Schistidium (Bryophyta, Grimmiaceae) based on the primary and secondary structure of nuclear rDNA internal transcribed spacers. Mol Biol 2010. [DOI: 10.1134/s0026893310060051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pröschold T, Darienko T, Silva PC, Reisser W, Krienitz L. The systematics of Zoochlorella revisited employing an integrative approach. Environ Microbiol 2010; 13:350-64. [PMID: 20874732 DOI: 10.1111/j.1462-2920.2010.02333.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Symbiosis of green algae with protozoa and invertebrates has been studied for more than 100 years. Endosymbiotic green algae are widely distributed in ciliates (e.g. Paramecium, Stentor, Climacostomum, Coleps, Euplotes), heliozoa (e.g. Acanthocystis) and invertebrates (e.g. Hydra, Spongilla), and have traditionally been identified as named or unnamed species of Chlorella Beij. or Zoochlorella K. Brandt or referred to as Chlorella-like algae or zoochlorellae. We studied 17 strains of endosymbionts isolated from various hosts and geographical localities using an integrative approach (nuclear encoded small subunit and internal transcribed spacer regions of rRNA gene sequences including their secondary structures, morphology, physiology and virus sensitivity). Phylogenetic analyses have revealed them to be polyphyletic. The strains examined belong to five independent clades within the Trebouxiophyceae (Choricystis-, Elliptochloris-, Auxenochlorella- and Chlorella-clades) and Chlorophyceae (Scenedesmus-clade). The most studied host organism, Paramecium bursaria, harbours endosymbionts representing at least five different species. On the basis of our results, we propose a taxonomic revision of endosymbiotic 'Chlorella'-like green algae. Zoochlorella conductrix K. Brandt is transferred to Micractinium Fresen. and Zoochlorella parasitica K. Brandt to Choricystis (Skuja) Fott. It was shown that Choricystis minor (Skuja) Fott, the generitype, is a later heterotypic synonym of Choricystis parasitica (K. Brandt) comb. nov. A new species, Chlorella heliozoae, is proposed to accommodate the endosymbiont of Acanthocystis turfacea.
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Affiliation(s)
- Thomas Pröschold
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Argyll, Scotland, UK.
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Ueki N, Matsunaga S, Inouye I, Hallmann A. How 5000 independent rowers coordinate their strokes in order to row into the sunlight: phototaxis in the multicellular green alga Volvox. BMC Biol 2010; 8:103. [PMID: 20663212 PMCID: PMC2920248 DOI: 10.1186/1741-7007-8-103] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/27/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The evolution of multicellular motile organisms from unicellular ancestors required the utilization of previously evolved tactic behavior in a multicellular context. Volvocine green algae are uniquely suited for studying tactic responses during the transition to multicellularity because they range in complexity from unicellular to multicellular genera. Phototactic responses are essential for these flagellates because they need to orientate themselves to receive sufficient light for photosynthesis, but how does a multicellular organism accomplish phototaxis without any known direct communication among cells? Several aspects of the photoresponse have previously been analyzed in volvocine algae, particularly in the unicellular alga Chlamydomonas. RESULTS In this study, the phototactic behavior in the spheroidal, multicellular volvocine green alga Volvox rousseletii (Volvocales, Chlorophyta) was analyzed. In response to light stimuli, not only did the flagella waveform and beat frequency change, but the effective stroke was reversed. Moreover, there was a photoresponse gradient from the anterior to the posterior pole of the spheroid, and only cells of the anterior hemisphere showed an effective response. The latter caused a reverse of the fluid flow that was confined to the anterior hemisphere. The responsiveness to light is consistent with an anterior-to-posterior size gradient of eyespots. At the posterior pole, the eyespots are tiny or absent, making the corresponding cells appear to be blind. Pulsed light stimulation of an immobilized spheroid was used to simulate the light fluctuation experienced by a rotating spheroid during phototaxis. The results demonstrated that in free-swimming spheroids, only those cells of the anterior hemisphere that face toward the light source reverse the beating direction in the presence of illumination; this behavior results in phototactic turning. Moreover, positive phototaxis is facilitated by gravitational forces. Under our conditions, V. rousseletii spheroids showed no negative phototaxis. CONCLUSIONS On the basis of our results, we developed a mechanistic model that predicts the phototactic behavior in V. rousseletii. The model involves photoresponses, periodically changing light conditions, morphological polarity, rotation of the spheroid, two modes of flagellar beating, and the impact of gravity. Our results also indicate how recently evolved multicellular organisms adapted the phototactic capabilities of their unicellular ancestors to multicellular life.
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Affiliation(s)
- Noriko Ueki
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
- Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577 Japan
| | - Shigeru Matsunaga
- Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577 Japan
- The Promotion Center for Research and Education, Graduate University for Advanced Studies (Sokendai), Hayama, Kanagawa, 240-0193 Japan
| | - Isao Inouye
- Institute of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577 Japan
| | - Armin Hallmann
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
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NAKADA TAKASHI, NOZAKI HISAYOSHI, TOMITA MASARU. Another Origin of Coloniality in Volvocaleans: The Phylogenetic Position of Pyrobotrys Arnoldi (Spondylomoraceae, Volvocales). J Eukaryot Microbiol 2010; 57:379-82. [DOI: 10.1111/j.1550-7408.2010.00488.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hejazi MA, Barzegari A, Gharajeh NH, Hejazi MS. Introduction of a novel 18S rDNA gene arrangement along with distinct ITS region in the saline water microalga Dunaliella. SALINE SYSTEMS 2010; 6:4. [PMID: 20377865 PMCID: PMC2867797 DOI: 10.1186/1746-1448-6-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 04/08/2010] [Indexed: 11/10/2022]
Abstract
Comparison of 18S rDNA gene sequences is a very promising method for identification and classification of living organisms. Molecular identification and discrimination of different Dunaliella species were carried out based on the size of 18S rDNA gene and, number and position of introns in the gene. Three types of 18S rDNA structure have already been reported: the gene with a size of ~1770 bp lacking any intron, with a size of ~2170 bp consisting one intron near 5' terminus, and with a size of ~2570 bp harbouring two introns near 5' and 3' termini. Hereby, we report a new 18S rDNA gene arrangement in terms of intron localization and nucleotide sequence in a Dunaliella isolated from Iranian salt lakes (ABRIINW-M1/2). PCR amplification with genus-specific primers resulted in production of a ~2170 bp DNA band, which is similar to that of D. salina 18S rDNA gene containing only one intron near 5' terminus. Whilst, sequence composition of the gene revealed the lack of any intron near 5' terminus in our isolate. Furthermore, another alteration was observed due to the presence of a 440 bp DNA fragment near 3' terminus. Accordingly, 18S rDNA gene of the isolate is clearly different from those of D. salina and any other Dunaliella species reported so far. Moreover, analysis of ITS region sequence showed the diversity of this region compared to the previously reported species. 18S rDNA and ITS sequences of our isolate were submitted with accesion numbers of EU678868 and EU927373 in NCBI database, respectively. The optimum growth rate of this isolate occured at the salinity level of 1 M NaCl. The maximum carotenoid content under stress condition of intense light (400 mumol photon m-2 s-1), high salinity (4 M NaCl) and deficiency of nitrate and phosphate nutritions reached to 240 ng/cell after 15 days.
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Affiliation(s)
- Mohammad A Hejazi
- Branch for the Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Tabriz, I. R. Iran
| | - Abolfazl Barzegari
- Branch for the Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Tabriz, I. R. Iran
| | - Nahid Hosseinzadeh Gharajeh
- Branch for the Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Tabriz, I. R. Iran
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Nakada T, Shinkawa H, Ito T, Tomita M. Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan. JOURNAL OF PLANT RESEARCH 2010; 123:67-78. [PMID: 19882207 DOI: 10.1007/s10265-009-0266-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 09/10/2009] [Indexed: 05/22/2023]
Abstract
Chlamydomonas reinhardtii P. A. Dang. (Volvocales, Chlorophyceae) is one of the most intensely studied algae, and its whole genome was sequenced. Although this species was originally described based on materials from France and is often referred to as a cosmopolitan species, all culture strains available today have been isolated from eastern North America. The distinctions with similar and/or closely related species, such as Chlamydomonas globosa J. Snow and Chlamydomonas orbicularis E. G. Pringsh., are also contentious. In this study, new strains of C. reinhardtii and C. globosa were isolated from Japan and compared with several strains similar to C. reinhardtii. Based on the morphological, genealogical, phylogenetical, and mating studies including the new Japanese strains, the circumscription of C. reinhardtii was clarified. C. reinhardtii was most closely related to C. globosa, and they were shown to be different species. Although C. reinhardtii was similar to C. orbicularis, the authentic strain of C. orbicularis was morphologically distinguishable and phylogenetically distant from C. reinhardtii. Discovery of the Japanese strains of C. reinhardtii supports the cosmopolitan distribution of this species. Based on Japanese strains and/or strains from other countries, emended descriptions of C. reinhardtii, C. globosa, and C. orbicularis are given.
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Affiliation(s)
- Takashi Nakada
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan.
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Barcoding of Diatoms: Nuclear Encoded ITS Revisited. Protist 2010; 161:7-34. [DOI: 10.1016/j.protis.2009.07.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 07/04/2009] [Indexed: 11/21/2022]
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Coleman AW, Maria Preparata R, Mehrotra B, Mai JC. Derivation of the Secondary Structure of the ITS-1 Transcript in Volvocales and its Taxonomic Correlations. Protist 2009. [PMID: 23196163 DOI: 10.1016/s1434-4610(98)70018-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Knowledge of secondary structure, formed by the gene spacer regions of the primary transcript of nuclear rDNA cistrons, is lacking for most phyla of eukaryotes. We have sequenced the first internal transcribed spacer region (ITS-1) of multiple representatives of the Volvocales, and from comparisons of these, derived a secondary structure common to the entire group. The secondary structure model is supported by numerous compensating base pair changes located within the paired regions of the stem-loops. Within the morphological species, such as those of Astrephomene and Gonium, the three basal nucleotide pairs of helices are highly conserved in primary sequence, and the single stranded region rich in CCAA is identical in sequence, even when isolates come from all continents of the earth. In other Volvocacean species known to include many pairs of mating types, this same level of conservation is found to correlate with the mating subgroups of the species. Thus a comparable degree of sequence similarity appears to characterize all isolates of a "biological" species; this is valid for taxonomic species only where the biological and taxonomic species levels coincide. In addition, the ITS-1 contains information useful for population analyses, and spacer secondary structure may have additional phylogenetic utility at the level of class or subclass when that information becomes available for other protistan groups.
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Affiliation(s)
- A W Coleman
- Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, USA
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Johansen T, Repolho T, Hellebø A, Raae AJ. Strict conservation of the ITS regions of the ribosomal RNA genes in Atlantic cod (Gadus morhuaL.). ACTA ACUST UNITED AC 2009; 17:107-14. [PMID: 17076252 DOI: 10.1080/10425170600624701] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The nucleotide sequence of the internal transcribed region (ITS) of ribosomal RNA genes from Atlantic cod (Gadus morhua L.) was determined. The complete ITS region spanned approximately 1113 base pairs. The ITS1 region comprised 532 base pairs, the 5.8S region 159, and the ITS2 region contained 422 base pairs. Sequence data were obtained from a total of 12 samples, one pool from six cod and 11 individuals. The sequencing was carried out in two separate experimental periods employing slightly different methodology. The samples were from two different cod stocks, Norwegian costal cod and North East Arctic cod. The sequence analysis showed that in the 12 samples, the ITS region, including the 5.8S RNA, was identical. The ITS region is thus totally conserved in these two cod stocks. The extreme conservation of the ITS regions in the cod rDNA could reflect the small genome size of cod and/or indicate a specific critical role in the processing of the ribosomal units in cold-adapted species.
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Affiliation(s)
- Torild Johansen
- Department of Biology, University of Bergen, PO Box 7800, Bergen 5020, Norway
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Lerche K, Hallmann A. Stable nuclear transformation of Gonium pectorale. BMC Biotechnol 2009; 9:64. [PMID: 19591675 PMCID: PMC2720962 DOI: 10.1186/1472-6750-9-64] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 07/10/2009] [Indexed: 11/21/2022] Open
Abstract
Background Green algae of the family Volvocaceae are a model lineage for studying the molecular evolution of multicellularity and cellular differentiation. The volvocine alga Gonium is intermediate in organizational complexity between its unicellular relative, Chlamydomonas, and its multicellular relatives with differentiated cell types, such as Volvox. Gonium pectorale consists of ~16 biflagellate cells arranged in a flat plate. The detailed molecular analysis of any species necessitates its accessibility to genetic manipulation, but, in volvocine algae, transformation procedures have so far only been established for Chlamydomonas reinhardtii and Volvox carteri. Results Stable nuclear transformation of G. pectorale was achieved using a heterologous dominant antibiotic resistance gene, the aminoglycoside 3'-phosphotransferase VIII gene (aphVIII) of Streptomyces rimosus, as a selectable marker. Heterologous 3'- and 5'-untranslated flanking sequences, including promoters, were from Chlamydomonas reinhardtii or from Volvox carteri. After particle gun bombardment of wild type Gonium cells with plasmid-coated gold particles, transformants were recovered. The transformants were able to grow in the presence of the antibiotic paromomycin and produced a detectable level of the AphVIII protein. The plasmids integrated into the genome, and stable integration was verified after propagation for over 1400 colony generations. Co-transformants were recovered with a frequency of ~30–50% when cells were co-bombarded with aphVIII-based selectable marker plasmids along with unselectable plasmids containing heterologous genes. The transcription of the co-transformed, unselectable genes was confirmed. After heterologous expression of the luciferase gene from the marine copepod Gaussia princeps, which was previously engineered to match the codon usage in C. reinhardtii, Gonium transformants show luciferase activity through light emission in bioluminescence assays. Conclusion Flanking sequences that include promoters from C. reinhardtii and from V. carteri work in G. pectorale and allow the functional expression of heterologous genes, such as the selectable marker gene aphVIII of S. rimosus or the co-transformed, codon-optimized G. princeps luciferase gene, which turned out to be a suitable reporter gene in Gonium. The availability of a method for transformation of Gonium makes genetic engineering of this species possible and allows for detailed studies in molecular evolution using the unicellular Chlamydomonas, the 16-celled Gonium, and the multicellular Volvox.
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Affiliation(s)
- Kai Lerche
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Universitätsstr, 25, D-33615 Bielefeld, Germany.
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Baguñà J, Carranza S, Pala M, Ribera C, Giribet G, Arnedo MA, Ribas M, Riutort M. From morphology and karyology to molecules. New methods for taxonomical identification of asexual populations of freshwater planarians. A tribute to Professor Mario Benazzi. ACTA ACUST UNITED AC 2009. [DOI: 10.1080/11250009909356258] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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