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Adrián-Serrano S, Pavlek M, Arnedo MA. A targeted gene phylogenetic framework to investigate diversification in the highly diverse yet geographically restricted red devil spiders (Araneae, Dysderidae). Cladistics 2024. [PMID: 39105704 DOI: 10.1111/cla.12595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/12/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
The family Dysderidae is a highly diverse group of nocturnal ground-dwelling and active-hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased-80% of its 644 documented species belong to just two genera, Dysdera (326) and Harpactea (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi-locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post-dated the break-up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus Dysdera. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis.
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Affiliation(s)
- Silvia Adrián-Serrano
- Departament Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
| | - Martina Pavlek
- Departament Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
- Croatian Biospeleological Society, Roosveltov trg 6, Zagreb, Croatia
| | - Miquel A Arnedo
- Departament Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Av. Diagonal 645, E-08028, Barcelona, Spain
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Antifungal and Aflatoxin-Reducing Activity of β-Glucan Isolated from Pichia norvegensis Grown on Tofu Wastewater. Foods 2021; 10:foods10112619. [PMID: 34828900 PMCID: PMC8618602 DOI: 10.3390/foods10112619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 12/02/2022] Open
Abstract
Yeast can be isolated from tofu wastewater and the cell wall in the form of β-glucan can act as a natural decontaminant agent. This study aimed to isolate and characterize native yeast from tofu wastewater, which can be extracted to obtain β-glucan and then identify the yeast and its β-glucan activity regarding antifungal ability against Aspergillus flavus and aflatoxin-reducing activity towards aflatoxin B1 (AFB1) and B2 (AFB2). Tofu wastewater native yeast was molecularly identified, and the growth observed based on optical density for 96 h and the pH also measured. β-glucan was extracted from native yeast cell walls with the acid-base method and then the inhibition activity towards A. flavus was tested using the well diffusion method and microscopic observation. AFB1 and AFB2 reduction were identified using HPLC LC-MS/MS. The results showed that the native yeast isolated was Pichia norvegensis with a β-glucan yield of 6.59%. Pichia norvegensis and its β-glucan showed an inhibition zone against Aspergillus flavus of 11.33 ± 4.93 and 7.33 ± 3.51 mm, respectively. Total aflatoxin-reducing activity was also shown by Pichia norvegensis of 26.85 ± 2.87%, and β-glucan of 27.30 ± 1.49%, while AFB1- and AFB2-reducing activity by Pichia norvegensis was 36.97 ± 3.07% and 27.13 ± 1.69%, and β-glucan was 27.13 ± 1.69% and 32.59 ± 4.20%, respectively.
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Chaliha C, Kaladhar VC, Doley R, Verma PK, Kumar A, Kalita E. Bipartite molecular approach for species delimitation and resolving cryptic speciation of Exobasidium vexans within the Exobasidium genus. Comput Biol Chem 2021; 92:107496. [PMID: 33930740 DOI: 10.1016/j.compbiolchem.2021.107496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/21/2021] [Indexed: 02/07/2023]
Abstract
Exobasidium vexans, a basidiomycete pathogen, is the causal organism of blister blight disease in tea. The molecular identification of the pathogen remains a challenge due to the limited availability of genomic data in sequence repositories and cryptic speciation within its genus Exobasidium. In this study, the nuclear internal transcribed spacer rDNA region (ITS) based DNA barcode was developed for E. vexans, to address the problem of molecular identification within the background of cryptic speciation. The isolation of E. vexans strain was confirmed through morphological studies followed by molecular identification utilizing the developed ITS barcode. Phylogenetic analysis based on Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian Inference (BI) confirmed the molecular identification of the pathogen as E. vexans strain. Further, BI analysis using BEAST mediated the estimation of the divergence time and evolutionary relationship of E. vexans within genus Exobasidium. The speciation process followed the Yule diversification model wherein the genus Exobasidium is approximated to have diverged in the Paleozoic era. The study thus sheds light on the molecular barcode-based species delimitation and evolutionary relationship of E. vexans within its genus Exobasidium.
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Affiliation(s)
- Chayanika Chaliha
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - V Chandra Kaladhar
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Robin Doley
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India; School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Eeshan Kalita
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India; Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
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Jung T, Horta Jung M, Webber JF, Kageyama K, Hieno A, Masuya H, Uematsu S, Pérez-Sierra A, Harris AR, Forster J, Rees H, Scanu B, Patra S, Kudláček T, Janoušek J, Corcobado T, Milenković I, Nagy Z, Csorba I, Bakonyi J, Brasier CM. The Destructive Tree Pathogen Phytophthora ramorum Originates from the Laurosilva Forests of East Asia. J Fungi (Basel) 2021; 7:jof7030226. [PMID: 33803849 PMCID: PMC8003361 DOI: 10.3390/jof7030226] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022] Open
Abstract
As global plant trade expands, tree disease epidemics caused by pathogen introductions are increasing. Since ca 2000, the introduced oomycete Phytophthora ramorum has caused devastating epidemics in Europe and North America, spreading as four ancient clonal lineages, each of a single mating type, suggesting different geographical origins. We surveyed laurosilva forests for P. ramorum around Fansipan mountain on the Vietnam-China border and on Shikoku and Kyushu islands, southwest Japan. The surveys yielded 71 P. ramorum isolates which we assigned to eight new lineages, IC1 to IC5 from Vietnam and NP1 to NP3 from Japan, based on differences in colony characteristics, gene x environment responses and multigene phylogeny. Molecular phylogenetic trees and networks revealed the eight Asian lineages were dispersed across the topology of the introduced European and North American lineages. The deepest node within P. ramorum, the divergence of lineages NP1 and NP2, was estimated at 0.5 to 1.6 Myr. The Asian lineages were each of a single mating type, and at some locations, lineages of "opposite" mating type were present, suggesting opportunities for inter-lineage recombination. Based on the high level of phenotypic and phylogenetic diversity in the sample populations, the coalescence results and the absence of overt host symptoms, we conclude that P. ramorum comprises many anciently divergent lineages native to the laurosilva forests between eastern Indochina and Japan.
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Affiliation(s)
- Thomas Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
- Correspondence: (T.J.); (C.M.B.); Tel.: +420-545136172 (T.J.)
| | - Marília Horta Jung
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
- Phytophthora Research and Consultancy, 83131 Nußdorf, Germany
| | - Joan F. Webber
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan; (K.K.); (A.H.)
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan; (K.K.); (A.H.)
| | - Hayato Masuya
- Forestry and Forest Products Research Institute (FFPRI), Tsukuba, Ibaraki 305-8687, Japan;
| | - Seiji Uematsu
- Departament of Bioregulation and Biointeraction, Laboratory of Molecular and Cellular Biology, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan;
| | - Ana Pérez-Sierra
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Anna R. Harris
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Jack Forster
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Helen Rees
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
| | - Bruno Scanu
- Department of Agricultural Sciences, University of Sassari, 07100 Sassari, Italy;
| | - Sneha Patra
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
- Laboratory of Ecological Plant Physiology, CzechGlobe, Global Change Research Institute of the Czech Academy of Sciences, 603 00 Brno, Czech Republic
| | - Tomáš Kudláček
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Josef Janoušek
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Tamara Corcobado
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Ivan Milenković
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Zoltán Nagy
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Mendel University in Brno, 613 00 Brno, Czech Republic; (M.H.J.); (S.P.); (T.K.); (J.J.); (T.C.); (I.M.); (Z.N.)
| | - Ildikó Csorba
- Centre for Agricultural Research, Plant Protection Institute, ELKH, H-1022 Budapest, Hungary; (I.C.); (J.B.)
| | - József Bakonyi
- Centre for Agricultural Research, Plant Protection Institute, ELKH, H-1022 Budapest, Hungary; (I.C.); (J.B.)
| | - Clive M. Brasier
- Forest Research, Alice Holt Lodge, Farnham GU10 4LH, Surrey, UK; (J.F.W.); (A.P.-S.); (A.R.H.); (J.F.); (H.R.)
- Correspondence: (T.J.); (C.M.B.); Tel.: +420-545136172 (T.J.)
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Salas-Leiva DE, Meerow AW, Francisco-Ortega J, Calonje M, Griffith MP, Stevenson DW, Nakamura K. Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads. Mol Ecol Resour 2014; 14:831-45. [PMID: 24444413 DOI: 10.1111/1755-0998.12228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 01/09/2014] [Accepted: 01/13/2014] [Indexed: 01/28/2023]
Abstract
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
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Affiliation(s)
- Dayana E Salas-Leiva
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156, USA
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