scholarly journals Phylogeny and species delimitations in the entomopathogenic genus Beauveria (Hypocreales, Ascomycota), including the description of B. peruviensis sp. nov.

MycoKeys ◽  
2019 ◽  
Vol 58 ◽  
pp. 47-68 ◽  
Author(s):  
Danilo E. Bustamante ◽  
Manuel Oliva ◽  
Santos Leiva ◽  
Jani E. Mendoza ◽  
Leidy Bobadilla ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Sequence Data ◽  
Pathogenic Fungi ◽  
Species Boundaries ◽  
New Taxon ◽  
Important Species ◽  
Genealogical Concordance ◽  
Structural Simplicity ◽  
Molecular Makers ◽  
Multilocus Phylogeny

The genus Beauveria is considered a cosmopolitan anamorphic and teleomorphic genus of soilborne necrotrophic arthropod-pathogenic fungi that includes ecologically and economically important species. Species identification in Beauveria is difficult because of its structural simplicity and the lack of distinctive phenotypic variation. Therefore, the use of multi-locus sequence data is essential to establish robust species boundaries in addition to DNA-based species delimitation methods using genetic distance, coalescent, and genealogical concordance approaches (polyphasic approaches). In this regard, our study used multilocus phylogeny and five DNA-based methods to delimit species in Beauveria using three molecular makers. These polyphasic analyses allowed for the delimitation of 20–28 species in Beauveria, confirming cryptic diversity in five species (i.e. B. amorpha, B. bassiana, B. diapheromeriphila, and B. pseudobassiana) and supporting the description of B. peruviensis as a new taxon from northeastern Peru. The other five species were not evaluated as they did not have enough data (i.e. B. araneola, B. gryllotalpidicola, B. loeiensis, B. medogensis, and B. rudraprayagi). Our results demonstrate that the congruence among different methods in a polyphasic approach (e.g. genetic distance and coalescence methods) is more likely to show reliably supported species boundaries. Among the methods applied in this study, genetic distance, coalescent approaches, and multilocus phylogeny are crucial when establishing species boundaries in Beauveria.

scholarly journals The Promise and Pitfalls of Sequence-Based Identification of Plant-Pathogenic Fungi and Oomycetes

2010 ◽  
Vol 100 (8) ◽  
pp. 732-737 ◽  
Author(s):  
Seogchan Kang ◽  
Michele A. Mansfield ◽  
Bongsoo Park ◽  
David M. Geiser ◽  
Kelly L. Ivors ◽  
...  
Keyword(s):  
Incomplete Data ◽  
Sequence Data ◽  
Pathogenic Fungi ◽  
Diagnostic Methods ◽  
Species Boundaries ◽  
Plant Pathogenic Fungi ◽  
Marker Loci ◽  
Potential Benefits ◽  
Reference Databases ◽  
Pathogen Diagnosis

Sequences of selected marker loci have been widely used for the identification of specific pathogens and the development of sequence-based diagnostic methods. Although such approaches offer several advantages over traditional culture-based methods for pathogen diagnosis and identification, they have their own pitfalls. These include erroneous and incomplete data in reference databases, poor or oversimplified interpretation of search results, and problems associated with defining species boundaries. In this letter, we outline the potential benefits and drawbacks of using sequence data for identification and taxonomic deductions of plant-pathogenic fungi and oomycetes, using Phytophthora as a primary example. We also discuss potential remedies for these pitfalls and address why coordinated community efforts are essential to make such remedies more efficient and robust.

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 316-324 ◽  
Author(s):  
Jongsik Chun ◽  
Fred A. Rainey
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Original Research ◽  
Rrna Gene ◽  
New Taxon ◽  
Genome Sequences ◽  
Microbial World ◽  
Content Type ◽  
Link Type ◽  
Type Strains

The polyphasic approach used today in the taxonomy and systematics of the Bacteria and Archaea includes the use of phenotypic, chemotaxonomic and genotypic data. The use of 16S rRNA gene sequence data has revolutionized our understanding of the microbial world and led to a rapid increase in the number of descriptions of novel taxa, especially at the species level. It has allowed in many cases for the demarcation of taxa into distinct species, but its limitations in a number of groups have resulted in the continued use of DNA–DNA hybridization. As technology has improved, next-generation sequencing (NGS) has provided a rapid and cost-effective approach to obtaining whole-genome sequences of microbial strains. Although some 12 000 bacterial or archaeal genome sequences are available for comparison, only 1725 of these are of actual type strains, limiting the use of genomic data in comparative taxonomic studies when there are nearly 11 000 type strains. Efforts to obtain complete genome sequences of all type strains are critical to the future of microbial systematics. The incorporation of genomics into the taxonomy and systematics of the Bacteria and Archaea coupled with computational advances will boost the credibility of taxonomy in the genomic era. This special issue of International Journal of Systematic and Evolutionary Microbiology contains both original research and review articles covering the use of genomic sequence data in microbial taxonomy and systematics. It includes contributions on specific taxa as well as outlines of approaches for incorporating genomics into new strain isolation to new taxon description workflows.

Addition to Micropeltidaceae: Micropeltis goniothalamicola sp. nov. and new record of Scolecopeltidium menglaense from Chiang Rai, Thailand

Phytotaxa ◽  
2021 ◽  
Vol 487 (1) ◽  
pp. 56-64
Author(s):  
DIANA S. MARASINGHE ◽  
SINANG HONGSANAN ◽  
SARANYAPHAT BOONMEE ◽  
NING XIE
Keyword(s):  
New Record ◽  
Sequence Data ◽  
Novel Species ◽  
Host Record ◽  
Its Sequence ◽  
New Taxon ◽  
Morphological Comparison ◽  
New Host ◽  
Mucilaginous Sheath ◽  
New Host Record

A novel species, Micropeltis goniothalamicola and a new record Scolecopeltidium menglaense were collected from Mae Fah Luang Botanical Gardens, Thailand. Our new taxon is different from other species in Micropeltis in having relatively smaller ascomata, 6–8-spored asci and 4–5-septate ascospores covering with mucilaginous sheath. Our new record, S. menglaense is the first host recorded from Jasmine grandiflorum (Oleaceae). Morphological comparison coupled with phylogenetic analysis of combined LSU and ITS sequence data provide evidence for the new species and new host record.

Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

2012 ◽  
Vol 60 (1) ◽  
pp. 32 ◽  
Author(s):  
Laurence J. Clarke ◽  
Duncan I. Jardine ◽  
Margaret Byrne ◽  
Kelly Shepherd ◽  
Andrew J. Lowe
Keyword(s):  
Genetic Variation ◽  
New Species ◽  
Genetic Structure ◽  
Western Australia ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Conservation Strategies ◽  
New Taxon ◽  
Near Surface ◽  
Two Populations

Atriplex sp. Yeelirrie Station (L. Trotter & A. Douglas LCH 25025) is a highly restricted, potentially new species of saltbush, known from only two sites ~30 km apart in central Western Australia. Knowledge of genetic structure within the species is required to inform conservation strategies as both populations occur within a palaeovalley that contains significant near-surface uranium mineralisation. We investigate the structure of genetic variation within populations and subpopulations of this taxon using nuclear microsatellites. Internal transcribed spacer sequence data places this new taxon within a clade of polyploid Atriplex species, and the maximum number of alleles per locus suggests it is hexaploid. The two populations possessed similar levels of genetic diversity, but exhibited a surprising level of genetic differentiation given their proximity. Significant isolation by distance over scales of less than 5 km suggests dispersal is highly restricted. In addition, the proportion of variation between the populations (12%) is similar to that among A. nummularia populations sampled at a continent-wide scale (several thousand kilometres), and only marginally less than that between distinct A. nummularia subspecies. Additional work is required to further clarify the exact taxonomic status of the two populations. We propose management recommendations for this potentially new species in light of its highly structured genetic variation.

scholarly journals Mismatch induced speciation in Salmonella : model and data

2006 ◽  
Vol 361 (1475) ◽  
pp. 2045-2053 ◽  
Author(s):  
Daniel Falush ◽  
Mia Torpdahl ◽  
Xavier Didelot ◽  
Donald F Conrad ◽  
Daniel J Wilson ◽  
...  
Keyword(s):  
New Species ◽  
Natural Selection ◽  
Dna Sequence ◽  
Computer Simulations ◽  
De Novo ◽  
Sequence Data ◽  
Biological Species ◽  
Species Boundaries ◽  
Population Subdivision ◽  
Geographical Population

In bacteria, DNA sequence mismatches act as a barrier to recombination between distantly related organisms and can potentially promote the cohesion of species. We have performed computer simulations which show that the homology dependence of recombination can cause de novo speciation in a neutrally evolving population once a critical population size has been exceeded. Our model can explain the patterns of divergence and genetic exchange observed in the genus Salmonella , without invoking either natural selection or geographical population subdivision. If this model was validated, based on extensive sequence data, it would imply that the named subspecies of Salmonella enterica correspond to good biological species, making species boundaries objective. However, multilocus sequence typing data, analysed using several conventional tools, provide a misleading impression of relationships within S. enterica subspecies enterica and do not provide the resolution to establish whether new species are presently being formed.

Combined multi-gene backbone tree for the genus Coniochaeta with two new species from Uzbekistan

Phytotaxa ◽  
2018 ◽  
Vol 336 (1) ◽  
pp. 43 ◽  
Author(s):  
MILAN C. SAMARAKOON ◽  
YUSUFJON GAFFOROV ◽  
NINGGUO LIU ◽  
SAJEEWA S. N. MAHARACHCHIKUMBURA ◽  
JAYARAMA D. BHAT ◽  
...  
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Species Recognition ◽  
Phylogenetic Species ◽  
Phylogenetic Studies ◽  
Genealogical Concordance ◽  
Two New Species ◽  
Backbone Tree

The genus Coniochaeta is an important ascomycete because its members live in diversified habitats and nutritional modes. In this study, two new species, C. acaciae and C. coluteae, are introduced from dead branches of Acacia sp. and Colutea paulsenii Freyn (both Fabaceae) respectively from Uzbekistan, based on morphological and phylogenetic studies. Analyses of combined ITS and LSU sequence data with Genealogical Concordance Phylogenetic Species Recognition (GCPSR) and comparison of similar taxa, provide evidences for placement of these new species in Coniochaeta, as distinct lineages.

Mimaporia, a new genus of Epicopeiidae (Lepidoptera), with description of a new species from Vietnam

Zootaxa ◽  
2017 ◽  
Vol 4254 (5) ◽  
pp. 537 ◽  
Author(s):  
CHIA-HSUAN WEI ◽  
SHEN-HORN YEN
Keyword(s):  
New Species ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Sister Group ◽  
Morphological Evidence ◽  
New Taxon ◽  
The Family ◽  
A New Species

The Epicopeiidae is a small geometroid family distributed in the East Palaearctic and Oriental regions. It exhibits high morphological diversity in body size and wing shape, while their wing patterns involve in various complex mimicry rings. In the present study, we attempted to describe a new genus, and a new species from Vietnam, with comments on two assumed congeneric novel species from China and India. To address its phylogenetic affinity, we reconstructed the phylogeny of the family by using sequence data of COI, EF-1α, and 28S gene regions obtained from seven genera of Epicopeiidae with Pseudobiston pinratanai as the outgroup. We also compared the morphology of the new taxon to other epicopeiid genera to affirm its taxonomic status. The results suggest that the undescribed taxon deserve a new genus, namely Mimaporia gen. n. The species from Vietnam, Mimaporia hmong sp. n., is described as new to science. Under different tree building strategies, the new genus is the sister group of either Chatamla Moore, 1881 or Parabraxas Leech, 1897. The morphological evidence, which was not included in phylogenetic analyses, however, suggests its potential affinity with Burmeia Minet, 2003. This study also provides the first, although preliminary, molecular phylogeny of the family on which the revised systematics and interpretation of character evolution can be based. 

scholarly journals Morphological and genetic evaluation of the thumbprint emperor, Lethrinus harak (Forsskål, 1775) in the Pacific and Indian Oceans

F1000Research ◽  
2021 ◽  
Vol 9 ◽  
pp. 915
Author(s):  
Muhammad Afrisal ◽  
Yukio Iwatsuki ◽  
Andi Iqbal Burhanuddin
Keyword(s):  
Pacific Ocean ◽  
Indian Ocean ◽  
Genetic Distance ◽  
Marine Biology ◽  
Sequence Data ◽  
Statistical Tests ◽  
Accurate Determination ◽  
Morphometric Character ◽  
Morphometric Characters ◽  
The Pacific

Background: The Lethrinidae (emperors) include many important food fish species. Accurate determination of species and stocks is important for fisheries management. The taxonomy of the genus Lethrinus is problematic, for example with regards to the identification of the thumbprint emperor Lethrinus harak. Little research has been done on L. harak diversity in the Pacific and Indian Oceans. This study aimed to evaluate the morphometric and genetic characters of the thumbprint emperor, L. harak (Forsskål, 1775) in the Pacific and Indian Oceans. Methods: This research was conducted in the Marine Biology Laboratory, Faculty of Marine Science and Fisheries, Hasanuddin University, and Division of Fisheries Science, University of Miyazaki. Morphometric character measurements were based on holotype character data, while genetic analysis was performed on cytochrome oxidase subunit I (COI) sequence data. Morphometric data were analysed using principal component analysis (PCA) statistical tests in MINITAB, and genetic data were analysed in MEGA 6. Results: Statistical test results based on morphometric characters revealed groupings largely representative of the Indian and Pacific Oceans. The Seychelles was separated from other Indian Ocean sites and Australian populations were closer to the Pacific than the Indian Ocean group. The genetic distance between the groups was in the low category (0.000 - 0.042). The phylogenetic topology reconstruction accorded well with the morphometric character analysis, with two main L. harak clades representing Indian and Pacific Ocean, and Australia in the Pacific Ocean clade. Conclusions: These results indicate that the morphological character size of L. harak from Makassar and the holotype from Saudi Arabia have changed. Genetic distance and phylogeny reconstruction are closely related to low genetic distance.

scholarly journals Pyrenochaetopsis kuksensis (Pyrenochaetopsidaceae), a new species associated with an ornamental boxwood in the Czech Republic

Phytotaxa ◽  
2021 ◽  
Vol 498 (3) ◽  
pp. 177-185
Author(s):  
MILAN ŠPETÍK ◽  
AKILA BERRAF-TEBBAL ◽  
ROBERT POKLUDA ◽  
ALEŠ EICHMEIER
Keyword(s):  
Czech Republic ◽  
New Species ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
New Taxon ◽  
The Czech Republic ◽  
Buxus Sempervirens ◽  
Fungal Microbiome ◽  
A New Species

During the investigation of fungal microbiome associated with boxwood in the Czech Republic, samples from Buxus sempervirens L. (Buxaceae) plants were collected and used for isolation. Two fungal strains were proposed as a new species Pyrenochaetopsis kuksensis based on morphology as well as phylogenetic analyses of ITS, LSU, rpb2, and tub2 sequence data. Detailed descriptions and phylogenetic relationships of the new taxon are provided.

Introduction of Neolophiotrema xiaokongense gen. et sp. nov. to the poorly represented Anteagloniaceae (Pleosporales, Dothideomycetes)

Phytotaxa ◽  
2021 ◽  
Vol 482 (1) ◽  
pp. 25-35
Author(s):  
GUANG-CONG REN ◽  
DHANUSHKA N. WANASINGHE ◽  
JUTAMART MONKAI ◽  
KEVIN D. HYDE ◽  
PETER E. MORTIMER ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Species Boundaries ◽  
Identification Of Species

The monotypic Neolophiotrema (typified by N. xiaokongense) is introduced for a wood-inhabiting taxon classified in Dothideomycetes. The genus is characterized by, coriaceous, immersed to semi-immersed ascomata, hamathecium with cellular pseudoparaphyses and overlapping 1–2-seriate, hyaline ascospores. Phylogenetic analysis of combined SSU, LSU, ITS, tef1-α and rpb2 sequence data supports the placement of Neolophiotrema in Anteagloniaceae (Pleosporales). A morphology-based synopsis key is provided to facilitate the identification of species of Anteagloniaceae. The classification and nature of species boundaries in Anteagloniaceae are discussed.

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