Molecular phylogenetic analysis of Dendrobium (Orchidaceae), with emphasis on the Australian section Dendrocoryne, and implications for generic classification

2008 ◽  
Vol 21 (1) ◽  
pp. 1 ◽  
Author(s):  
Jacinta M. Burke ◽  
Michael J. Bayly ◽  
Peter B. Adams ◽  
Pauline Y. Ladiges
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Divergence ◽  
Its Region ◽  
Sister Group ◽  
Main Group ◽  
Internal Transcribed Spacers ◽  
Nuclear Rdna ◽  
Sister Relationship ◽  
Asian Clade ◽  
Molecular Phylogenetic

Sequences of the internal transcribed spacers (ITS) of nuclear rDNA were obtained for a broad range of dendrobium orchids for phylogenetic analysis using parsimony. A progressive approach was used to identify functional outgroups for analysis of all taxa in Dendrobium sect. Dendrocoryne. Our first, broadest analysis confirmed the results of other workers that Dendrobium sensu lato includes a major Australasian clade and a sister Asian clade. In the Australasian clade, the New Zealand species D. cunninghamii (=gen. Winika, Clements et al. 1997) was identified as the sister group to a well supported clade that includes the genera Cadetia, Diplocaulobium and Flickingeria, and Dendrobium sects Grastidium, Latouria, Spatulata, Australorchis (=gen. Australorchis), Rhizobium (= gen. Dockrillia) and Dendrocoryne. Sect. Dendrocoryne is probably polyphyletic, with two species, D. aemulum and D. callitrophilum (=gen. Tropilis), outside the main group and sect. Rhizobium (= gen. Dockrillia) nested within it. Sect. Australorchis (= gen. Australorchis) is possibly the sister group to the clade of Rhizobium plus the main group of Dendrocoryne. Thelychiton (a genus reinstated for several species in Dendrocoryne) is polyphyletic, given that Tetrabaculum (=D. tetragonum complex) and Dockrillia fall within the same clade. The splitting of the Australasian dendrobiums into various genera by other authors is excessive and unnecessary, and alternative taxonomic treatments are offered here for debate. Our study included accessions for all varieties in the following three widespread eastern Australian species: D. speciosum, D. kingianum and D. tetragonum. Each of these species showed significant sequence divergence between particular geographic regions, but some varieties had identical sequences. The splitting of D. speciosum into 11 species is not supported. We identified pseudogenes in the ITS region for D. fleckeri and D. finniganense, which appear to have evolved before these two species diverged, but support their sister relationship. Sequences for D. callitrophilum and D. (Grastidium) baileyi (the latter from GenBank) also appear to be pseudogenes, and these taxa need further study.

A framework for a phylogenetic classification in the genus Cortinarius (Basidiomycota, Agaricales) derived from morphological and molecular data

2005 ◽  
Vol 83 (11) ◽  
pp. 1457-1477 ◽  
Author(s):  
Sigisfredo Garnica ◽  
Michael Weiß ◽  
Bernhard Oertel ◽  
Franz Oberwinkler
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Phylogenetic Analysis ◽  
Nuclear Rdna ◽  
Ecological Data ◽  
Natural Classification ◽  
Geographical Patterns ◽  
Rdna Sequences ◽  
Molecular Phylogenetic

Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species including most of the recognised subgenera from Europe, South America, Australia, Tasmania, New Zealand, and Asia were sequenced and analysed by maximum likelihood and neighbour joining. Our morphological and molecular analyses showed considerable disagreement with earlier morphology-based hypotheses concerning the infrageneric delimitations in Cortinarius. We propose a new base for a more natural classification system in Cortinarius involving the taxonomic rearrangement of the species into the following major lineages that we informally designate as “clades” at this time: (1) phlegmacioid species are included in Alluti, Amarescentes, Arguti, Calochroi, Caerulescentes, Percomes, Phlegmacioides, Phlegmacium, Purpurascentes, Scauri, and Vulpini; (2) the Heterocliti clade includes species of the subgenera Leprocybe and Cystogenes ; (3) most of the Myxacium species are included in the Delibuti and Myxacium clades; (4) part of Rozites are included in the Rozites clade; (5) the north-hemispheric species of subgenus Dermocybe are included in the Dermocybe clade and part of the south-hemispheric species in the Splendidi clade; (6) part of Sericeocybe are integrated in the Anomali and Telamonia clades; (7) members of subgenus Cortinarius are assigned to the Cortinarius clade; (8) telamonioid taxa are included in the Obtusi, Renidentes, and Telamonia clades. Several Cortinarius species with peculiar patterns of morphology and basidiome coloration had isolated positions in the sequence analysis, and the evolutionary relationships among the major lineages remained unresolved. Our results suggest the convergent evolution of certain morphological traits across phylogenetically divergent lineages in Cortinarius. However, combinations of features such as pileipellis anatomy, spore shape, veil coloration, basidiome pigments, and stipe shape appear useful to circumscribe clades. Our molecular phylogenetic analysis allows insights in global geographical patterns of species distribution within the major lineages in the genus Cortinarius. The clade structure proposed here could be used as backbone for further more detailed systematic studies.

ORIGIN AND RELATIONSHIPS OF ALPINIA GALANGA (ZINGIBERACEAE) BASED ON MOLECULAR DATA

2000 ◽  
Vol 57 (1) ◽  
pp. 9-37 ◽  
Author(s):  
A. RANGSIRUJI ◽  
M. F. NEWMAN ◽  
Q. C. B. CRONK
Keyword(s):  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Sister Relationship ◽  
Important Species ◽  
Alpinia Galanga ◽  
Decay Index ◽  
Molecular Phylogenetic

Alpinia galanga is an important species cultivated as a culinary spice and is the type species of the genus. It is hence a member of sect. Alpinia subsect. Alpinia (with non-tubular bracteoles). However, molecular phylogenetic analyses suggest that A. galanga is closely related to A. nigra in sect. Allughas (with tubular bracteoles). This clade, which includes A. conchigera, is strongly supported with a bootstrap value (BS) of 100% and a decay index (DI) of >+6. These results are based on the internal transcribed spacer (ITS) region of the 18S–25S nuclear ribosomal DNA. The region (405–423bp) was sequenced from 17 accessions representing 16 taxa of Zingiberaceae, including 15 species of Alpinia and one outgroup. The sequence divergence ranged from 0.5 to 15.6% among the ingroup and from 10.1 to 13.3% between the ingroup and the outgroup. The results also strongly support the sister relationship of A. rafflesiana and A. javanica in section Allughas (BS=100%, DI=>+6), thus the whole section is paraphyletic. Section Alpinia subsect. Catimbium is monophyletic (BS=100%, DI=+5). On the other hand, sect. Alpinia subsect. Alpinia is paraphyletic (BS=100%, DI=>+6) with respect to sect. Alpinia subsect. Catimbium. The results from a phylogenetic analysis of a subset of the taxa using the spacer between trnL (UAA) 3′ exon and trnF (GAA) of chloroplast DNA confirmed the position of A. galanga in sect. Allughas. It appears that A. galanga has evolved within sect. Allughas and the absence of tubular bracteoles is a convergence with sect. Alpinia, possibly as a result of evolution under domestication.

Pilaira australis sp. nov. (Mucorales, Mucoromycota) isolated from emu faeces in Australia

Phytotaxa ◽  
2017 ◽  
Vol 329 (3) ◽  
pp. 277 ◽  
Author(s):  
ANDREW S. URQUHART ◽  
PAULINE M. L. COULON ◽  
ALEXANDER IDNURM
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Species Identification ◽  
Internal Transcribed Spacers ◽  
Molecular Phylogenetic Analysis ◽  
Unique Combination ◽  
Dromaius Novaehollandiae ◽  
Molecular Phylogenetic ◽  
Carbon Utilisation ◽  
A New Species

Pilaira australis, a new species of fungus in the coprophilous genus Pilaira, was isolated from emu (Dromaius novaehollandiae) faeces and is described. Morphologically, the species resembles other species in the genus, particularly P. moreaui, except differs in its unique combination of sporangiophore height and sporangiospore length. Molecular phylogenetic analysis indicates that P. australis is distinct from other species in the genus with two regions, the internal transcribed spacers (ITS) and a fragment of the pyrG gene, showing 91% and 90% identity to the nearest species, respectively. Ultrastructure features and carbon utilisation were determined for P. australis, and may provide characteristics for species identification in this genus.

scholarly journals Savitreea pentosicarens gen. nov., sp. nov., a yeast species in the family Saccharomycetaceae isolated from a grease trap

2020 ◽  
Vol 70 (11) ◽  
pp. 5665-5670
Author(s):  
Varunya Sakpuntoon ◽  
Jirameth Angchuan ◽  
Chanita Boonmak ◽  
Pannida Khunnamwong ◽  
Noémie Jacques ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Yeast Species ◽  
Sequence Divergence ◽  
Its Region ◽  
Rrna Gene ◽  
Nucleotide Substitutions ◽  
D2 Domain ◽  
The Family ◽  
Lsu Rrna Gene ◽  
Lsu Rrna

Two strains (DMKU-GTCP10-8 and CLIB 1740) representing a novel anamorphic yeast species were isolated from a grease sample collected from a grease trap in Thailand and from an unidentified fungus collected in French Guiana, respectively. On the basis of phylogenetic analysis based on the combined D1/D2 domain of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region, Lachancea fermentati CBS 707T was the closely related species with 12.8 % sequence divergence (70 nucleotide substitutions and three gaps in 571 nucleotides) and 28.1 % sequence divergence (93 nucleotide substitutions and 90 gaps in 651 nucleotides) in the D1/D2 domain of the LSU rRNA gene and the ITS region, respectively. Phylogenetic analysis based on the concatenated sequences of the five genes including the small subunit rRNA gene, the D1/D2 domain of the LSU rRNA gene, the ITS region, translation elongation factor-1 alpha (TEF1) and RNA polymerase II subunit 2 (RPB2) genes confirmed that the two strains (DMKU-GTCP10-8 and CLIB 1740) were well-separated from other described yeast genera in Saccharomycetaceae. Hence, Savitreea pentosicarens gen. nov., sp. nov. is proposed to accommodate these two strains as members of the family Saccharomycetaceae. The holotype is S. pentosicarens DMKU-GTCP10-8T (ex-type strain TBRC 12159=PYCC 8490; MycoBank number 835044).

Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure

2020 ◽  
Vol 190 (3) ◽  
pp. 1002-1019 ◽  
Author(s):  
Donald L J Quicke ◽  
Sergey A Belokobylskij ◽  
Yves Braet ◽  
Cornelis van Achterberg ◽  
Paul D N Hebert ◽  
...  
Keyword(s):  
Sequence Data ◽  
Elongation Factor ◽  
Sequence Divergence ◽  
Sister Group ◽  
Morphological Characters ◽  
Dna Sequence Data ◽  
Elongation Factor 1 Alpha ◽  
Molecular Phylogenetic ◽  
Molecular Dataset ◽  
First Time

Abstract A new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.

A new species of Conocybe (Bolbitaceae) from Punjab, Pakistan

Phytotaxa ◽  
2019 ◽  
Vol 402 (5) ◽  
pp. 251
Author(s):  
AIMAN IZHAR ◽  
HIRA BASHIR ◽  
ABDUL NASIR KHALID
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Its Region ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Evidence ◽  
Fruiting Bodies ◽  
Germ Pore ◽  
Central Disc ◽  
Molecular Phylogenetic ◽  
A New Species

Conocybe punjabensis sp. nov., a species belonging to the saprobic family Bolbitaceae, is illustrated and described from Pakistan based on morphology and molecular evidence. The species can be distinguished on the basis of medium-sized fruiting bodies, a pileus with a dark brown central disc, a fibrillose stipe, forked lamellae near pileus margin, ellipsoid angular basidiospores with an apical germ pore, cheilocystidia and pleurocystidia varying from catenulate, lecythiform to clavate, and lecythiform caulocystidia. Molecular phylogenetic analysis of the nuclear ribosomal ITS region also supports the recognition of this new species in Conocybe. Detailed descriptions, photographs, illustrations and comparison with allied taxa are given.

scholarly journals Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region

Horticulturae ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 87
Author(s):  
Kumpei Shiragaki ◽  
Shuji Yokoi ◽  
Takahiro Tezuka
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Wild Species ◽  
Morphological Characteristics ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Rdna Its ◽  
Rdna Its Region ◽  
Genus Capsicum

The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.

Two Erysiphe species associated with recent outbreak of soybean powdery mildew: results of molecular phylogenetic analysis based on nuclear rDNA sequences

Mycoscience ◽  
2002 ◽  
Vol 43 (4) ◽  
pp. 333-341 ◽  
Author(s):  
Susumu Takamatsu ◽  
Yusuke Taguchi ◽  
Hyeon-Dong Shin ◽  
Urailak Paksiri ◽  
Saranya Limkaisang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Molecular Phylogenetic Analysis ◽  
Nuclear Rdna ◽  
Rdna Sequences ◽  
Recent Outbreak ◽  
Molecular Phylogenetic

Infundibulicybe macrospora sp. nov., a new and noteworthy species from Himalayan moist temperate forests of Pakistan

Phytotaxa ◽  
2020 ◽  
Vol 452 (4) ◽  
pp. 268-277
Author(s):  
MUHAMMAD ALI ◽  
JUNAID KHAN ◽  
HIRA BASHIR ◽  
ABDUL REHMAN NIAZI ◽  
HASSAN SHER ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Temperate Forests ◽  
Its Region ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
A New Species ◽  
Reddish Orange ◽  
Light Orange

Infundibulicybe macrospora, a new species, is described and illustrated from the Himalayan moist temperate forests of Pakistan. The new species can be differentiated from close allies by its reddish orange to light orange pileus, whitish lamellae and stipe, and larger and broader basidiospores. The new species is also supported by molecular phylogenetic analysis inferred from internal transcribed spacer (ITS) region.

scholarly journals Ectomycorrhizae of Tomentella badia: description and molecular identification

2013 ◽  
Vol 48 (2) ◽  
pp. 155-171 ◽  
Author(s):  
Andrea Binder ◽  
Derek Peršoh ◽  
Nourou S. Yorou ◽  
Rita Verma ◽  
Claus Bässler ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Picea Abies ◽  
Molecular Identification ◽  
Its Region ◽  
Molecular Phylogenetic Analysis ◽  
Functional Characteristics ◽  
Molecular Phylogenetic ◽  
Dark Blue

Species within the genera <em>Tomentella </em>are among the most important ECM in forests. However, our knowledge about their functional characteristics is still rather limited. The ectomycorrhizae of <em>Tomentella badia </em>on <em>Picea abies </em>are described here in detail and compared to the non-identified ECM <em>Piceirhiza obscura</em>. A pseudoparenchymatous mantle formed by epidermoid cells is covered by heaps of epidermoid cells. This mantle type is regarded as a new one and designated as mantle type R. Many cells filled with dark blue contents and/or blue granules, together with clampless hyphae, are distinct characters of these ectomycorrhizae. Molecular-phylogenetic analysis of the ITS region was used for identification.

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