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.

Pseudosperma albobrunneum sp. nov. from coniferous forests of Pakistan

Mycotaxon ◽  
2021 ◽  
Vol 136 (2) ◽  
pp. 361-372
Author(s):  
Sana Jabeen ◽  
Zainab ◽  
Hira Bashir ◽  
Abdul Nasir Khalid
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Its Region ◽  
Morphological Characters ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Coniferous Forests ◽  
Molecular Phylogenetic ◽  
Khyber Pakhtunkhwa Province ◽  
A New Species

A new species, Pseudosperma albobrunneum, is described and illustrated. The specimens are from different areas of Khyber Pakhtunkhwa province, Pakistan. The identification is based on morphological characters, in combination with molecular phylogenetic analysis of sequences of the ITS region of nuclear ribosomal DNA. The species is found distinct morphologically from all closely related taxa, and molecular data confirm its novelty.

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.

Phylogenetic and genomic relationships in the genus Glycine Willd. based on sequences from the ITS region of nuclear rDNA

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 57-68 ◽  
Author(s):  
Krishna P. Kollipara ◽  
Ram J. Singh ◽  
Theodore Hymowitz
Keyword(s):  
Sequence Variation ◽  
Glycine Soja ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Single Nucleotide ◽  
Nucleotide Sequence Variation ◽  
Genomic Relationships ◽  
Its1 And Its2

Phylogenetic relationships among all 18 species of the genus Glycine were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. Pairwise sequence divergence values ranged from 0.2% (a single nucleotide) between Glycine max and Glycine soja to 8.6% between Glycine hirticaulis and Glycine falcata. The length of the ITS1 and ITS2 sequences ranged from 215 to 238 nucleotides and from 205 to 222 nucleotides, respectively, and that of 5.8S was 168 nucleotides across all the species. Phylogenetic analyses of the ITS region clearly resolved all the genomic groups that were established previously based on cytogenetic and biochemical studies. Based on this study, we assign new genome symbols: HH to Glycine arenaria, H1H1 to Glycine hirticaulis, H2H2 to Glycine pindanica, II to Glycine albicans, and I1I1 to Glycine lactovirens. Parsimony analysis of the entire ITS region, using subgenus Soja as outgroup, resulted in a trichotomy consisting of the clades: G. falcata (F genome), Glycine cyrtoloba and Glycine curvata (C genome), and all other species (A, B, D, E, H, and I genomes) of the subgenus Glycine.Key words: Glycine spp., soybean, genomes, ITS region, rDNA.

scholarly journals TRIBES AND CLADES WITHIN APIACEAE SUBFAMILY APIOIDEAE: THE CONTRIBUTION OF MOLECULAR DATA

2001 ◽  
Vol 58 (2) ◽  
pp. 301-330 ◽  
Author(s):  
S. R. DOWNIE ◽  
G. M. PLUNKETT ◽  
M. F. WATSON ◽  
K. SPALIK ◽  
D. S. KATZ-DOWNIE ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Data Sets ◽  
Combining Data ◽  
Restriction Sites ◽  
Dna Restriction ◽  
Cladistic Analyses

Phylogenetic analyses of chloroplast gene (rbcL, matK), intron (rpl16, rps16, rpoC1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae (Umbelliferae) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets. Ten tribes (Aciphylleae M. F. Watson & S. R. Downie, Bupleureae Spreng., Careae Baill., Echinophoreae Benth., Heteromorpheae M. F. Watson & S. R. Downie, Oenantheae Dumort., Pleurospermeae M. F. Watson & S. R. Downie, Pyramidoptereae Boiss., Scandiceae Spreng. and Smyrnieae Spreng.) are erected or confirmed as monophyletic, with Scandiceae comprising subtribes Daucinae Dumort., Scandicinae Tausch and Torilidinae Dumort. Seven additional clades are also recognized but have yet to be treated formally, and at least 23 genera examined to date are of dubious tribal or clade placement. The utility of these different molecular markers for phylogenetic inference in Apioideae is compared based on maximum parsimony analyses of subsets of previously published molecular data sets. Of the six loci sequenced, the ITS region is seen to be evolving most rapidly and rbcL is the most conservative. Intermediate in rate of evolution are matK and the three chloroplast introns; with rpl16 and rps16 evolving slightly faster than matK or rpoC1. The analysis of restriction sites, however, provided 2–4 times more parsimony informative characters than any single DNA locus sequenced, with estimates of divergence just slightly lower than that of the ITS region. The trees obtained from separate analyses of these reduced data sets are consistent with regard to the major clades inferred and the relationships among them. Similar phylogenies are obtained by combining data or combining trees, representing the supermatrix and supertree approaches to phylogenetic analysis, respectively. The inferred relationship among the tribes and informally recognized major clades within Apioideae is presented.

scholarly journals Disentangling relationships among eastern Mediterranean Cymbalaria including description of a novel species from the southern Peloponnese (Greece)

2021 ◽  
Vol 307 (2) ◽  
Author(s):  
Pau Carnicero ◽  
Núria Garcia-Jacas ◽  
Llorenç Sáez ◽  
Theophanis Constantinidis ◽  
Mercè Galbany-Casals
Keyword(s):  
Eastern Mediterranean ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Distribution Patterns ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Long Distance ◽  
Aegean Islands ◽  
Molecular Phylogenetic

AbstractThe eastern Mediterranean basin hosts a remarkably high plant diversity. Historical connections between currently isolated areas across the Aegean region and long-distance dispersal events have been invoked to explain current distribution patterns of species. According to most recent treatments, at least two Cymbalaria species occur in this area, Cymbalaria microcalyx and C. longipes. The former comprises several intraspecific taxa, treated at different ranks by different authors based on morphological data, evidencing the need of a taxonomic revision. Additionally, some populations of C. microcalyx show exclusive morphological characters that do not match any described taxon. Here, we aim to shed light on the systematics of eastern Mediterranean Cymbalaria and to propose a classification informed by various sources of evidence. We performed molecular phylogenetic analyses using ITS, 3’ETS, ndhF and rpl32-trnL sequences and estimated the ploidy level of some taxa performing relative genome size measures. Molecular data combined with morphology support the division of traditionally delimited C. microcalyx into C. acutiloba, C. microcalyx and C. minor, corresponding to well-delimited nrDNA lineages. Furthermore, we propose to combine C. microcalyx subsp. paradoxa at the species level. A group of specimens previously thought to belong to Cymbalaria microcalyx constitute a well-defined phylogenetic and morphological entity and are described here as a new species, Cymbalaria spetae. Cymbalaria longipes is non-monophyletic, but characterized by being glabrous and diploid, unlike other eastern species. The nrDNA data suggest at least two dispersals from the mainland to the Aegean Islands, potentially facilitated by marine regressions.

Infundibulicybe rufa sp. nov. (Tricholomataceae), a reddish brown species from southwestern China

Phytotaxa ◽  
2016 ◽  
Vol 266 (2) ◽  
pp. 134 ◽  
Author(s):  
QI ZHAO ◽  
YAN-JIA HAO ◽  
JIAN-KUI LIU ◽  
KEVIN D. HYDE ◽  
YANG-YANG CUI ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Biosphere Reserve ◽  
Its Region ◽  
Southwestern China ◽  
New Taxon ◽  
Line Drawings ◽  
Phylogenetic Placement ◽  
Molecular Phylogenetic ◽  
Pileus Surface

Infundibulicybe rufa sp. nov., is described from Jiuzhaigou Biosphere Reserve, southwestern China. It is characterized by the combination of the following characters: umbilicate to slightly infundibuliform, reddish brown pileus; decurrent, cream lamellae; cylindrical stipe concolorous with the pileus surface. Molecular phylogenetic analyses using the nuclear ribosomal internal transcribed spacer (ITS) region indicates that I. rufa is closely related to I. mediterranea and I. bresadolana. A description, line drawings, phylogenetic placement and comparison with allied taxa for the new taxon are presented.

Higher-level relationships among the eucalypts are resolved by ITS-sequence data

2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Phylogenetic Groups ◽  
Single Section ◽  
Western Australian ◽  
Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

scholarly journals Noteworthy record of the Ethiopian genet, Genetta abyssinica, (Carnivora, Viverridae) from Djibouti informs its phylogenetic position within Genetta

Mammalia ◽  
2019 ◽  
Vol 83 (2) ◽  
pp. 180-189 ◽  
Author(s):  
Adam W. Ferguson ◽  
Houssein R. Roble ◽  
Molly M. McDonough
Keyword(s):  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Sister Relationship ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Molecular Phylogenetic ◽  
Relationship Of

AbstractThe molecular phylogeny of extant genets (Carnivora, Viverridae,Genetta) was generated using all species with the exception of the Ethiopian genetGenetta abyssinica. Herein, we provide the first molecular phylogenetic assessment ofG. abyssinicausing molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen ofG. abyssinicacollected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship ofG. abyssinicato otherGenettaspecies, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships amongGenettaspecies remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore.

scholarly journals Polulichloris henanensis gen. et sp. nov. (Trebouxiophyceae, Chlorophyta), a novel subaerial coccoid green alga

Phytotaxa ◽  
2015 ◽  
Vol 218 (2) ◽  
pp. 137 ◽  
Author(s):  
Huiyin Song ◽  
Qi Zhang ◽  
Guoxiang Liu ◽  
Zhengyu Hu
Keyword(s):  
Green Alga ◽  
New Genus ◽  
Cultured Cells ◽  
Phylogenetic Analyses ◽  
Light And Electron Microscopy ◽  
Molecular Data ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Molecular Phylogenetic ◽  
18S Rdna Gene

Coccoid green algae are abundant in subaerial habitats, but they are largely unexplored because of their morphological uniformity. Several new genus-level lineages have recently been described on the basis of molecular data. In this study, a coccoid green alga was isolated from surface soil in Zhoukou, Henan Province, China, and the cultured cells were described using light and electron microscopy. The ellipsoidal cell had smooth cell wall and parietal chloroplast with a pyrenoid surrounded by a starch envelope. Reproduction occurred by formation of 2‒16 autospores. Molecular phylogenetic analyses based on the nuclear 18S rDNA gene and the chloroplast ribulose-bisphosphate carboxylase gene (rbcL) indicated that this coccoid green alga represents a new lineage of the Watanabea clade (Trebouxiophyceae, Chlorophyta). Here, we describe this organism as a new genus and species, Polulichloris henanensis, gen. et sp. nov.

scholarly journals First Report of the Cereal Cyst Nematode Heterodera filipjevi on Wheat in Serbia

Plant Disease ◽  
2012 ◽  
Vol 96 (10) ◽  
pp. 1583-1583 ◽  
Author(s):  
V. Oro ◽  
S. Živković ◽  
Ž. Ivanović ◽  
L. Waeyenberge
Keyword(s):  
New York ◽  
Tail Length ◽  
Its Region ◽  
Molecular Data ◽  
Cyst Nematode ◽  
Cereal Cyst Nematode ◽  
Important Species ◽  
First Report ◽  
Wheat Field ◽  
Heterodera Filipjevi

The most globally recognized and economically important nematode on wheat is the cereal cyst nematode (CCN) complex (1). One of the most important species of this group is Heterodera filipjevi (Madžidov, 1981) Mulvey and Golden, 1983. During regular soil quarantine control in September 2010, Heterodera sp. cysts were found in soil samples originating from a wheat field in Gunaroš, Vojvodina Province, in northern Serbia. The wheat was a winter crop grown in a dryland production system and had an average cyst density of 2.50/100 cm3 of soil. Morphologically, the cysts were golden brown and lemon shaped with a posterior protuberance. The vulval cone was bifenestrate with horseshoe-shaped semifenestra, bullae, and underbridge. Cyst measurements (n = 30) ranged as follows: cyst length (without neck): 511.50 to 899.00 μm, cyst width: 201.50 to 682.00 μm, fenestral length: 44.80 to 65.60 μm, fenestral width: 24.00 to 40.00 μm, vulval bridge length: 12.80 to 20.80 μm, vulval bridge width: 6.40 to 14.40 μm, vulval slit: 6.00 to 12.80 μm, and underbridge length: 60.00 to 112.00 μm. The second-stage juveniles had an offset head, stylet with characteristic anchor-shaped basal knobs, four incisures, and a conical tail with a rounded tip. The J2 morphometrics (n = 30) were: length: 447.30 to 611.10 μm, width: 22.40 to 25.60 μm, stylet: 20.80 to 24.00 μm, tail length: 56.00 to 68.80 μm, tail width: 14.40 to 19.20 μm, and hyaline length: 35.20 to 44.80 μm. The ITS region was used for molecular analysis. Each DNA sample was extracted from a single cyst. Sequencing was done with primers TW81 and AB28 (2). In comparison with other H. filipjevi populations, the obtained sequence (GenBank Accession No. JX235959) revealed 99 to 100% similarity. Morphological and molecular data confirmed the existence of H. filipjevi. This is, to our knowledge, the first report of H. filipjevi from Serbia. Since wheat has important socioeconomic value for Serbia, after extensive surveys, additional phytosanitary measures may be necessary to prevent the spread of this parasite. References: (1) J. M. Nicol et al. Current Nematode Threats to World Agriculture. Genomics and Molecular Genetics of Plant-Nematode Interactions, Springer, New York, 2011. (2) A. M. Skantar et al. J. Nematol. 39:133, 2007.

Sign in / Sign up

Export Citation Format

Share Document