Phylogenetic Analysis within Genera Morchella (Ascomycota, Pezizales) and Macrolepiota (Basidiomycota, Agaricales) Inferred from rDNA ITS and EF-1a Sequences

2012 ◽  
pp. 171-218 ◽  
Keyword(s):  
Phylogenetic Analysis ◽  
Rdna Its

scholarly journals Molecular and phylogenetic analysis reveals new diversity of Dunaliella salina from hypersaline environments

2021 ◽  
pp. 1-11
Author(s):  
Andrea Highfield ◽  
Angela Ward ◽  
Richard Pipe ◽  
Declan C. Schroeder
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Dunaliella Salina ◽  
Phylogenetic Analyses ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Hypersaline Environments ◽  
Rdna Its ◽  
Β Carotene ◽  
Selection Of

Abstract Twelve hyper-β carotene-producing strains of algae assigned to the genus Dunaliella salina have been isolated from various hypersaline environments in Israel, South Africa, Namibia and Spain. Intron-sizing of the SSU rDNA and phylogenetic analysis of these isolates were undertaken using four commonly employed markers for genotyping, LSU rDNA, ITS, rbcL and tufA and their application to the study of Dunaliella evaluated. Novel isolates have been identified and phylogenetic analyses have shown the need for clarification on the taxonomy of Dunaliella salina. We propose the division of D. salina into four sub-clades as defined by a robust phylogeny based on the concatenation of four genes. This study further demonstrates the considerable genetic diversity within D. salina and the potential of genetic analyses for aiding in the selection of prospective economically important strains.

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.

scholarly journals Morphological and molecular characterization of Sarcocystis wenzeli in chickens (Gallus gallus) in China

2020 ◽  
Author(s):  
Jing Pan ◽  
Chunli Ma ◽  
Zhumei Huang ◽  
Yulong Ye ◽  
Hongxia Zeng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rdna ◽  
Sequence Similarity ◽  
28S Rdna ◽  
Ground Substance ◽  
Molecular Characteristics ◽  
Cox1 Gene ◽  
Intermediate Hosts ◽  
Rdna Its ◽  
Sarcocystis Spp

Abstract Background: There has been considerable confusion concerning the number and classification of Sarcocystis spp. in chickens. Scarce nucleotide data of Sarcocystis spp. from chickens are provided in GenBank. The study aimed to investigate the morphological and molecular characteristics of Sarcocystis spp. found in chickens in China. Methods: Tissues from 33 chickens were collected in 2019. Sarcocysts were observed using light (LM) and transmission electron microscopy (TEM). Individual sarcocysts from different chickens were selected for DNA extraction, and five loci, 18S rDNA, 28S rDNA, the ITS-1 region ( ITS-1 ), the mitochondrial cox1 gene ( cox1 ), and the apicoplastic rpoB gene ( rpoB ), were amplified from each sarcocyst, sequenced and analyzed. Results: Only S . wenzeli was found in 14 of 33 (42.4%) chickens. Under LM, the sarcocysts were microscopic and exhibited palisade-like villar protrusions measuring 1.5–2.8 μm. Ultrastructurally, the sarcocyst wall contained numerous stubby hill-like villar protrusions. The protrusions included scattered microtubules, which extended from the tips of the protrusions into the ground substance. The five loci were successfully sequenced and deposited in GenBank. At 18S rDNA, ITS-1 and cox1 , the most similar sequences in GenBank were those of Sarcocystis sp. obtained from the brains of chickens, i.e., 99.9–100%, 98.1–98.5%, and 99.3% identity, respectively. The five loci (18S rDNA, 28S rDNA, ITS-1 , cox1 and rpoB ) showed different levels of interspecific sequence similarity with other closely related species of Sarcocystis (e.g., 99.8%, 99.0–99.2%, 89.3-89.7%, 98.5%, and 97.5%, respectively, with S . anasi ). Phylogenetic analysis based on three of the loci (18S rDNA, cox1 , and rpoB ) revealed that S . wenzeli formed an independent clade with Sarcocystis spp. that employ geese or ducks as intermediate hosts and canines as the known or presumed definitive host. Conclusions: The sequences of 28S rDNA and rpoB reported here constitute the first records of genetic markers of Sarcocystis spp. in chickens. Based on molecular analysis, S . wenzeli might be responsible for the neurological disease in chickens, and ITS-1 and rpoB are more suitable for discriminating it from closely related Sarcocystis spp. Phylogenetic analysis revealed that S . wenzeli presents a close relationship with Sarcocystis spp. in geese or ducks.

A new and threatened species of Trichaptum (Basidiomycota, Hymenochaetales) from urban mangroves of Santa Catarina Island, Southern Brazil

Phytotaxa ◽  
2021 ◽  
Vol 482 (2) ◽  
pp. 197-207
Author(s):  
THIAGO KOSSMANN ◽  
DIOGO HENRIQUE COSTA-REZENDE ◽  
ARISTÓTELES GÓES-NETO ◽  
ELISANDRO RICARDO DRECHSLER-SANTOS
Keyword(s):  
Phylogenetic Analysis ◽  
Threatened Species ◽  
Mangrove Forests ◽  
Southern Brazil ◽  
Santa Catarina ◽  
Rdna Its ◽  
Worldwide Distribution ◽  
Variable Morphology ◽  
Iucn Criteria

Trichaptum comprises around 36 polypore species, with variable morphology and worldwide distribution. During polypore surveys in Santa Catarina Island (Southern Brazil), specimens of a remarkable species, with large, mostly resupinate basidiomata, large (6–11µm long) spores and two kinds of cystidia, were collected in mangrove forests and their vicinities. Morphological and phylogenetic analysis (rDNA ITS) revealed it as new, and is described herein as T. fissile sp. nov. Moreover, the species is proposed as Vulnerable according to the IUCN criteria. The taxonomic placement and delimitation of Trichaptum are also discussed.

Geopora ramila sp. nov. (Pezizales, Pyronemataceae) evidenced by morphological characters and phylogenetic analyses in Iran

Phytotaxa ◽  
2020 ◽  
Vol 475 (1) ◽  
pp. 29-42
Author(s):  
MASOUD SHEIBANI ◽  
SAMAD JAMALI
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Its Sequence ◽  
Fars Province ◽  
Annual Plant ◽  
Blast Search ◽  
Rdna Its ◽  
Internally Transcribed Spacer ◽  
Close Relatives

A new Geopora species (Pyronemataceae), Geopora ramila was described and illustrated from the soil, under or in the vicinity of Helianthemum ledifolium var. ledifolium annual plant in Fars province, Iran. Morphologically, G. ramila is similar to G. pinyonensis and G. arenicola but distinguished from both by a combination of morphological characters including, color and size of ascocarps, size and shape of ascospores, habit and associated host. The ribosomal DNA internally transcribed spacer (rDNA ITS) sequence of the new species (Acc. No. MT108930 to MT108934) showed 87.82% identity with G. pinyonensis in the BLAST search in GenBank. ITS-based phylogenetic analysis clearly supports G. ramila is a new and distinctive species lacking close relatives among described species of Geopora.

scholarly journals Phylogenetic Analysis of Different Ploidy Saccharum spontaneum Based on rDNA-ITS Sequences

PLoS ONE ◽  
2016 ◽  
Vol 11 (3) ◽  
pp. e0151524 ◽  
Author(s):  
Xinlong Liu ◽  
Xujuan Li ◽  
Hongbo Liu ◽  
Chaohua Xu ◽  
Xiuqin Lin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Its Sequences ◽  
Saccharum Spontaneum ◽  
Rdna Its ◽  
Rdna Its Sequences

Phylogenetic analysis of the phytopathogenic fungus Fusarium solani based on the rDNA-ITS region

2000 ◽  
Vol 104 (10) ◽  
pp. 1175-1183 ◽  
Author(s):  
H. Suga ◽  
T. Hasegawa ◽  
H. Mitsui ◽  
K. Kageyama ◽  
M. Hyakumachi
Keyword(s):  
Phylogenetic Analysis ◽  
Fusarium Solani ◽  
Its Region ◽  
Phytopathogenic Fungus ◽  
Rdna Its ◽  
Rdna Its Region
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