A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region

Crocus asymmetricus (Iridaceae) is described as a new species endemic to the southern part of the Anatolian diagonal in Turkey. It is phylogenetically related to C. vitellinus and morphologically to C. antalyensis, but differs from these species in showing an asymmetric corm and a single point of root emergence. Both C. antalyensis and C. asymmetricus are illustrated and compared in this paper. A Bayesian phylogenetic tree of the nuclear rDNA ITS region confirms the affiliation of C. asymmetricus to C. ser. Flavi, and its close relationship to C. vitellinus. A new identification key to the species of C. ser. Flavi occurring in Turkey is also presented.

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Intra-individual and intra-species heterogeneity in nuclear rDNA ITS region of Vigna species from subgenus Ceratotropis

Genetics Research ◽

10.1017/s001667230800983x ◽

2008 ◽

Vol 90 (4) ◽

pp. 299-316 ◽

Cited By ~ 20

Author(s):

AJAY SAINI ◽

SREENIVASULU K. REDDY ◽

NARENDRA JAWALI

Keyword(s):

Process Analysis ◽

Pcr Amplification ◽

Its Region ◽

Pcr Analysis ◽

Rdna Repeat ◽

Nuclear Rdna ◽

Rdna Its ◽

Secondary Structure Analysis ◽

Repeat Units ◽

Rdna Its Region

SummaryThe extent of intra-individual and intra-species heterogeneity in the nuclear rDNA internal transcribed spacer (ITS) was investigated among the ‘Asiatic Vigna’ species (subgenus Ceratotropis). High intra- and inter-individual ITS polymorphism was observed among Vigna radiata accessions, where multiple ITS length variants ranging from ~700 to ~770 bp were detected on PCR amplification. Subsequent analysis revealed that the variants are ‘heteroduplex ITS fragments’ generated during the PCR process. Analysis of ITS from wild and cultivated forms of ten Vigna species from subgenus Ceratotropis revealed substantial intra-species divergence in four species: Vigna umbellata, Vigna trilobata, V. radiata and Vigna minima. However, no other species analysed showed intra-individual ITS heterogeneity as observed in V. radiata. The results demonstrate differential evolution of ITS sequence among wild and cultivated forms of V. radiata. Evidence indicates that intra-species hybridization and a slow ‘molecular drive’ are responsible for this phenomenon. Sequence analysis of 5·8S, ITS1 and ITS2 and secondary-structure analysis of ITS regions indicate that the ITS variants do not belong to pseudogenic rDNA repeat units. Further, reverse transcriptase-PCR (RT-PCR) analysis showed that rDNA repeat units harbouring certain intra-individual ITS variants were transcriptionally inactive, indicating the regulation of these loci by epigenetic gene silencing. The V. radiata ITS variants, when analysed together, did not cause any phylogenetic errors at the species level.

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Phylogenetic utility of the nuclear rDNA ITS region in subfamilyIxoroideae (Rubiaceae): Comparisons with cpDNArbcL sequence data

Plant Systematics and Evolution ◽

10.1007/bf00984925 ◽

1999 ◽

Vol 217 (1-2) ◽

pp. 119-135 ◽

Cited By ~ 42

Author(s):

K. Andreasen ◽

B. G. Baldwin ◽

B. Bremer

Keyword(s):

Sequence Data ◽

Its Region ◽

Nuclear Rdna ◽

Rdna Its ◽

Rdna Its Region

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PCR-RFLP ITS-based analysis of wine yeast autochthonous strains isolated from different grape cultivars in Taman subregion

E3S Web of Conferences ◽

10.1051/e3sconf/202128505020 ◽

2021 ◽

Vol 285 ◽

pp. 05020

Author(s):

Elena Lobodina ◽

Ivan Suprun ◽

Natalya Ageeva ◽

Ekaterina Al-Nakib

Keyword(s):

Genetic Analysis ◽

Restriction Analysis ◽

Its Region ◽

Wine Yeast ◽

Product Size ◽

Rdna Its ◽

Hanseniaspora Uvarum ◽

Pcr Rflp ◽

Autochthonous Yeast ◽

Rdna Its Region

The studies present the results of morphological, cultural and genetic analysis of the ITS1-ITS4 region of the autochthonous yeast strains genome by using the HaeIII restriction enzyme. On the red and white grapes varieties, based on the morphology of the cells, autochthonous strains belonging to the genus Saccharomyces prevail – 83.3%, what is confirmed by genetic analysis of rDNA ITS region. Restriction analysis showed that all strains of the genus Saccharomyces belong to the species Saccharomyces cerevisiae / S. paradoxus. The percentage of Saccharomyces isolated on the Pervenets Magaracha variety is 86.7%, Krasnostop Anapsky - 80%. The non-Saccharomyces yeast had a product size of 750 bp, presumably of the species Hanseniaspora uvarum.

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Phylogenetic structure of the genus Leveillula (Erysiphales: Erysiphaceae) inferred from the nucleotide sequences of the rDNA ITS region with special reference to the L. taurica species complex

Mycological Research ◽

10.1016/s0953-7562(08)61946-2 ◽

2001 ◽

Vol 105 (8) ◽

pp. 909-918 ◽

Cited By ~ 29

Author(s):

Seyed Akbar Khodaparast ◽

Susumu Takamatsu ◽

Ghorban-Ali Hedjaroude

Keyword(s):

Special Reference ◽

Species Complex ◽

Its Region ◽

Nucleotide Sequences ◽

Phylogenetic Structure ◽

Rdna Its ◽

Rdna Its Region

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

Horticulturae ◽

10.3390/horticulturae6040087 ◽

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.

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Molecular identification and artificial cultivation of a wild isolate of oyster mushroom in Albania

Italian Journal of Agronomy ◽

10.4081/ija.2016.704 ◽

2016 ◽

Vol 10 (1s) ◽

pp. 35

Author(s):

Jordan Merkuri ◽

Stefania Mirela Mang ◽

Ippolito Camele ◽

Magdalena Cara ◽

Gian Luigi Rana

Keyword(s):

Its Region ◽

Edible Mushroom ◽

Biological Efficiency ◽

Potato Dextrose Agar Medium ◽

Wild Isolate ◽

Rdna Its ◽

Pure Cultures ◽

Rdna Its Region ◽

And Diffusion ◽

Artificial Cultivation

Basidiomata of a wild mushroom macroscopically recognised as Pleurotus ostreatus were observed on an oak trunk in a mixed wood of northern Albania. Pure cultures of the fungus were then obtained on potato-dextrose-agar medium. Molecular analyses of genomic DNA of the fungus confirmed its identification. The rDNA ITS region nucleotide sequence of the studied Pleurotacea matched at 99% those of two P. ostreatus strains already present in NCBI GenBank database. The rDNA ITS nucelotide sequences of two pure cultures of the Albanian P. ostreatus were deposited in EMBL database under the accession numbers LN849458 and LN849459. One of the fungus isolates was subsequently cultivated under protected and semi-natural conditions. Productivity and biological efficiency of the Albanian P. ostreatus ranged from about 10% to 16% and from 33 to 53.33%, respectively. This seems to be the first report on the artificial cultivation of P. ostreatus in Albania and could have, in the next future, a high economic impact on development and diffusion of this important edible mushroom over the country.

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