Dataset Information

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis.

ABSTRACT: Owing to their significant medicinal and edible values, the natural Dendrobium species have underdone over-collection and habitat destruction, and cultivated species emerged for candidates. However, these Dendrobium plants are similar in shape to be easily confused, leading to extreme difficulties for identification based on their morphological and chemical features. In this study, the rDNA ITS region sequence analysis was developed for rapid and accurate identification of thirteen wild and cultivated Dendrobium species belonging to two sections Formosae and Chrysotoxae. By cloning and sequencing the rDNA ITS region genes from 13 Dendrobium species, the phylogenetic relationships among them were analyzed. Results showed that the variation of the ITS region, together with the lengths and Guanine and Cytosine contents of ITS, 5.8s rDNA, ITS1 and ITS2 sequences occurred in the tested Dendrobium species, and which from section Chrysotoxae was higher than that from section Formsae. Phylogenetic analysis based on neighbor-joining and maximum p-arsimony trees indicated that the Dendrobium species of sections Formosae and Chrysotoxae could be well divided into two groups. A majority of Dendrobium species exhibited distinctive ITS2 secondary structures, while for those with close genetic relationships were similar. Therefore, the ITS2 region sequence analysis is simple, quick, and highly reliable that can be used as an effective tool for molecular identification and classification, as well as the reconstruction of the phylogeny of wild and cultivated Dendrobium species belonging to different sections.

SUBMITTER: Liu H

PROVIDER: S-EPMC6474905 | biostudies-literature | 2019 Apr

REPOSITORIES: biostudies-literature

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Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis.

Liu Hongmei H Fang Chengxin C Zhang Tingmo T Guo Li L Ye Qiang Q

AMB Express 20190419 1

Owing to their significant medicinal and edible values, the natural Dendrobium species have underdone over-collection and habitat destruction, and cultivated species emerged for candidates. However, these Dendrobium plants are similar in shape to be easily confused, leading to extreme difficulties for identification based on their morphological and chemical features. In this study, the rDNA ITS region sequence analysis was developed for rapid and accurate identification of thirteen wild and cult ...[more]

PMID: 31004252

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Project description:Background and aimsDendrobium species show tremendous morphological diversity and have broad geographical distribution. As repetitive sequence analysis is a useful tool to investigate the evolution of chromosomes and genomes, the aim of the present study was the characterization of repetitive sequences from Dendrobium moschatum for comparative molecular and cytogenetic studies in the related species Dendrobium aphyllum, Dendrobium aggregatum and representatives from other orchid genera.MethodsIn order to isolate highly repetitive sequences, a c(0)t-1 DNA plasmid library was established. Repeats were sequenced and used as probes for Southern hybridization. Sequence divergence was analysed using bioinformatic tools. Repetitive sequences were localized along orchid chromosomes by fluorescence in situ hybridization (FISH).Key resultsCharacterization of the c(0)t-1 library resulted in the detection of repetitive sequences including the (GA)(n) dinucleotide DmoO11, numerous Arabidopsis-like telomeric repeats and the highly amplified dispersed repeat DmoF14. The DmoF14 repeat is conserved in six Dendrobium species but diversified in representative species of three other orchid genera. FISH analyses showed the genome-wide distribution of DmoF14 in D. moschatum, D. aphyllum and D. aggregatum. Hybridization with the telomeric repeats demonstrated Arabidopsis-like telomeres at the chromosome ends of Dendrobium species. However, FISH using the telomeric probe revealed two pairs of chromosomes with strong intercalary signals in D. aphyllum. FISH showed the terminal position of 5S and 18S-5.8S-25S rRNA genes and a characteristic number of rDNA sites in the three Dendrobium species.ConclusionsThe repeated sequences isolated from D. moschatum c(0)t-1 DNA constitute major DNA families of the D. moschatum, D. aphyllum and D. aggregatum genomes with DmoF14 representing an ancient component of orchid genomes. Large intercalary telomere-like arrays suggest chromosomal rearrangements in D. aphyllum while the number and localization of rRNA genes as well as the species-specific distribution pattern of an abundant microsatellite reflect the genomic diversity of the three Dendrobium species.

Dataset Information

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis.

Publications

Molecular authentication and differentiation of Dendrobium species by rDNA ITS region sequence analysis.

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