Comparative chloroplast DNA analysis of phalaenopsis orchids and evaluation of cpDNA markers for distinguishing moth orchids

Ching-Chun Chang, Wen-Luan Wu, Yu Chang Liu, Cheng Fong Jheng, Tien Chih Chen, Bo Yen Lin, Jhong Yi Lin, Ting Chieh Chen, Yuech Feng Lee

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The chloroplast DNA (cpDNA) of P. equestris was determined and compared to that of P. aphrodite. The two moth orchids showed similar genome size, structure, gene order, codon usage, and AT content. The ndh genes were either lost or nonfunctional in two endemic moth orchids. The rate of interspecies variation between moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The intergenic spacers were the most divergent, followed by introns, and were used for the evaluation of molecular markers. Fifteen out of 27 cpDNA regions were highly variable among the moth orchids. The rps16-trnQ marker showed the best discriminatory power: 15 endemic moth orchids could be successfully separated into 13 groups. From the sequences of the 7 selected cpDNA regions, the rps16-trnQ intergenic spacer was the best DNA barcode: 19 endemic moth orchids could be completely distinguished.

Original languageEnglish
Title of host publicationOrchid biotechnology III
PublisherWorld Scientific Publishing Co. Pte Ltd
Pages61-90
Number of pages30
ISBN (Electronic)9789813109230
ISBN (Print)9813109211, 9789813109216
DOIs
Publication statusPublished - 2017 Jan 25

Fingerprint

Orchidaceae
Chloroplast DNA
Phalaenopsis
Moths
chloroplast DNA
Genetic Markers
chloroplast
moth
moths
DNA
Genes
genetic markers
intergenic DNA
Introns
Substitution reactions
Nucleotides
Genome Size
Gene Order
gene
DNA barcoding

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Engineering(all)
  • Agricultural and Biological Sciences(all)
  • Environmental Science(all)

Cite this

Chang, C-C., Wu, W-L., Liu, Y. C., Jheng, C. F., Chen, T. C., Lin, B. Y., ... Lee, Y. F. (2017). Comparative chloroplast DNA analysis of phalaenopsis orchids and evaluation of cpDNA markers for distinguishing moth orchids. In Orchid biotechnology III (pp. 61-90). World Scientific Publishing Co. Pte Ltd. https://doi.org/10.1142/9789813109223_0004
Chang, Ching-Chun ; Wu, Wen-Luan ; Liu, Yu Chang ; Jheng, Cheng Fong ; Chen, Tien Chih ; Lin, Bo Yen ; Lin, Jhong Yi ; Chen, Ting Chieh ; Lee, Yuech Feng. / Comparative chloroplast DNA analysis of phalaenopsis orchids and evaluation of cpDNA markers for distinguishing moth orchids. Orchid biotechnology III. World Scientific Publishing Co. Pte Ltd, 2017. pp. 61-90
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Chang, C-C, Wu, W-L, Liu, YC, Jheng, CF, Chen, TC, Lin, BY, Lin, JY, Chen, TC & Lee, YF 2017, Comparative chloroplast DNA analysis of phalaenopsis orchids and evaluation of cpDNA markers for distinguishing moth orchids. in Orchid biotechnology III. World Scientific Publishing Co. Pte Ltd, pp. 61-90. https://doi.org/10.1142/9789813109223_0004

Comparative chloroplast DNA analysis of phalaenopsis orchids and evaluation of cpDNA markers for distinguishing moth orchids. / Chang, Ching-Chun; Wu, Wen-Luan; Liu, Yu Chang; Jheng, Cheng Fong; Chen, Tien Chih; Lin, Bo Yen; Lin, Jhong Yi; Chen, Ting Chieh; Lee, Yuech Feng.

Orchid biotechnology III. World Scientific Publishing Co. Pte Ltd, 2017. p. 61-90.

Research output: Chapter in Book/Report/Conference proceedingChapter

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AU - Chen, Tien Chih

AU - Lin, Bo Yen

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AU - Chen, Ting Chieh

AU - Lee, Yuech Feng

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N2 - The chloroplast DNA (cpDNA) of P. equestris was determined and compared to that of P. aphrodite. The two moth orchids showed similar genome size, structure, gene order, codon usage, and AT content. The ndh genes were either lost or nonfunctional in two endemic moth orchids. The rate of interspecies variation between moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The intergenic spacers were the most divergent, followed by introns, and were used for the evaluation of molecular markers. Fifteen out of 27 cpDNA regions were highly variable among the moth orchids. The rps16-trnQ marker showed the best discriminatory power: 15 endemic moth orchids could be successfully separated into 13 groups. From the sequences of the 7 selected cpDNA regions, the rps16-trnQ intergenic spacer was the best DNA barcode: 19 endemic moth orchids could be completely distinguished.

AB - The chloroplast DNA (cpDNA) of P. equestris was determined and compared to that of P. aphrodite. The two moth orchids showed similar genome size, structure, gene order, codon usage, and AT content. The ndh genes were either lost or nonfunctional in two endemic moth orchids. The rate of interspecies variation between moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The intergenic spacers were the most divergent, followed by introns, and were used for the evaluation of molecular markers. Fifteen out of 27 cpDNA regions were highly variable among the moth orchids. The rps16-trnQ marker showed the best discriminatory power: 15 endemic moth orchids could be successfully separated into 13 groups. From the sequences of the 7 selected cpDNA regions, the rps16-trnQ intergenic spacer was the best DNA barcode: 19 endemic moth orchids could be completely distinguished.

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M3 - Chapter

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BT - Orchid biotechnology III

PB - World Scientific Publishing Co. Pte Ltd

ER -

Chang C-C, Wu W-L, Liu YC, Jheng CF, Chen TC, Lin BY et al. Comparative chloroplast DNA analysis of phalaenopsis orchids and evaluation of cpDNA markers for distinguishing moth orchids. In Orchid biotechnology III. World Scientific Publishing Co. Pte Ltd. 2017. p. 61-90 https://doi.org/10.1142/9789813109223_0004