The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

Cheng Fong Jheng, Tien Chih Chen, Jhong Yi Lin, Ting Chieh Chen, Wen-Luan Wu, Ching-Chun Chang

Research output: Contribution to journalArticle

42 Citations (Scopus)

Abstract

The chloroplast genome of . Phalaenopsis equestris was determined and compared to those of . Phalaenopsis aphrodite and . Oncidium Gower Ramsey in Orchidaceae. The chloroplast genome of . P. equestris is 148,959. bp, and a pair of inverted repeats (25,846. bp) separates the genome into large single-copy (85,967. bp) and small single-copy (11,300. bp) regions. The genome encodes 109 genes, including 4 rRNA, 30 tRNA and 75 protein-coding genes, but loses four . ndh genes (. ndhA, . E, . F and . H) and seven other . ndh genes are pseudogenes. The rate of inter-species variation between the two 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 IR regions have a lower rate of nucleotide substitution (3.5-5.8-fold) and indels (4.3-7.1-fold) than single-copy regions. The intergenic spacers are the most divergent, and based on the length variation of the three intergenic spacers, 11 native . Phalaenopsis orchids could be successfully distinguished. The coding genes, IR junction and RNA editing sites are relatively more conserved between the two moth orchids than between those of . Phalaenopsis and . Oncidium spp.

Original languageEnglish
Pages (from-to)62-73
Number of pages12
JournalPlant Science
Volume190
DOIs
Publication statusPublished - 2012 Jul 1

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Orchidaceae
Phalaenopsis
Chloroplasts
Genetic Markers
chloroplasts
genomics
genetic markers
Oncidium
Chloroplast Genome
intergenic DNA
genes
moths
Moths
nucleotides
RNA editing
Genes
genome
pseudogenes
Nucleotides
Genome

All Science Journal Classification (ASJC) codes

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

Cite this

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abstract = "The chloroplast genome of . Phalaenopsis equestris was determined and compared to those of . Phalaenopsis aphrodite and . Oncidium Gower Ramsey in Orchidaceae. The chloroplast genome of . P. equestris is 148,959. bp, and a pair of inverted repeats (25,846. bp) separates the genome into large single-copy (85,967. bp) and small single-copy (11,300. bp) regions. The genome encodes 109 genes, including 4 rRNA, 30 tRNA and 75 protein-coding genes, but loses four . ndh genes (. ndhA, . E, . F and . H) and seven other . ndh genes are pseudogenes. The rate of inter-species variation between the two 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 IR regions have a lower rate of nucleotide substitution (3.5-5.8-fold) and indels (4.3-7.1-fold) than single-copy regions. The intergenic spacers are the most divergent, and based on the length variation of the three intergenic spacers, 11 native . Phalaenopsis orchids could be successfully distinguished. The coding genes, IR junction and RNA editing sites are relatively more conserved between the two moth orchids than between those of . Phalaenopsis and . Oncidium spp.",
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The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. / Jheng, Cheng Fong; Chen, Tien Chih; Lin, Jhong Yi; Chen, Ting Chieh; Wu, Wen-Luan; Chang, Ching-Chun.

In: Plant Science, Vol. 190, 01.07.2012, p. 62-73.

Research output: Contribution to journalArticle

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