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 language | English |
|---|---|
| Pages (from-to) | 62-73 |
| Number of pages | 12 |
| Journal | Plant Science |
| Volume | 190 |
| DOIs | |
| Publication status | Published - 2012 Jul 1 |
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All Science Journal Classification (ASJC) codes
- Genetics
- Agronomy and Crop Science
- Plant Science
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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 journal › Article
TY - JOUR
T1 - The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids
AU - Jheng, Cheng Fong
AU - Chen, Tien Chih
AU - Lin, Jhong Yi
AU - Chen, Ting Chieh
AU - Wu, Wen-Luan
AU - Chang, Ching-Chun
PY - 2012/7/1
Y1 - 2012/7/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84860137960&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84860137960&partnerID=8YFLogxK
U2 - 10.1016/j.plantsci.2012.04.001
DO - 10.1016/j.plantsci.2012.04.001
M3 - Article
C2 - 22608520
AN - SCOPUS:84860137960
VL - 190
SP - 62
EP - 73
JO - Plant Science
JF - Plant Science
SN - 0168-9452
ER -