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

研究成果: Article

44 引文 (Scopus)

摘要

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.

原文English
頁(從 - 到)62-73
頁數12
期刊Plant Science
190
DOIs
出版狀態Published - 2012 七月 1

指紋

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

引用此文

@article{4ebd545cf0eb40bd9f02dd1486b4ad42,
title = "The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids",
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.",
author = "Jheng, {Cheng Fong} and Chen, {Tien Chih} and Lin, {Jhong Yi} and Chen, {Ting Chieh} and Wu, {Wen Luan} and Chang, {Ching Chun}",
year = "2012",
month = "7",
day = "1",
doi = "10.1016/j.plantsci.2012.04.001",
language = "English",
volume = "190",
pages = "62--73",
journal = "Plant Science",
issn = "0168-9452",
publisher = "Elsevier Ireland Ltd",

}

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.

於: Plant Science, 卷 190, 01.07.2012, p. 62-73.

研究成果: 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 -