The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny

B. Y. Lin; C. D. Chang; L. L.H. Huang; Y. C. Liu; Y. Y. Su; T. C. Chen; R. H. Lee; H. J. Huang; W. L. Wu; C. C. Chang

doi:10.1007/s10535-015-0566-2

The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny

B. Y. Lin, C. D. Chang, L. L.H. Huang, Y. C. Liu, Y. Y. Su, T. C. Chen, R. H. Lee, H. J. Huang, W. L. Wu, C. C. Chang

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

Abstract

Moth orchids (Phalaenopsis) are among the top-traded blooming potted plants in the world. To explore mitochondrial DNA (mtDNA) markers for species identification, we located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana and then pre-screened them for polymorphic markers by their comparison with corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish 15 endemic moth orchids. Five most variable markers with polymorphic information content (PIC) ≥ 0.7 could be combined to classify 18 of 19 endemic moth orchids including parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids, evolutionary hotspots, such as variable simple sequence repeats and minisatellite repeats, were identified as useful markers. Furthermore, a marker technology was applied to reveal the maternal inheritance mode of mtDNA in the moth orchids. Moreover, phylogenetic analysis indicates that the mtDNA was nonmonophyletic below the Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.

Original language	English
Pages (from-to)	68-78
Number of pages	11
Journal	Biologia Plantarum
Volume	60
Issue number	1
DOIs	https://doi.org/10.1007/s10535-015-0566-2
Publication status	Published - 2016 Jan 1

All Science Journal Classification (ASJC) codes

Plant Science
Horticulture

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10.1007/s10535-015-0566-2

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@article{ca568b5f700949d598a6d76309cc91b4,

title = "The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny",

abstract = "Moth orchids (Phalaenopsis) are among the top-traded blooming potted plants in the world. To explore mitochondrial DNA (mtDNA) markers for species identification, we located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana and then pre-screened them for polymorphic markers by their comparison with corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish 15 endemic moth orchids. Five most variable markers with polymorphic information content (PIC) ≥ 0.7 could be combined to classify 18 of 19 endemic moth orchids including parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids, evolutionary hotspots, such as variable simple sequence repeats and minisatellite repeats, were identified as useful markers. Furthermore, a marker technology was applied to reveal the maternal inheritance mode of mtDNA in the moth orchids. Moreover, phylogenetic analysis indicates that the mtDNA was nonmonophyletic below the Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.",

author = "Lin, {B. Y.} and Chang, {C. D.} and Huang, {L. L.H.} and Liu, {Y. C.} and Su, {Y. Y.} and Chen, {T. C.} and Lee, {R. H.} and Huang, {H. J.} and Wu, {W. L.} and Chang, {C. C.}",

note = "Funding Information: We thank Dr. Chi-Chu Tsai for sparing the moth orchids. We are also grateful to the anonymous reviewers for their comments that helped to improve the quality of this manuscript. This work was financially supported by the grant (MOST 102-2321-B-006-017 and 103-2321-B-006-009) from the Ministry of Science and Technology to C.-C. Chang. Publisher Copyright: {\textcopyright} 2016, Springer Science+Business Media Dordrecht.",

year = "2016",

month = jan,

day = "1",

doi = "10.1007/s10535-015-0566-2",

language = "English",

volume = "60",

pages = "68--78",

journal = "Biologia Plantarum",

issn = "0006-3134",

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T1 - The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny

AU - Lin, B. Y.

AU - Chang, C. D.

AU - Huang, L. L.H.

AU - Liu, Y. C.

AU - Su, Y. Y.

AU - Chen, T. C.

AU - Lee, R. H.

AU - Huang, H. J.

AU - Wu, W. L.

AU - Chang, C. C.

N1 - Funding Information: We thank Dr. Chi-Chu Tsai for sparing the moth orchids. We are also grateful to the anonymous reviewers for their comments that helped to improve the quality of this manuscript. This work was financially supported by the grant (MOST 102-2321-B-006-017 and 103-2321-B-006-009) from the Ministry of Science and Technology to C.-C. Chang. Publisher Copyright: © 2016, Springer Science+Business Media Dordrecht.

PY - 2016/1/1

Y1 - 2016/1/1

N2 - Moth orchids (Phalaenopsis) are among the top-traded blooming potted plants in the world. To explore mitochondrial DNA (mtDNA) markers for species identification, we located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana and then pre-screened them for polymorphic markers by their comparison with corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish 15 endemic moth orchids. Five most variable markers with polymorphic information content (PIC) ≥ 0.7 could be combined to classify 18 of 19 endemic moth orchids including parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids, evolutionary hotspots, such as variable simple sequence repeats and minisatellite repeats, were identified as useful markers. Furthermore, a marker technology was applied to reveal the maternal inheritance mode of mtDNA in the moth orchids. Moreover, phylogenetic analysis indicates that the mtDNA was nonmonophyletic below the Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.

AB - Moth orchids (Phalaenopsis) are among the top-traded blooming potted plants in the world. To explore mitochondrial DNA (mtDNA) markers for species identification, we located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana and then pre-screened them for polymorphic markers by their comparison with corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish 15 endemic moth orchids. Five most variable markers with polymorphic information content (PIC) ≥ 0.7 could be combined to classify 18 of 19 endemic moth orchids including parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids, evolutionary hotspots, such as variable simple sequence repeats and minisatellite repeats, were identified as useful markers. Furthermore, a marker technology was applied to reveal the maternal inheritance mode of mtDNA in the moth orchids. Moreover, phylogenetic analysis indicates that the mtDNA was nonmonophyletic below the Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.

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U2 - 10.1007/s10535-015-0566-2

DO - 10.1007/s10535-015-0566-2

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SN - 0006-3134

VL - 60

SP - 68

EP - 78

JO - Biologia Plantarum

JF - Biologia Plantarum

IS - 1

ER -

The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny

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