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Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding

Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle in vitro...

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Autores principales: Pan, I-Chun, Liao, Der-Chih, Wu, Fu-Huei, Daniell, Henry, Singh, Nameirakpam Dolendro, Chang, Chen, Shih, Ming-Che, Chan, Ming-Tsair, Lin, Choun-Sea
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319614/
https://www.ncbi.nlm.nih.gov/pubmed/22496851
http://dx.doi.org/10.1371/journal.pone.0034738
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author Pan, I-Chun
Liao, Der-Chih
Wu, Fu-Huei
Daniell, Henry
Singh, Nameirakpam Dolendro
Chang, Chen
Shih, Ming-Che
Chan, Ming-Tsair
Lin, Choun-Sea
author_facet Pan, I-Chun
Liao, Der-Chih
Wu, Fu-Huei
Daniell, Henry
Singh, Nameirakpam Dolendro
Chang, Chen
Shih, Ming-Che
Chan, Ming-Tsair
Lin, Choun-Sea
author_sort Pan, I-Chun
collection PubMed
description Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle in vitro make E. pusilla a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of E. pusilla was sequenced accurately, efficiently and economically. The cp genome of E. pusilla shares 89 and 84% similarity with Oncidium Gower Ramsey and Phalanopsis aphrodite, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the rps15-trnN region of the Cymbidieae tribe. Because commercial Oncidium varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of E. pusilla, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that trnF-ndhJ and trnH-psbA were suitable for phylogenetic analysis. E. pusilla proved to be phylogenetically closer to Rodriguezia and Tolumnia than Oncidium, despite its similar floral appearance to Oncidium. These results indicate the hybrid compatibility of E. pusilla, its cp genome providing important information for Oncidium breeding.
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spelling pubmed-33196142012-04-11 Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding Pan, I-Chun Liao, Der-Chih Wu, Fu-Huei Daniell, Henry Singh, Nameirakpam Dolendro Chang, Chen Shih, Ming-Che Chan, Ming-Tsair Lin, Choun-Sea PLoS One Research Article Oncidium is an important ornamental plant but the study of its functional genomics is difficult. Erycina pusilla is a fast-growing Oncidiinae species. Several characteristics including low chromosome number, small genome size, short growth period, and its ability to complete its life cycle in vitro make E. pusilla a good model candidate and parent for hybridization for orchids. Although genetic information remains limited, systematic molecular analysis of its chloroplast genome might provide useful genetic information. By combining bacterial artificial chromosome (BAC) clones and next-generation sequencing (NGS), the chloroplast (cp) genome of E. pusilla was sequenced accurately, efficiently and economically. The cp genome of E. pusilla shares 89 and 84% similarity with Oncidium Gower Ramsey and Phalanopsis aphrodite, respectively. Comparing these 3 cp genomes, 5 regions have been identified as showing diversity. Using PCR analysis of 19 species belonging to the Epidendroideae subfamily, a conserved deletion was found in the rps15-trnN region of the Cymbidieae tribe. Because commercial Oncidium varieties in Taiwan are limited, identification of potential parents using molecular breeding method has become very important. To demonstrate the relationship between taxonomic position and hybrid compatibility of E. pusilla, 4 DNA regions of 36 tropically adapted Oncidiinae varieties have been analyzed. The results indicated that trnF-ndhJ and trnH-psbA were suitable for phylogenetic analysis. E. pusilla proved to be phylogenetically closer to Rodriguezia and Tolumnia than Oncidium, despite its similar floral appearance to Oncidium. These results indicate the hybrid compatibility of E. pusilla, its cp genome providing important information for Oncidium breeding. Public Library of Science 2012-04-04 /pmc/articles/PMC3319614/ /pubmed/22496851 http://dx.doi.org/10.1371/journal.pone.0034738 Text en Pan et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Pan, I-Chun
Liao, Der-Chih
Wu, Fu-Huei
Daniell, Henry
Singh, Nameirakpam Dolendro
Chang, Chen
Shih, Ming-Che
Chan, Ming-Tsair
Lin, Choun-Sea
Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
title Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
title_full Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
title_fullStr Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
title_full_unstemmed Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
title_short Complete Chloroplast Genome Sequence of an Orchid Model Plant Candidate: Erycina pusilla Apply in Tropical Oncidium Breeding
title_sort complete chloroplast genome sequence of an orchid model plant candidate: erycina pusilla apply in tropical oncidium breeding
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319614/
https://www.ncbi.nlm.nih.gov/pubmed/22496851
http://dx.doi.org/10.1371/journal.pone.0034738
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