Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding

Ya Ting Chao, Wan Chieh Chen, Chun Yi Chen, Hsiu Yin Ho, Chih Hsin Yeh, Yi Tzu Kuo, Chun Lin Su, Shao Hua Yen, Hao Yen Hsueh, Jen Hau Yeh, Hui Lan Hsu, Yi Hui Tsai, Tzu Yen Kuo, Song Bin Chang, Kai Yi Chen, Ming Che Shih

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

The Orchidaceae is a diverse and ecologically important plant family. Approximately 69% of all orchid species are epiphytes, which provide diverse microhabitats for many small animals and fungi in the canopy of tropical rainforests. Moreover, many orchids are of economic importance as food flavourings or ornamental plants. Phalaenopsis aphrodite, an epiphytic orchid, is a major breeding parent of many commercial orchid hybrids. We provide a high-quality chromosome-scale assembly of the P. aphrodite genome. The total length of all scaffolds is 1025.1 Mb, with N50 scaffold size of 19.7 Mb. A total of 28 902 protein-coding genes were identified. We constructed an orchid genetic linkage map, and then anchored and ordered the genomic scaffolds along the linkage groups. We also established a high-resolution pachytene karyotype of P. aphrodite and completed the assignment of linkage groups to the 19 chromosomes using fluorescence in situ hybridization. We identified an expansion in the epiphytic orchid lineage of FRS5-like subclade associated with adaptations to the life in the canopy. Phylogenetic analysis further provides new insights into the orchid lineage-specific duplications of MADS-box genes, which might have contributed to the variation in labellum and pollinium morphology and its accessory structure. To our knowledge, this is the first orchid genome to be integrated with a SNP-based genetic linkage map and validated by physical mapping. The genome and genetic map not only offer unprecedented resources for increasing breeding efficiency in horticultural orchids but also provide an important foundation for future studies in adaptation genomics of epiphytes.

Original languageEnglish
Pages (from-to)2027-2041
Number of pages15
JournalPlant Biotechnology Journal
Volume16
Issue number12
DOIs
Publication statusPublished - 2018 Dec

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Physical Chromosome Mapping
Orchidaceae
Phalaenopsis
physical chromosome mapping
chromosome mapping
Breeding
Genetic Linkage
Chromosomes
epiphytes
Genome
chromosomes
linkage groups
genome
breeding
canopy
pollinia (pollen)
Chromosomes, Human, Pair 19
genomics
pachytene stage
flavorings

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science

Cite this

Chao, Ya Ting ; Chen, Wan Chieh ; Chen, Chun Yi ; Ho, Hsiu Yin ; Yeh, Chih Hsin ; Kuo, Yi Tzu ; Su, Chun Lin ; Yen, Shao Hua ; Hsueh, Hao Yen ; Yeh, Jen Hau ; Hsu, Hui Lan ; Tsai, Yi Hui ; Kuo, Tzu Yen ; Chang, Song Bin ; Chen, Kai Yi ; Shih, Ming Che. / Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding. In: Plant Biotechnology Journal. 2018 ; Vol. 16, No. 12. pp. 2027-2041.
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abstract = "The Orchidaceae is a diverse and ecologically important plant family. Approximately 69{\%} of all orchid species are epiphytes, which provide diverse microhabitats for many small animals and fungi in the canopy of tropical rainforests. Moreover, many orchids are of economic importance as food flavourings or ornamental plants. Phalaenopsis aphrodite, an epiphytic orchid, is a major breeding parent of many commercial orchid hybrids. We provide a high-quality chromosome-scale assembly of the P. aphrodite genome. The total length of all scaffolds is 1025.1 Mb, with N50 scaffold size of 19.7 Mb. A total of 28 902 protein-coding genes were identified. We constructed an orchid genetic linkage map, and then anchored and ordered the genomic scaffolds along the linkage groups. We also established a high-resolution pachytene karyotype of P. aphrodite and completed the assignment of linkage groups to the 19 chromosomes using fluorescence in situ hybridization. We identified an expansion in the epiphytic orchid lineage of FRS5-like subclade associated with adaptations to the life in the canopy. Phylogenetic analysis further provides new insights into the orchid lineage-specific duplications of MADS-box genes, which might have contributed to the variation in labellum and pollinium morphology and its accessory structure. To our knowledge, this is the first orchid genome to be integrated with a SNP-based genetic linkage map and validated by physical mapping. The genome and genetic map not only offer unprecedented resources for increasing breeding efficiency in horticultural orchids but also provide an important foundation for future studies in adaptation genomics of epiphytes.",
author = "Chao, {Ya Ting} and Chen, {Wan Chieh} and Chen, {Chun Yi} and Ho, {Hsiu Yin} and Yeh, {Chih Hsin} and Kuo, {Yi Tzu} and Su, {Chun Lin} and Yen, {Shao Hua} and Hsueh, {Hao Yen} and Yeh, {Jen Hau} and Hsu, {Hui Lan} and Tsai, {Yi Hui} and Kuo, {Tzu Yen} and Chang, {Song Bin} and Chen, {Kai Yi} and Shih, {Ming Che}",
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Chao, YT, Chen, WC, Chen, CY, Ho, HY, Yeh, CH, Kuo, YT, Su, CL, Yen, SH, Hsueh, HY, Yeh, JH, Hsu, HL, Tsai, YH, Kuo, TY, Chang, SB, Chen, KY & Shih, MC 2018, 'Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding', Plant Biotechnology Journal, vol. 16, no. 12, pp. 2027-2041. https://doi.org/10.1111/pbi.12936

Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding. / Chao, Ya Ting; Chen, Wan Chieh; Chen, Chun Yi; Ho, Hsiu Yin; Yeh, Chih Hsin; Kuo, Yi Tzu; Su, Chun Lin; Yen, Shao Hua; Hsueh, Hao Yen; Yeh, Jen Hau; Hsu, Hui Lan; Tsai, Yi Hui; Kuo, Tzu Yen; Chang, Song Bin; Chen, Kai Yi; Shih, Ming Che.

In: Plant Biotechnology Journal, Vol. 16, No. 12, 12.2018, p. 2027-2041.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Chromosome-level assembly, genetic and physical mapping of Phalaenopsis aphrodite genome provides new insights into species adaptation and resources for orchid breeding

AU - Chao, Ya Ting

AU - Chen, Wan Chieh

AU - Chen, Chun Yi

AU - Ho, Hsiu Yin

AU - Yeh, Chih Hsin

AU - Kuo, Yi Tzu

AU - Su, Chun Lin

AU - Yen, Shao Hua

AU - Hsueh, Hao Yen

AU - Yeh, Jen Hau

AU - Hsu, Hui Lan

AU - Tsai, Yi Hui

AU - Kuo, Tzu Yen

AU - Chang, Song Bin

AU - Chen, Kai Yi

AU - Shih, Ming Che

PY - 2018/12

Y1 - 2018/12

N2 - The Orchidaceae is a diverse and ecologically important plant family. Approximately 69% of all orchid species are epiphytes, which provide diverse microhabitats for many small animals and fungi in the canopy of tropical rainforests. Moreover, many orchids are of economic importance as food flavourings or ornamental plants. Phalaenopsis aphrodite, an epiphytic orchid, is a major breeding parent of many commercial orchid hybrids. We provide a high-quality chromosome-scale assembly of the P. aphrodite genome. The total length of all scaffolds is 1025.1 Mb, with N50 scaffold size of 19.7 Mb. A total of 28 902 protein-coding genes were identified. We constructed an orchid genetic linkage map, and then anchored and ordered the genomic scaffolds along the linkage groups. We also established a high-resolution pachytene karyotype of P. aphrodite and completed the assignment of linkage groups to the 19 chromosomes using fluorescence in situ hybridization. We identified an expansion in the epiphytic orchid lineage of FRS5-like subclade associated with adaptations to the life in the canopy. Phylogenetic analysis further provides new insights into the orchid lineage-specific duplications of MADS-box genes, which might have contributed to the variation in labellum and pollinium morphology and its accessory structure. To our knowledge, this is the first orchid genome to be integrated with a SNP-based genetic linkage map and validated by physical mapping. The genome and genetic map not only offer unprecedented resources for increasing breeding efficiency in horticultural orchids but also provide an important foundation for future studies in adaptation genomics of epiphytes.

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