Chromosome‐level assembly, genetic and physical mapping of <i>Phalaenopsis aphrodite</i> 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 Li; 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

doi:10.1111/pbi.12936

Cited by 79 publications

(75 citation statements)

References 44 publications

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“…The whole-genome sequence of P. aphrodite has been released ( Chao et al , 2018 ), and we identified only one MDS gene within it, consistent with the result of the transcriptome analysis. This indicated that the copy number of MDS genes varies among Phalaenopsis orchids.…”

Section: Discussionsupporting

confidence: 83%

PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids

Chuang

Hung

Tsai

et al. 2018

Journal of Experimental Botany

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Section: Discussionsupporting

confidence: 83%

PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids

Chuang

Hung

Tsai

et al. 2018

Journal of Experimental Botany

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“…The high-quality clean reads were mapped to the P. aphrodite subsp. formosana genome (Chao et al , 2018). We selected those with a fold-change higher than 2 and an adjusted P-value less than 0.05 as the differentially expressed genes (DEGs).…”

Section: Methodsmentioning

confidence: 99%

Ancestral duplicatedDL/CRCorthologs display function on orchid reproductive organ innovation

Chen

Hsiao

et al. 2020

Preprint

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27The orchid flower is renowned for complexity of flower organ morphogenesis and has 28 attracted great interest from scientists. The YABBY genes encode plant-specific transcription 29 factors with important roles in vegetative and reproductive development in seed plants. 30 DROOPING LEAF/CRABS CLAW (DL/CRC) orthologs are involved in reproductive organ 31 development (especially carpels) of angiosperms. Orchid gynostemium (the fused organ of 32 the androecium and gynoecium) and ovule development are unique developmental processes. 33 Understanding the DL/CRC-like genes controlling the developmental program of the 34 gynostemium and ovule could provide accessible information for reproductive organ 35 molecular regulation in orchids. Two DL/CRC-like genes, named PeDL1 and PeDL2, were 36 cloned from Phalaenopsis equestris. The orchid DL/CRC forms a monophyletic clade with 37 two subclades including AshDL, PeDL1 and DcaDL1 in subclade I, and PeDL2 and DcaDL2 38 in subclade II. The temporal and spatial expression analysis indicated PeDL genes are 39 specifically expressed in the gynostemium and at the early stages of ovule development. Both 40 PeDLs could partially complement an Arabidopsis crc-1 mutant. Transient overexpression of 41 PeDL1 in Phalaenopsis orchids caused abnormal development of ovule and stigmatic cavity 42 of gynostemium. PeDL1, instead of PeDL2, could form a heterodimer with PeCIN8. 43 Paralogue retention and subsequent divergence of the gene sequence of PeDL1 and PeDL2 in 44 P. equestris might result in the differentiation of function and protein behaviors. These results 45 reveal the important roles of PeDLs involved in orchid gynostemium and ovule development 46 and provide new insights for further understanding the molecular mechanisms underlying 47 orchid reproductive organ development. 48 49 52 Over the last couple of decades, genes involved in angiosperm floral organ specification 68 were identified and the 'ABCDE model' was proposed, with the combined effect of the A-, B-, 69 C-, D-, and E-class MADS-box genes determining the floral organ identity. In monocot 70 orchids, the Phalaenopsis species was used as a model plant to delineate the B-, C-, D-, and 71 E-class functions of MADS-box genes participating in specialized floral organ development 72 (Pan et al., 2014; Tsai et al., 2014). The most notable feature is that P. equestris contains four 73 B-class AP3-like genes with differential expression largely responsible for differentiation of 74 the two closely-spaced tripartite perianth whorls into three sepals of the outer whorl, versus 75 the inner whorl of two lateral petals and a median labellum (Tsai et al., 2004). Later, the 76 refined 'orchid code' and 'Homeotic Orchid Tepal (HOT)' models were, respectively, 77proposed to illustrate the regulation of perianth morphogenesis in orchids 78 4 (Mondragon- Palomino & Theissen, 2011; Pan et al., 2011). The studies of floral terata from 79Phalaenopsis and Cymbidium agreed that C-and D-class MADS-box genes correlated with 80 the gynostemium and...

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“…In the past decade, the next-generation sequencing (NGS) tools were widely applied in whole genome sequencing and RNA sequencing (RNA-seq). The first whole genome sequence of the orchid Phalaenopsis equestris was published in 2015 [51] and the number of orchid genomes has continuously increased [52][53][54][55][56]. The whole genome sequencing of Orchidaceae provides a gateway into orchid research, including flower morphology, sexual deception, environmental stress responses and symbiosis.…”

Section: Molecular Studies On Orchid Mycorrhizal Symbiosis By Next-gementioning

confidence: 99%

New Insights into the Symbiotic Relationship between Orchids and Fungi

Yeh¹,

Chung

Liang

et al. 2019

Applied Sciences

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Mycorrhizas play an important role in plant growth and development. In mycorrhizal symbioses, fungi supply soil mineral nutrients, such as nitrogen and phosphorus, to their host plants in exchange for carbon resources. Plants gain as much as 80% of mineral nutrient requirements from mycorrhizal fungi, which form associations with the roots of over 90% of all plant species. Orchid seeds lack endosperms and contain very limited storage reserves. Therefore, the symbiosis with mycorrhizal fungi that form endomycorrhizas is essential for orchid seed germination and protocorm development under natural conditions. The rapid advancement of next-generation sequencing contributes to identifying the orchid and fungal genes involved in the orchid mycorrhizal symbiosis and unraveling the molecular mechanisms regulating the symbiosis. We aim to update and summarize the current understanding of the mechanisms on orchid-fungus symbiosis, and the main focus will be on the nutrient exchange between orchids and their fungal partners. Appl. Sci. 2019, 9, 585 2 of 14 sheath, which functions as a plant-fungus interface, surrounding the epidermal and outer cortical cells. The interface is used for the bidirectional nutrient transfer between a plant and its fungal partner [7]. (2) Endomycorrhiza: the fungi possess specific types of hyphae such as arbuscules and coils to penetrate and grow inside of the root cells of host plants [3]. Endomycorrhizas can be further classified as ectendomycorrhizas, ericoid, arbutoid, monotropoid, orchid and arbuscular mycorrhizas based on the specificity of plant families and the type of internal hyphae [3,8]. Ectomycorrhizas are also alternatively represented as arbuscular mycorrhizas because the class is the most prevalent type of mycorrhizae, as shown in approximately 71% of all vascular plant species [1,9].The Orchidaceae is the largest family of flowering plants including over 700 genera and about 30,000-35,000 species and still hundreds of new species displaying variable floral features, lifestyles, habitat distributions and trophic patterns are being discovered and developed every year [10,11]. Mycorrhizas in orchid species are highly important throughout their whole life including germination and further development. In this article, we provide a brief review of the roles of mycorrhizas in orchid growth and development and the current understanding of the mechanisms in nutrient exchange between orchids and their fungal partners.

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

Cited by 79 publications

References 44 publications

PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids

PbbHLH4 regulates floral monoterpene biosynthesis in Phalaenopsis orchids

Ancestral duplicatedDL/CRCorthologs display function on orchid reproductive organ innovation

New Insights into the Symbiotic Relationship between Orchids and Fungi

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