The &lt;i&gt;Cymbidium goeringii&lt;/i&gt; genome provides insight into organ development and adaptive evolution in orchids

Sun, Ye; Chen, Gui-Zhen; Huang, Jie; Liu, Ding-Kun; Feng, Xue; Chen, Xiu-Lan; Chen, Shiqiang; Chungui, Liu; Liu, Hong; Ma, Hongyu; Yuan, Yuan; Zhang, Diyang; Sun, Weihong; Peng, Donghui; Wang, Zhiwen; Lan, Siren; Li, Fengtong; Liu, Zhong‐Jian; PubBio-Tech, Wuhan

doi:10.48130/opr-2021-0010

Cited by 15 publications

(20 citation statements)

References 71 publications

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“…The Orchidaceae is one of the largest families of flowering plants. However, due to the difficulty of assembling and annotating of genomes of Cymbidium , only Cymbidium goeringii [ 38 ] and Cymbidium sinense [ 39 ] had been sequenced and published. Morphological and phylogenetic analyses revealed a close relationship between C. lowianum and C. tracyanum [ 6 ].…”

Section: Discussionmentioning

confidence: 99%

Selection and Validation of Reference Genes for Quantitative Real-Time PCR Analysis of Development and Tissue-Dependent Flower Color Formation in Cymbidium lowianum

Dong

Zhang

2022

IJMS

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The development and tissue-dependent color formation of the horticultural plant results in various color pattern flowers. Anthocyanins and carotenoids contribute to the red and yellow colors, respectively. In this study, quantitative real-time polymerase chain reaction (qRT-PCR) is used to analyze the expression profiles of anthocyanin and carotenoids biosynthesis genes in Cymbidium lowianum (Rchb.f.) Rchb.f. Appropriate reference gene selection and validation are required before normalization of gene expression in qRT-PCR analysis. Thus, we firstly selected 12 candidate reference genes from transcriptome data, and used geNorm and Normfinder to evaluate their expression stability in lip (divided into abaxial and adaxial), petal, and sepal of the bud and flower of C. lowianum. Our results show that the two most stable reference genes in different tissues of C. lowianum bud and flower are EF1δ and 60S, the most unstable reference gene is 26S. The expression profiles of the CHS and BCH genes were similar to FPKM value profiles after normalization to the two most stable reference genes, EF1δ and 60S, with the upregulated CHS and BCH expression in flower stage, indicating that the ABP and CBP were activated across the stages of flower development. However, when the most unstable reference gene, 26S, was used to normalize the qRT-PCR data, the expression profiles of CHS and BCH differed from FPKM value profiles, indicating the necessity of selecting stable reference genes. Moreover, CHS and BCH expression was highest in the abaxial lip and adaxial lip, respectively, indicating that the ABP and CBP were activated in abaxial and adaxial lip, respectively, resulting in a presence of red or yellow segments in abaxial and adaxial lip. This study is the first to provide reference genes in C. lowianum, and also provide useful information for studies that aim to understand the molecular mechanisms of flower color formation in C. lowianum.

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Section: Discussionmentioning

confidence: 99%

Selection and Validation of Reference Genes for Quantitative Real-Time PCR Analysis of Development and Tissue-Dependent Flower Color Formation in Cymbidium lowianum

Dong

Zhang

2022

IJMS

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“…7a ). The real-time quantitative reverse transcription PCR (qRT-PCR) analyses show that the expression level of two trehalase genes in C. goeringii 69 (Supplementary Table 37 ) is upregulated in the samples from the mycoheterotrophic stage and downregulated in the samples from the autotrophic stage (Fig. 7b,c ).…”

Section: Resultsmentioning

confidence: 99%

“…Expression patterns of trehalase genes c249696_g1_i4 ( CL09234 (ref. 69 )) ( b ) and c232459_g1_i2 ( CL20246 (ref. 69 )) ( c ) in different stages.…”

Section: Resultsmentioning

confidence: 99%

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Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy

Liu

et al. 2022

Nat. Plants

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To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.

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“…We suspected that PhSEPs genes may act as the “glue” for MADS-box transcription factor complex formation to regulate perianth formation in P. henryanum . In recent years, the genomes of some orchids including Apostasia shenzhenica , Phalaenopsis aphrodite , Vanilla planifolia , C. goeringii , Dendrobium chrysotoxum , Platanthera zijinensis , and Platanthera guangdongensis were published ( Zhang et al, 2017 , 2021 ; Chao et al, 2018 ; Hasing et al, 2020 ; Sun et al, 2021 ; Li et al, 2022 ). By contrast, the occurrence of whole-genome duplication in Paphiopedilum results in a genome that is very large and complex Besides, A-, B-, C-, D-class MADS-box genes in P. henryanum have not been systematically identified, which restricts the analysis of the protein–protein interaction network.…”

Section: Discussionmentioning

confidence: 99%

Characterization of Three SEPALLATA-Like MADS-Box Genes Associated With Floral Development in Paphiopedilum henryanum (Orchidaceae)

et al. 2022

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Paphiopedilum (Orchidaceae) is one of the world’s most popular orchids that is found in tropical and subtropical forests and has an enormous ornamental value. SEPALLATA-like (SEP-like) MADS-box genes are responsible for floral organ specification. In this study, three SEP-like MADS-box genes, PhSEP1, PhSEP2, and PhSEP3, were identified in Paphiopedilum henryanum. These genes were 732–916 bp, with conserved SEPI and SEPII motifs. Phylogenetic analysis revealed that PhSEP genes were evolutionarily closer to the core eudicot SEP3 lineage, whereas none of them belonged to core eudicot SEP1/2/4 clades. PhSEP genes displayed non-ubiquitous expression, which was detectable across all floral organs at all developmental stages of the flower buds. Furthermore, subcellular localization experiments revealed the localization of PhSEP proteins in the nucleus. Yeast two-hybrid assays revealed no self-activation of PhSEPs. The protein–protein interactions revealed that PhSEPs possibly interact with B-class DEFICIENS-like and E-class MADS-box proteins. Our study suggests that the three SEP-like genes may play key roles in flower development in P. henryanum, which will improve our understanding of the roles of the SEP-like MADS-box gene family and provide crucial insights into the mechanisms underlying floral development in orchids.

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The <i>Cymbidium goeringii</i> genome provides insight into organ development and adaptive evolution in orchids

Cited by 15 publications

References 71 publications

Selection and Validation of Reference Genes for Quantitative Real-Time PCR Analysis of Development and Tissue-Dependent Flower Color Formation in Cymbidium lowianum

Selection and Validation of Reference Genes for Quantitative Real-Time PCR Analysis of Development and Tissue-Dependent Flower Color Formation in Cymbidium lowianum

Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy

Characterization of Three SEPALLATA-Like MADS-Box Genes Associated With Floral Development in Paphiopedilum henryanum (Orchidaceae)

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