The genome and transcriptome of<i>Phalaenopsis</i>yield insights into floral organ development and flowering regulation

Huang, Jui Hsien; Lin, Chih-Peng; Cheng, Ta-Chih; Huang, Yuanhao; Tsai, Yi-Jung; Cheng, Shu-Yun; Chen, Yiwen; Lee, Chueh-Pai; Chung, Wan-Chia; Chang, Bill C.H.; Chin, Shih-Wen; Lee, Chen‐Yu; Chen, Fure-Chyi

doi:10.7717/peerj.2017

Cited by 37 publications

(26 citation statements)

References 46 publications

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“…Recent studies with Phalaenopsis equestris genome sequencing [57], with 2n = 2x = 38 and 29,431 predicted protein-coding genes and Phalaenopsis Brother Spring Dancer 'KHM190' [58], 2n = 2x = 38 and 41,153 protein coding genes, make room for further detailed studies on the identification and expression of genes involved in the production of PLBs from different types of somatic tissue in orchids, which can be compared with other model species and in which the embryogenic pathway is already better elucidated, similar to the studies already carried out that brought new discoveries about flowering and the development of floral organs [58].…”

Section: Genus Phalaenopsis and Relatedmentioning

confidence: 99%

An Overview of Orchid Protocorm-Like Bodies: Mass Propagation, Biotechnology, Molecular Aspects, and Breeding

Cardoso

Zanello

Chen

2020

IJMS

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The process through induction, proliferation and regeneration of protocorm-like bodies (PLBs) is one of the most advantageous methods for mass propagation of orchids which applied to the world floricultural market. In addition, this method has been used as a tool to identify genes of interest associated with the production of PLBs, and also in breeding techniques that use biotechnology to produce new cultivars, such as to obtain transgenic plants. Most of the molecular studies developed have used model plants as species of Phalaenopsis, and interestingly, despite similarities to somatic embryogenesis, some molecular differences do not yet allow to characterize that PLB induction is in fact a type of somatic embryogenesis. Despite the importance of species for conservation and collection purposes, the flower market is supported by hybrid cultivars, usually polyploid, which makes more detailed molecular evaluations difficult. Studies on the effect of plant growth regulators on induction, proliferation, and regeneration of PLBs are the most numerous. However, studies of other factors and new technologies affecting PLB production such as the use of temporary immersion bioreactors and the use of lighting-emitting diodes have emerged as new tools for advancing the technique with increasing PLB production efficiency. In addition, recent studies on Phalaenopsis equestris genome sequencing have enabled more detailed molecular studies and the molecular characterization of plantlets obtained from this technique currently allow the technique to be evaluated in a more comprehensive way regarding its real applications and main limitations aiming at mass propagation, such as somaclonal variation.

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Section: Genus Phalaenopsis and Relatedmentioning

confidence: 99%

An Overview of Orchid Protocorm-Like Bodies: Mass Propagation, Biotechnology, Molecular Aspects, and Breeding

Cardoso

Zanello

Chen

2020

IJMS

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“…Recently, the roles of B-and E-class MADS-box genes were revealed for orchid tepal development (Tsai et al, 2004;Tsai et al, 2005;Lu et al, 2007;Hsieh et al, 2013a;Su et al, 2013b;Pan et al, 2014;Hsu et al, 2015b;Huang et al, 2015;Huang et al, 2016). We have shown that knock-down expression of Eclass PeSEP1-4 genes reduced the expression of PeERF1.…”

Section: Peerf1 As a Downstream Target Of Floral Morphogenesis Genesmentioning

confidence: 99%

PeERF1, a SHINE-Like Transcription Factor, Is Involved in Nanoridge Development on Lip Epidermis of Phalaenopsis Flowers

et al. 2020

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Phalaenopsis orchids have a spectacular floral morphology with a highly evolved lip that offers a landing platform for pollinators. The typical morphological orchid lip features are essential for the special pollination mechanism of Phalaenopsis flowers. Previously, we found that in the lip, a member of the AP2/EREBP protein family was highly expressed. Here, we further confirmed its high expression and characterized its function during lip development. Phylogenetic analysis showed that AP2/EREBP belongs to the Va2 subgroup of ERF transcription factors. We named it PeERF1. We found that PeERF1 was only expressed at stage 5, as flowers opened. This coincided with both thickening of the cuticle and development of nanoridges. We performed knockdown expression of PeERF1 using CymMV-based virus-induced gene silencing in either the AP2 conserved domain, producing PeERF1_AP2-silenced plants, or the SHN specific domain, producing PeERF1_SHN-silenced plants. Using cryo-SEM, we found that the number of nanoridges was reduced only in the PeERF1_AP2-silenced group. This change was found on both the abaxial and adaxial surfaces of the central lip lobe. Expression of PeERF1 was reduced significantly in PeERF1_AP2-silenced plants. In cutin biosynthesis genes, expression of both PeCYP86A2 and PeDCR was significantly decreased in both groups. The expression of PeCYP77A4 was reduced significantly only in the PeERF1_AP2-silenced plants.Although PeGPAT expression was reduced in both silenced plants, but to a lesser degree. The expression of PeERF1 was significantly reduced in the petal-like lip of a big-lip variant. PeCYP77A4 and PeGPAT in the lip were also reduced, but PeDCR was not. Furthermore, heterologous overexpression of PeERF1 in the genus Arabidopsis produced leaves that were shiny on the adaxial surface. Taken together, our results show that in Phalaenopsis orchids PeERF1 plays an important role in formation of nanoridges during lip epidermis development.

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“…In our previous study, we examined sequencing and quality checking of Phalaenopsis, and construction of draft genome (Huang et al, 2016). Here explained briefly, to sequence the Phalaenopsis genome from extracted DNA, we applied nextgeneration sequencing technologies using the Illumina HiSeq 2000 platform.…”

Section: Sequencing Quality Control and Draft Genome Constructionmentioning

confidence: 99%

“…In our previous report, we explained about sequence assembly and dataset annotation (Huang et al, 2016). Here we performed whole-genome assembly using Velvet (https://www.ebi.ac.uk/~zerbino/velvet/) (Zerbino et al, 2008) with K-mer 63.…”

Section: De Novo Assembly and Dataset Annotationmentioning

confidence: 99%

“…The transcript profile was analyzed and the labellum development was proposed to be regulated by the MADS-box genes, including PhAGL6a, PhAGL6b, and PhMADS4. In addition to this, we generated draft genomes for winter flowering Phalaenopsis Brother Spring Dancer 'KHM190' cultivar and summer flowering species Phalaenopsis pulcherrima 'B8802' (Huang et al, 2016). It revealed alternative splicing of PhAGL6b that led to differential labellum development, and we also proposed gibberellin pathway regulation of the flowering expression.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Research Article PhalDB:A comprehensive database for molecular mining of the <i>Phalaenopsis</i> genome, transcriptome and miRNome

Lee¹,

Viswanath²,

Huang³

et al. 2018

Genet. Mol. Res.

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©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 17 (4): gmr18051 C.Y. Lee. et al. 2 include information about somaclonal variations and cool temperature treatment, which are important for commercial variety development. PhalDB provides sequence information from 24 samples and covers the above-mentioned tissues or conditions so that comprehensive gene data related to flower development, somaclonal variation and some horticulture traits are available for searching. A user can access DNA level information and miRNA structure, etc. It also provides an opportunity to explore mRNA level information and interactions between genes and miRNA. PhalDB is equipped with a BLAST tool to perform similarity searches among the various gene sequences.

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The genome and transcriptome ofPhalaenopsisyield insights into floral organ development and flowering regulation

Cited by 37 publications

References 46 publications

An Overview of Orchid Protocorm-Like Bodies: Mass Propagation, Biotechnology, Molecular Aspects, and Breeding

An Overview of Orchid Protocorm-Like Bodies: Mass Propagation, Biotechnology, Molecular Aspects, and Breeding

PeERF1, a SHINE-Like Transcription Factor, Is Involved in Nanoridge Development on Lip Epidermis of Phalaenopsis Flowers

Research Article PhalDB:A comprehensive database for molecular mining of the <i>Phalaenopsis</i> genome, transcriptome and miRNome

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