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Phalaenopsis Genome and Transcriptome Exploitation and Its Application for Breeding

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The Orchid Genome

Part of the book series: Compendium of Plant Genomes ((CPG))

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Abstract

Orchidaceae is one of the largest families of flowering plants with about 30,000 species. Orchid flowers are highly valued because of their quite distinct and pretty features like spectacular floral shape, color, and elaborate adaptations to pollinators. Among the numerous species, the Phalaenopsis genus of about 66 species derived hybrids is the popular potted ornamental plant. Nowadays, there are more commercial demands for the various Phalaenopsis hybrids with diverse flower colors, fragrance, disease-free, environmentally protected with long-lasting blooming. To produce Phalaenopsis hybrids with diverse features, the whole-genome organization analysis plays a key role to deploy suitable strategies. Genome sequencing has been developed as an important discipline in the plant sciences. During the past decade, remarkable advancement has been made in next-generation sequencing technologies, including 454 pyrosequencing, Illumina/Solexa technology, and sequencing by oligo ligation detection. To accelerate genetic improvement through molecular breeding, wide-ranging analyses of genes and the genome of Phalaenopsis have been conducted using advanced technologies. Whole-genome and transcriptomes were sequenced, assembled, and annotated in (wild-type and peloric mutant plants) P. equestris, P. aphrodite and hybrids. The chloroplast DNA sequence information of P. equestris and P. aphrodite were  obtained. Various RNA-Seq reads were produced from flowers and temperature treated parts of Phalaenopsis orchids (wild-type and peloric mutant plants) and P. bellina. From these produced genome sequences, various databases were constructed for the Phalaenopsis genome. We expect Phalaenopsis genome sequences, microRNAs, expressed sequence tags, simple sequence repeats, linkage maps, and constructed databases will deliver a valued source for basic and applied research, including comparative genomic analysis, developmental studies and molecular breeding on Phalaenopsis.

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Abbreviations

Myr:

Million years

CAM:

Crassulacean acid metabolism

NGS:

Next-generation sequencing

SOLiD:

Sequencing by oligo ligation detection

PGM:

Personal genome machine

NCBI:

National Center for Biotechnology Information

TCV:

Total chromosome volume

CH:

Constitutive heterochromatin

ESTs:

Expressed sequence tags

BESs:

Bacterial artificial chromosome end sequences

TEs:

Transposable elements

LTRs:

Long terminal repeats

DEGs:

Differentially expressed genes

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

FISH:

Fluorescent in situ hybridization

sRNA:

small RNA

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Acknowledgements

The works by authors described in this chapter were supported by grants from the Ministry of Science and Technology (MOST 106-2321-B-020-002) and Agriculture and Food Agency, Council of Agriculture, Taiwan (107AS-7.6.3-FD-Z2, 107AS-7.5.3-FD-Z1 and 108AS-7.5.2-FD-Z1) to FCC.

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Authors and Affiliations

  1. Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan

    Kotapati Kasi Viswanath, Jian-Zhi Huang, Shih-Wen Chin & Fure-Chyi Chen

  2. General Research Service Center, National Pingtung University of Science and Technology, Pingtung, Taiwan

    Fure-Chyi Chen

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  1. Kotapati Kasi Viswanath
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  2. Jian-Zhi Huang
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  3. Shih-Wen Chin
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  4. Fure-Chyi Chen
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Correspondence to Fure-Chyi Chen .

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  1. Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung County, Nei-pu Town, Taiwan

    Fure-Chyi Chen

  2. Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung County, Nei-pu Town, Taiwan

    Shih-Wen Chin

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Viswanath, K.K., Huang, JZ., Chin, SW., Chen, FC. (2021). Phalaenopsis Genome and Transcriptome Exploitation and Its Application for Breeding. In: Chen, FC., Chin, SW. (eds) The Orchid Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-66826-6_4

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