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Table 1 Characteristics of findings in the literature for the application of next generation sequencing (NGS) to orchid transcriptomes

From: Post genomics era for orchid research

Subfamily Species Sequencing platform Tissue Study aim References
Apostasioideae Apostasia shenzhenica Illumina/Solexa Mature flower buds Study of floral development and evolutionary trends of orchid flowers Tsai et al. (2013)
Apostasioideae Neuwiedia malipoensis Illumina/Solexa Mature flower buds
Vanilloideae Vanilla shenzhenica Illumina/Solexa Mature flower buds
Vanilloideae Galeola faberi Illumina/Solexa Mature flower buds
Cypripedioideae Paphiopedilum armeniacum Illumina/Solexa Mature flower buds
Cypripedioideae Cypripedium singchii Illumina/Solexa Mature flower buds
Orchidoideae Habenaria delavayi Illumina/Solexa Mature flower buds
Orchidoideae Hemipilia forrestii Illumina/Solexa Mature flower buds
Epidendroideae Phalaenopsis equestris Illumina/Solexa Mature flower buds
Epidendroideae Cymbidium sinense Illumina/Solexa Mature flower buds
Vanilloideae Vanilla planifolia Illumina/Solexa
Roche/454
Pod tissues, seeds Study of biosynthetic routes to flavor components Rao et al. (2014)
Cypripedioideae Paphiopedilum concolor Illumina Hiseq 2000 Roots Identify the genes that control root growth and development Li et al. (2015b)
Orchidoideae Ophrys species Roche/454
Illumina/Solexa
Flowers, labellums, leaves, flower organ from open flowers and buds Identify genes responding for pollinator attraction Sedeek et al. (2013)
Orchidoideae Orchis italica Illumina/Solexa
(MiSeq)
Inflorescences The roles of small RNAs on the flower development Aceto et al. (2014)
Orchidoideae Orchis italica Illumina Hiseq 2500 Florets of inflorescence before anthesis Analyzing transcripts potentially involved in flower development De Paolo et al. (2014)
Orchidoideae Serapias vomeracea Roche/454 Protocorms Investigate the molecular bases of the orchid response to mycorrhizal invasion Perotto et al. (2014)
Orchidoideae Anoectochilus roxburghii (Wall.) Lindl. Illumina HiSeq 4000 Dry seeds, seeds from asymbiotic or symbiotic germination Study of seed germination process Liu et al. (2015)
Orchidoideae Gastrodia elata Blume Illumina Hiseq 2000 Vegetative tissues, corms, juvenile tubers Address the gene regulation mechanism in gastrodin biosynthesis Tsai et al. (2016)
Epidendroideae Phalaenopsis aphrodite Sanger: EST Protocorms Gene discovery and genomic annotation Fu et al. (2011)
, Hsiao et al. (2011a)
Epidendroideae Phalaenopsis equestris Sanger: EST Mature flower buds
Epidendroideae Phalaenopsis bellina Sanger: EST Mature flower buds without column
Epidendroideae Phalaenopsis aphrodite
Phalaenopsis equestris
Phalaenopsis bellina
Roche/454 Mixed tissues
Epidendroideae Phalaenopsis equestris Illumina/Solexa Leaves
Epidendroideae Phalaenopsis aphrodite Roche/454
Illumina/Solexa
Leaves, stems, roots, young inflorescences, stalks, flower buds, flowers, germinating seeds Investigate expressed genes involved in many biological processes of orchids Su et al. (2011)
Epidendroideae Phalaenopsis aphrodite Illumina/Solexa Leaves, stalks, flower buds Study the roles of small RNAs on the regulation of flowering An et al. (2011), An and Chan (2012)
Epidendroideae Phalaenopsis aphrodite Illumina/Solexa Leaves, roots, flowers, germinating seeds, young inflorescences Identify species- and tissue-specific miRNAs Chao et al. (2014)
Epidendroideae Phalaenopsis Brother Spring Dancer ‘KHM190’ Illumina Hiseq 2000 Petals, sepals or labellums from flower buds of wild-type and peloric petal mutant plants Study regulation of floral- organ development Huang et al. (2015)
Epidendroideae Phalaenopsis sp. Illumina Hiseq 2000 Explants Examine Phalaenopsis leaf explant browning Xu et al. (2015)
Epidendroideae Oncidium ‘Gower Ramsey’ Roche/454 Leaves, pseudobulbs, young inflorescences, inflorescences, flower buds, mature flowers Identify genes associated with flowering time Chang et al. (2011)
Epidendroideae Oncidium ‘Gower Ramsey’ Illumina/Solexa Roots with or without fungus Study the roles of small RNAs on the interaction between root and the fungus Ye et al. (2014)
Epidendroideae Erycina pusilla Illumina/Solexa Roots, leaves, peduncles, flowers, capsules Investigate photoperiod-dependent flowering genes Chou et al. (2013)
Epidendroideae Erycina pusilla Illumina/Solexa Roots, leaves, peduncles, flowers, capsules Study the roles of small RNAs on the regulation of flowering Lin et al. (2013a)
Epidendroideae Cymbidium ensifolium ‘Tiegusu’ Illumina HiSeq 2000 Flower buds, mature flower Identify genes associated with floral development Li et al. (2014)
Epidendroideae Cymbidium sinense ‘Qi Jian Bai Mo’ Illumina HiSeq 2000 Plants in vegetative phase/floral differentiation phase/reproductive phase Identify genes associated with floral development Zhang et al. (2013)
Epidendroideae Cymbidium hybridum ‘Golden Boy’ Illumina Hiseq 2000 Roots with or without fungus Study of orchid-mycorrhizal fungi interactions Zhao et al. (2014)
Epidendroideae Cymbidium ensifolium ‘Tiegusu’ Illumina/Solexa Flower bud Identify miRNAs related to floral development Li et al. (2015c)
Epidendroideae Cymbidium ensifolium ‘tianesu’ Roche/454 Sepals, petals, labellums, gynostemia from flower buds and mature flowers Reveal genes associated with floral organ differentiation Yang and Zhu (2015)
Epidendroideae Cymbidium sinense ‘Dharma’ Roche/454 Roots, leaves, pseudobulbs, flowers Analyze molecular mechanism underlying leaf-color variations Zhu et al. (2015)
Epidendroideae Cymbidium sinense
Cymbidium atropurpureum
Cymbidium mannii
Illumina Hiseq 2000 Leaves Explore the evolution and molecular regulation of CAM plants Zhang et al. (2016c)
Epidendroideae Dendrobium officinale Roche/454 Stems Study of alkaloid biosynthesis Guo et al. (2013)
Epidendroideae Dendrobium officinale Illumina Hiseq 2000 Juvenile and adult plants Identify genes associated with polysaccharide synthesis Zhang et al. (2016b)
Epidendroideae Dendrobium officinale Illumina Hiseq 2500 Flower, roots, leaves, stems Study of the regulatory networks of the production and accumulation of the medicinal constituents Meng et al. (2016)