Table 1.

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

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)