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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)