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Advanced Applications of Next-Generation Sequencing Technologies to Orchid Biology

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Advanced Applications of Next-Generation Sequencing Technologies to Orchid Biology Advanced Applications of Next-generation Sequencing Technologies to Orchid Biology Chuan-Ming Yeh1†, Zhong-Jian Liu2,3,4† and Wen-Chieh Tsai5,6,7* 1Division of Strategic Research and Development, Graduate School of Science and Engineering, Satitama University, Saitama, Japan. 2Shenzhen Key Laboratory for Orchid Conservation and Utilization, Te National Orchid Conservation Center of China and Te Orchid Conservation and Research Center of Shenzhen, Shenzhen, China. 3Te Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China. 4College of Arts, College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China. 5Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan. 6Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. 7Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan. *Correspondence: [email protected] †Tese authors contributed equally htps://doi.org/10.21775/cimb.027.051 Abstract Introduction Next-generation sequencing (NGS) technologies Te Chinese have been cultivating fragrant Cym- are revolutionizing biology by permiting tran- bidium species since 500 bc. Te earliest book on scriptome sequencing, whole-genome sequencing record about orchids is Shen Nung Pen Tsao Ching, and resequencing, and genome-wide single nucle- published during the Han dynasty. Tis book refers otide polymorphism profling. Orchid research to well-known orchids used as popular medicines, has benefted from this breakthrough, and a few including Dendrobium, Gsatrodia, and Bletilla. It orchid genomes are now available; new biological is generally agreed that the term orchid was frst questions can be approached and new breeding used by the Greek philosopher Teophrastus in strategies can be designed. Te frst part of this his inquiry into plants (Arditi, 1992). Orchid review describes the unique features of orchid cultivation and growth became popular in the late biology. Te second part provides an overview eighteenth century in Europe. Voyages around the of the current NGS platforms, many of which are world were sponsored by the wealthy to collect already used in plant laboratories. Te third part orchids, herbarium species, and other exotic plants. summarizes the state of orchid transcriptome Merchants, government ofcials, sea captains, plant and genome sequencing and illustrates current collectors, explorers, privateers, and other travel- achievements. Te genetic sequences currently lers began sending plants to their home countries obtained will not only provide a broad scope for soon afer they discovered them. Some of these the study of orchid biology, but also serves as a orchids were sent to botanical gardens; others starting point for uncovering the mystery of orchid reached private growers. Subsequently, the landed evolution. gentry, the wealthy, and commercial frms started Curr. Issues Mol. Biol. Vol. 27 52 | Yeh et al. to accumulate orchid collections. In 1794, 15 epi- Apostasioideae, Cypripedioideae, Vanilloideae, phytic orchids were cultivated at Kew Gardens in Orchidoideae and Epidendroideae. Te Aposta- London. To satisfy the needs of growers, large num- sioideae is considered the sister group to other bers of collectors were sent to faraway places. Tese orchids. Vanilloideae diverged just before Cypripe- collectors destroyed millions of plants, discovered dioideae. Both subfamilies have relatively low many new species, and sufered and died from numbers of genera and species. Most of the diseases and deprivation, but sent many orchids to taxonomic diversity in orchids is in two recently England. By about 1820, it became possible to heat expanded sister subfamilies: Orchidoideae and greenhouses with hot water fowing through pipes. especially Epidendroideae (Górniaka et al., 2010). Tese advances permited growers to simulate Orchids are known for their diversity of specialized what they considered to be appropriate conditions reproductive and ecological strategies (Tsai et al., for orchid culture – heat and humidity. Improved 2014). For successful reproduction, the production methods such as lower temperature, beter ventila- of labellum and gynostemium (a fused structure tion and poting contributed to higher survival of of androecium and gynoecium) to facilitate pol- the orchids and became even more popular. lination is well documented and the co-evolution Te family Orchidaceae is the largest family of of orchid fowers and pollinators is well known fowering plants and the number of species may (Schiestl et al., 2003). In addition, the especially exceed 25,000 (Atwood, 1986). Like all other living successful evolutionary progress of orchids may organisms, present-day orchids have evolved from be explained by mature pollen grains packaged ancestral forms as a result of selection pressure and as pollinia, pollination-regulated ovary/ovule adaptation. Tey show a wide diversity of epiphytic development, synchronized timing of micro- and and terrestrial growth forms and have successfully mega-gametogenesis for efective fertilization, and colonized almost every habitat on earth. Factors the release of thousands or millions of immature promoting orchid species richness include specifc embryos (seeds without endosperm) in a mature interaction between the orchid fower and pollina- capsule (Yu and Goh, 2001). However, despite their tor (Cozzolino and Widmer, 2005), sequential and unique developmental reproductive biology, as well rapid interplay between drif and natural selection as specialized pollination and ecological strategies, (Tremblay et al., 2005), obligate interaction with orchids remain under-represented in molecular mycorrhiza (Otero and Flanagan, 2006), and epi- studies relative to other species-rich plant families phytism which is true for most of all orchids and (Peakall, 2007). Te reasons may be associated probably two-thirds of the epiphytic fora of the with the large genome size, long life cycle, and inef- world. Te radiation of the orchid family has prob- fcient transformation system of orchids (Hsiao et ably taken place in a comparatively short period al., 2011b). as compared with that of most fowering plant During the last 30 years DNA sequencing has families, which had already started to diversify in completely changed our vision of biology and the Mid-Cretaceous period (Crane et al., 1995). particularly plant biology. It has been possible Te time of origin of orchids is in dispute, although to characterize a large number of genes by their Dressler suggests that they originated 80 to 40 mil- nucleotide sequences, thus providing a shortcut lion years ago (Mya; late Cretaceous to late Eocene) to the corresponding protein sequences and their (Dressler, 1981). Recently, the origin of the functions. Information on gene polymorphisms Orchidaceae was dated with a fossil orchid and its has facilitated genetic mapping, gene cloning and pollinator. Te authors showed that the most recent the understanding of evolutionary relationships common ancestor of extant orchids lived in the late and has allowed for the initiation of biodiversity Cretaceous (76 to 84 Mya) (Ramírez et al., 2007). studies. Te most popular sequencing method has Tey also suggested the largest orchid subfamilies, been the Sanger method (Sanger et al., 1977a). which together represent > 95% of living orchid When combined with the use of robotics, bioinfor- species, began to diversify early in the Tertiary (65 matics, computer databases and instrumentation, Mya) (Ramírez et al., 2007). the method has allowed for sequencing larger According to molecular phylogenetic stud- DNA fragments and, fnally, complete genomes. ies, Orchidaceae comprises fve subfamilies: As a result, a series of landmark genomes was Curr. Issues Mol. Biol. Vol. 27 Next-generation Sequencing Technologies in Orchid Biology | 53 obtained, such as Caenorabditis elegans, Drosophila Analyser in 2006 from Solexa, which was purchased melanogaster, Arabidopsis thaliana, Homo sapiens by Illumina 1 year later (Liu et al., 2012). Te and Oryza sativa (International Human Genome SOLiD (Sequencing by Oligo Ligation Detection) Sequencing Consortium, 2004; International Rice platform is the third NGS technology developed by Genome Sequencing Project, 2005; Te Arabidop- Applied Biosystems (now Termo Fisher) in 2007 sis Genome Initiative, 2000). Te deciphering of (Valouev et al., 2008). Tese Solexa (Illumina) these genomes led to the era of functional genomics and SOLiD sequencers generated short reads with and completely modifed biological investigation. only 35-bp lengths comparing to the 110-bp reads However, this technology remained tedious and by the 454 system. However, their numbers of expensive. Tese limiting factors stimulated the reads (30 and 100 million reads, respectively) are development and commercialization of next- much larger than that of the 454 sequencer (200 generation sequencing (NGS) technologies, as thousand reads). In 2010, PGM (Personal Genome opposed to the automated Sanger method, which Machine), the frst NGS platform developed by is considered a frst-generation technology. When semiconductor technology which generates 100-bp coupled with the appropriate computational algo- reads, was released by Ion Torrent (now Termo rithms, the development of NGS technologies has Fisher). Without using optical-sensing device, opened new avenues on a genome-wide scale to the detection for sequencing by Ion Torren PGM radically alter our understanding
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