Open Access
How to translate text using browser tools
5 June 2015 Characterization of Microsatellite Loci for an Australian Epiphytic Orchid, Dendrobium calamiforme, Using Illumina Sequencing
Dorset W. Trapnell, Rochelle R. Beasley, Stacey L. Lance, Ashley R. Field, Kenneth L. Jones
Author Affiliations +

Molecular phylogeographic approaches can provide potent tests of historical biogeographic hypotheses, such as the influence of historical barriers to gene flow on evolutionary diversification. The tropical rainforests of northeastern Australia harbor a diverse flora rich in basal angiosperm lineages that has long been thought to have been assembled principally through ecological filtering of relict Gondwanan stock and exchange of lineages with Malesia and Southeast Asia (e.g., Webb and Tracey, 1981; Crayn et al., 2015). However, the role of in situ diversification in this old biome may be underappreciated. Within this biome, a congruent genetic discontinuity has been found in various fauna groups (e.g., Schneider et al., 1998) and tree species (Rossetto et al., 2009) across the biogeographic barrier known as the Black Mountain Corridor (BMC), located between Cairns and Cape Tribulation. To better understand the processes that gave rise to this pattern, and the significance of in situ diversification to the origins and maintenance of tropical rainforest diversity, we aim to determine the phylogeographic structure of a codistributed epiphytic orchid. These orchids release tiny, wind-borne seeds high in the air column, where they can be picked up by wind currents and potentially transported great distances.

Dendrobium calamiforme Lodd. ex Lindl., commonly known as the pencil orchid in reference to the long, terete leaves, had been renamed Dockrillia calamiformis (Lodd. ex Lindl.) M. A. Clem. & D. L. Jones (Clements and Jones, 1996); however, this was rejected by Adams (2011). This orchid is indigenous to coastal tropical Queensland, Australia, ranging from Badu Island in the Torres Strait to Mount Elliott near Townsville, with nearly continuous distribution in its habitat across its range. It is a canopy and subcanopy epiphyte that grows in vine forest, swamp forest, beach forest, and riparian forest but is uncommon in ever-wet closed canopy rainforest. Although it can occur on large boulders, populations reach their highest density in large mature trees and can be locally abundant. Individuals become reproductive within five years and can live for several decades. Dendrobium calamiforme flowers in the dry season (July to September) and, while the pollination syndrome has not been verified, Hymenoptera, Coleoptera, and birds have been observed visiting flowering plants.

The development of highly polymorphic microsatellite markers will allow insights into the levels and partitioning of neutral genetic variation in this common epiphytic orchid. With these markers, patterns of seed dispersal, colonization, and genetic connectivity across the BMC will be investigated. Based on the dispersal ability of D. calamiforme, we predict low genetic structure among populations straddling the BMC; however, biogeographic disjunctions have been found in Costa Rican epiphytic orchids (Trapnell and Hamrick, 2004; Kartzinel et al., 2013; Trapnell et al., unpublished) that appear to be maintained by cryptic processes.


Total DNA was extracted from one individual of D. calamiforme, following the cetyltrimethylammonium bromide (CTAB) protocol of Doyle and Doyle (1990). After shearing 1 µg of genomic DNA with a Covaris S220 Focused-ultrasonicator (Covaris, Woburn, Massachusetts, USA), a paired-end shotgun library was prepared with the Illumina TruSeq DNA Library Kit (Illumina, San Diego, California, USA). During library preparation, a multiplex identified adapter was incorporated as multiple species were run together on an Illumina MiSeq using 100-bp paired-end reads. The program PAL_FINDER_v0.02.03 (Castoe et al., 2012) was used to examine 5 million reads and identify those containing microsatellite repeats; positive reads were targeted for primer design using Primer3 (version 2.0.0; Rozen and Skaletsky, 1999). The frequency of designed primer sequences in all reads was assessed by the software, and only primers whose sequences occurred ≤2 times were selected to avoid duplicated loci. Forty-eight loci of the 5412 that met this criterion were chosen. To use a three-primer PCR with one universally labeled primer (CAG tag 5′-CAGTCGGGCGTCATCA-3′), one primer from each pair was modified at the 5′ end with the addition of the CAG tag sequence and the 5′ end of the second primer from each pair was modified with the addition of GTTT.

Table 1.

Characteristics of 19 polymorphic microsatellite loci developed for Dendrobium calamiforme.a


The selected 48 primer pairs were tested for clean amplification and polymorphism across four individuals. The PCR amplifications were performed in a 12.5-µL volume (10 mM Tris [pH 8.4], 50 mM KCl, 0.25 µg bovine serum albumin [BSA], 0.4 µM unlabeled primer, 0.04 µM tag-labeled primer, 0.36 µM universal dye-labeled primer, 3.0 mM MgCl2, 0.8 mM dNTPs [Thermo Scientific, Waltham, Massachusetts, USA], 0.5 units AmpliTaq Gold Polymerase [Life Technologies, Carlsbad, California, USA], and 20 ng DNA template) using an Applied Biosystems GeneAmp PCR System 9700 (Life Technologies). For all loci, a touchdown thermal cycling program (Don et al., 1991) was used that had a 10°C span of annealing temperatures ranging between 65–55°C (TD65). The cycling profile consisted of an initial denaturation step of 5 min at 95°C followed by 20 cycles of 95°C for 30 s, highest annealing temperature (decreased 0.5°C per cycle) for 30 s, and 72°C for 30 s; and 20 cycles of 95°C for 30 s, lowest annealing temperature for 30 s, and 72°C for 30 s; and a final extension at 72°C for 5 min. After amplification, all PCR products were genotyped by running on an ABI-3130x1 sequencer (Life Technologies) and using a size standard prepared according to DeWoody et al. (2004), with the exception that primers that were not fluorescently labeled had GTTT added to their 5′ ends. Results of fragment analysis were analyzed using GeneMapper version 3.7 (Life Technologies). Of the 48 loci tested, 19 yielded high-quality polymorphic PCR products and were characterized by trinucleotide (12 loci) and tetranucleotide (7 loci) repeat motifs (Table 1). The remaining 29 loci did not amplify well and therefore were not used.

Table 2.

Genetic diversity values for five populations of Dendrobium calamiforme in Queensland, Australia, using 19 newly developed polymorphic microsatellite loci.a


We assessed the variability of these 19 loci in 24 specimens of D. calamiforme collected from five sites, spanning a distance of 79.7 km (Appendix 1). Vouchers from each site were deposited at the Australian Tropical Herbarium (CNS) (Appendix 1). Each site consisted of a small number of D. calamiforme individuals in each of two to five host trees. We used GenAlEx version 6.4 (Peakall and Smouse, 2006) to estimate the number of alleles per locus (A), observed heterozygosity (Ho), expected heterozygosity (He), and the probability of identity (PID). To test for deviations from Hardy-Weinberg equilibrium (HWE) and for linkage disequilibrium, GENEPOP version 4.0 (Rousset, 2008) was used.

These 19 loci were highly polymorphic with mean per locus values of A = 8.4 (range = 2−14), He = 0.754 (0.486−0.902), and Ho = 0.496 (0.043−0.957). Mean population values were A = 3.7 (range = 2.5−5.0), He = 0.591 (0.484−0.693), Ho = 0.489 (0.432−0.588), and = 0.259 (0.161−0.370) (Table 2). After Bonferroni correction for multiple comparisons, 14 loci showed significant deviation from expectations under HWE (Table 2). Linkage disequilibrium was detected for 61 of the 171 paired loci comparisons, which is not surprising considering that our samples came from multiple small populations.


The 19 novel microsatellites developed for D. calamiforme revealed high levels of polymorphism and genetic diversity and thus should prove valuable for elucidating levels and patterns of genetic variation in future population genetic and phylogeographic investigations of this species in northeastern Australia. These highly variable markers may also be useful for discerning species boundaries among D. calamiforme and the putative taxa D. baseyanum St. Cloud and D. ×foederatum St. Cloud, which have in the past been recognized as occurring in the Cairns area of northeastern Australia (Field and Zich, 2012).



P. B. Adams 2011. Systematics of Dendrobiinae (Orchidaceae), with special reference to Australian taxa. Botanical Journal of the Linnean Society 166: 105–126. Google Scholar


T. A. Castoe , A. W. Poole , A. P. J. de Koning , K. L. Jones , D. F. Tomback , S. J. Oyler-McCance , J. A. Fike , et al. 2012. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE 7: e30953. Google Scholar


M. A. Clements , and D. L. Jones . 1996. New species of Dendrobiinae (Orchidaceae) from Papua New Guinea. Lasianthera 1: 8–25. Google Scholar


D. M. Crayn , C. Costion , and M. G. Harrington . 2015. The Sahul-Sunda floristic exchange: Dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics. Journal of Biogeography 42: 11–24. Google Scholar


A. J. DeWoody , J. Schupp , L. Kenefic , J. Busch , L. Murfitt , and P. Keim . 2004. Universal method for producing ROX-labeled size standards suitable for automated genotyping. BioTechniques 37: 348–350. Google Scholar


R. H. Don , P. T. Cox , B. J. Wainwright , K. Baker , and J. S. Mattick . 1991. ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Research 19: 4008. Google Scholar


J. J. Doyle , and J. L. Doyle . 1990. Isolation of plant DNA from fresh tissue. Focus (San Francisco, Calif.) 12: 13–15. Google Scholar


A. R. Field , and F. A. Zich . 2012. Types of enigmatic north-Queensland orchids from the Dockrill herbarium. Austrobaileya 8: 696–698. Google Scholar


T. R. Kartzinel , R. P. Shefferson , and D. W. Trapnell . 2013. Relative importance of pollen and seed dispersal across a Neotropical mountain landscape for an epiphytic orchid. Molecular Ecology 22: 6048–6059. Google Scholar


R. Peakall , and P. E. Smouse . 2006. GenAlEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295. Google Scholar


M. Rossetto , D. Crayn , A. Ford, R. Mellick , and K. Sommerville . 2009. The influence of environment and life-history traits on the distribution of genes and individuals: A comparative study of 11 rainforest trees. Molecular Ecology 18: 1422–1438. Google Scholar


F. Rousset 2008. GENEPOP'007: A complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8: 103–106. Google Scholar


S. Rozen , and H. Skaletsky . 1999. Primer3 on the WWW for general users and for biologist programmers. In S. Misener and S. A. Krawetz [eds.], Methods in molecular biology, vol. 132: Bioinformatics methods and protocols. 365–386. Humana Press, Totowa, New Jersey, USA. Google Scholar


C. J. Schneider , M. Cunningham , and C. Moritz . 1998. Comparative phylogeography and the history of endemic vertebrates in the Wet Tropics rainforests of Australia. Molecular Ecology 7: 487–498. Google Scholar


D. W. Trapnell , and J. L. Hamrick . 2004. Partitioning nuclear and chloroplast variation at multiple spatial scales in the Neotropical epiphytic orchid, Laelia rubescens. Molecular Ecology 13: 2655–2666. Google Scholar


L. J. Webb , and J. G. Tracey . 1981. Australian rainforests: Patterns and change. In A. Keast [ed.], Ecological biogeography of Australia, vol. 1, 605–694. W. Junk, The Hague, The Netherlands. Google Scholar


Appendix 1.

Geographic locations and voucher information for Dendrobium calamiforme samples collected from five sites in Queensland, Australia, and deposited in the Australian Tropical Herbarium (CNS) by Ashley R. Field (ARF).



[1] The authors thank Dat Hoang for laboratory assistance, the Biostatistics/Bioinformatics Shared Resource at the University of Colorado Cancer Center (5P30CA046934) for bioinformatics support, Darren Crayn for valuable feedback on the manuscript, and an anonymous reviewer. Funding was provided by a University of Georgia Faculty Research Grant (D.W.T.), the University of Georgia Office of the Vice President of Research (D.W.T.), and by the U.S. Department of Energy under Award Number DEFC09-07SR22506 to the University of Georgia Research Foundation.

Dorset W. Trapnell, Rochelle R. Beasley, Stacey L. Lance, Ashley R. Field, and Kenneth L. Jones "Characterization of Microsatellite Loci for an Australian Epiphytic Orchid, Dendrobium calamiforme, Using Illumina Sequencing," Applications in Plant Sciences 3(6), (5 June 2015).
Received: 19 February 2015; Accepted: 1 April 2015; Published: 5 June 2015
Dendrobium calamiforme
Dockrillia calamiformis
genetic diversity
simple sequence repeat (SSR) markers
Back to Top