References
- Cameron KM, Chase MW, Whitten WM, Kores PJ, Jarrell DC, Albert VA, Yukawa T, et al. (1999). A phylogenetic analysis of the Orchidaceae: Evidence from rbcL nucleotide. Am J Bot 86:208–24
- Carver T, Harris SR, Berriman M, Parkhill J, McQuillan JA. (2012). Artemis: An integrated platform for visualization and analysis of highthroughput sequence-based experimental data. Bioinformatics 28:464–9
- Chase MW. (2005). Classification of Orchidaceae in the age of DNA data. Curtis’s Bot Mag 22:2–7
- Chevreux B, Wetter T, Suhai S. (1999). Genome sequence assembly using trace signals and additional sequence information. Comput Sci Biol: Proc German Conf Bioinform 99:45–56
- Doyle JJ, Doyle JL. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
- Dressler RL. (1990). The Orchids: Natural history and classification. Cambridge, MA: Harvard University Press
- Jheng C-F, Chen T-C, Lin J-Y, Chen T-C, Wu W-L, Chang C-C. (2012). The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids. Plant Sci 190:62–73
- Lowe TM, Eddy SR (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–64
- Langmead B, Salzberg S. (2012). Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–9
- Luo J, Hou B-W, Niu Z-T, Liu W, Xue Q-Y, Ding X-Y. (2014). Comparative chloroplast genomes of photosynthetic orchids: Insights into evolution of the orchidaceae and development of molecular markers for phylogenetic applications. PloS One 9:e99016
- Mendonça MP, Lins LV. (2007). Revisão das listas das espécies da flora e da fauna Ameaçadas de extinção do estado de minas gerais. Belo Horizonte, MG, Brasil: Fundação Biodiversitas
- Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D. (2013). Using tablet for visual exploration of second-generation sequencing data. Brief Bioinform 14:193–202
- Van den Berg C, Goldman DH, Freudenstein JV, Pridgeon AM, Cameron KM, Chase MW. (2005). An overview of the phylogenetic relationships within Epidendroideae inferred from multiple DNA regions and recircumscription of Epidendreae and Arethuseae (Orchidaceae). Am J Bot 92:613–24
- Van den Berg C, Higgins WE, Dressler RL, Whitten WM, Soto-Arenas M, Chase MW. (2009). A phylogenetic study of Laeliinae (Orchidaceae) based on combined nuclear and plastid DNA sequences. Ann Bot 104:417–30
- Wyman SK, Jansen RK, Boore JL. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics 20:3252–5
- Yang J-B, Tang M, Li H-T, Zhang Z-R, Li D-Z. (2013). Complete chloroplast genome of the genus Cymbidium: Lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evol Biol 13:84