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Phylogenetic Classification of Gongora S pecies ( Orchidaceae ) Based on DNA Barcode Regions matK, rpoB, rpoC1, and trn‐H‐psbA
Author(s) -
Guardado Christopher,
Rodriguez Olivia,
Foss Keagan,
Ludovic Daniela,
Ribadeneyra Clara,
Trivino Cesar,
Baenziger Edward,
RibesZamora Albert,
Simmons Alexandra D
Publication year - 2016
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.30.1_supplement.572.3
Subject(s) - rpob , dna barcoding , phylogenetic tree , biology , barcode , dna sequencing , evolutionary biology , phylogenetics , orchidaceae , amplicon , mitochondrial dna , genome , genetics , polymerase chain reaction , dna , gene , botany , 16s ribosomal rna , computer science , operating system
Objectives Traditional species classification of orchids is based upon morphology, which is often hindered by inherent limitations such as species similarities. According to the American Orchid Society, the genus Gongora shows extensive morphological affinities, which result in mislabeling in the collections; however, advancements in gene sequencing technology enable the economic feasibility for species identification based on the orchid's genome. Specifically, DNA Barcoding is a molecular technique that uses “DNA barcodes”, which are short DNA regions, that can be used for species identification among other applications (Feng et al , 2015). Additionally, barcoding allows for the study of the evolutionary relationship between species examined and would therefore facilitate classification of unknown species (Singh, 2012). Our objective is to elucidate the classification of 38 Gongora species using four DNA barcode sequences. Methods and Results DNA was extracted from 82 individuals from 38 Gongora species. Then, PCR was employed to amplify the four DNA barcode regions of interest ( matK, rpoB, rpoC1, and trn‐H‐psbA ). The effectiveness of the PCR was analyzed by gel electrophoresis. Subsequently, amplicons were sent for DNA sequencing at an outside sequencing laboratory. The sequenced DNA was analyzed using MUSCLE in Mega 6.0 program. We developed a phylogenetic tree for about 32 species of orchids for each DNA barcode region. The rpoB and rpoC1 sequences provided similar phylogenetic trees thereby supporting the current classification of those Gongora as individual species. Furthermore, the phylogenetic trees also imply a possible evolutionary scheme. The highly variable trnH‐psbA provided a similar species identification but contradicting species evolution. Conclusions DNA barcodes provide unique insights into possible Gongora species identification; however, the need to combine all four DNA barcodes into one phylogenetic tree is necessary to provide conclusive results for species classification and evolutionary relationships. The current results suggest that the rpoB and rpoC1 are useful markers for evolutionary analysis and trnH‐psbA could elucidate the differences between closely related species. Support or Funding Information University of St. Thomas Research Committee and Biology Department