title: Analysis of whole chloroplast genomes from the genera of the Clauseneae, the curry tribe (Rutaceae, Citrus family).
abstract: The Clauseneae (Aurantioideae, Rutaceae) is a tribe in the Citrus family that, although economically important as it contains the culinary and medicinally-useful curry tree (Bergera koenigii), has been relatively understudied. Due to the recent significant taxonomic changes made to this tribe, a closer inspection of the genetic relationships among its genera has been warranted. Whole genome skimming was used to generate chloroplast genomes from six species, representing each of the four genera (Bergera, Clausena, Glycosmis, Micromelum) in the Clauseneae tribe plus one closely related outgroup (Merrillia), using the published plastome sequence of Citrus sinensis as a reference. Phylogenetically informative character (PIC) data were analyzed using a genome alignment of the seven species, and variability frequency among the species was recorded for each coding and non-coding region, with the regions of highest variability identified for future phylogenetic studies. Non-coding regions exhibited a higher percentage of variable characters as expected, and the phylogenetic markers ycf1, matK, rpoC2, ndhF, trnS-trnG spacer, and trnH-psbA spacer proved to be among the most variable regions. Other markers that are frequently used in phylogenetic studies, e.g. rps16, atpB-rbcL, rps4-trnT, and trnL-trnF, proved to be far less variable. Phylogenetic analyses of the aligned sequences were conducted using Bayesian inference (MrBayes) and Maximum Likelihood (RAxML), yielding highly supported divisions among the four genera.
authors.affiliation: Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA; Thomas Jefferson High School for Science and Technology, 6560 Braddock Rd, Alexandria, VA 22312, USA. Electronic address: vikram.shivakumar@gmail.com.
authors.forename: Vikram S
authors.initials: VS
authors.lastname: Shivakumar
authors.affiliation: Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA; Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Untere Karspüle 2, 37073 Göttingen, Germany.
authors.forename: Marc S
authors.initials: MS
authors.lastname: Appelhans
authors.affiliation: Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Johnson
authors.affiliation: Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA.
authors.forename: Monica
authors.initials: M
authors.lastname: Carlsen
authors.affiliation: Department of Botany and Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA. Electronic address: zimmerl@si.edu.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Zimmer
mesh_terms: D001499:Bayes Theorem; D002957:Citrus / Q000235:genetics; D054628:Genome, Chloroplast / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D016013:Likelihood Functions; D032101:Murraya / Q000235:genetics; D010802:Phylogeny; D027821:Rutaceae / Q000145:classification* / Q000235:genetics*; D016415:Sequence Alignment
keywords: Bergera koenigii; Chloroplast genome; Clauseneae; Next-generation sequencing; Phylogenetically informative characters; Rutaceae; Single nucleotide polymorphism