title: The complete chloroplast genome sequence ofGentiana lawrenceivar. farreri(Gentianaceae) and comparative analysis with its congeneric species.
abstract: BACKGROUND
  The chloroplast (cp) genome is useful in plant systematics, genetic diversity analysis, molecular identification and divergence dating. The genusGentianacontains 362 species, but there are only two valuable complete cp genomes. The purpose of this study is to report the characterization of complete cp genome ofG. lawrenceivar.farreri, which is endemic to the Qinghai-Tibetan Plateau (QTP).
  
  
  METHODS
  Using high throughput sequencing technology, we got the complete nucleotide sequence of theG. lawrenceivar.farrericp genome. The comparison analysis including genome difference and gene divergence was performed with its congeneric speciesG. straminea. The simple sequence repeats (SSRs) and phylogenetics were studied as well.
  
  
  RESULTS
  The cp genome ofG. lawrenceivar.farreriis a circular molecule of 138,750 bp, containing a pair of 24,653 bp inverted repeats which are separated by small and large single-copy regions of 11,365 and 78,082 bp, respectively. The cp genome contains 130 known genes, including 85 protein coding genes (PCGs), eight ribosomal RNA genes and 37 tRNA genes. Comparative analyses indicated thatG. lawrenceivar.farreriis 10,241 bp shorter than its congeneric speciesG. straminea.Four large gaps were detected that are responsible for 85% of the total sequence loss. Further detailed analyses revealed that 10 PCGs were included in the four gaps that encode nine NADH dehydrogenase subunits. The cp gene content, order and orientation are similar to those of its congeneric species, but with some variation among the PCGs. Three genes,ndhB,ndhFandclpP, have high nonsynonymous to synonymous values. There are 34 SSRs in theG. lawrenceivar.farrericp genome, of which 25 are mononucleotide repeats: no dinucleotide repeats were detected. Comparison with theG. stramineacp genome indicated that five SSRs have length polymorphisms and 23 SSRs are species-specific. The phylogenetic analysis of 48 PCGs from 12 Gentianales taxa cp genomes clearly identified three clades, which indicated the potential of cp genomes in phylogenetics.
  
  
  CONCLUSIONS
  The "missing" sequence ofG. lawrenceivar.farrerimainly consistent ofndhgenes which could be dispensable under chilling-stressed conditions in the QTP. The complete cp genome sequence ofG. lawrenceivar.farreriprovides intragenic information that will contribute to genetic and phylogenetic research in the Gentianaceae.
authors.affiliation: College of Life Science, Luoyang Normal University , Luoyang , China.
authors.forename: Peng-Cheng
authors.initials: PC
authors.lastname: Fu
authors.affiliation: College of Life Science, Luoyang Normal University , Luoyang , China.
authors.forename: Yan-Zhao
authors.initials: YZ
authors.lastname: Zhang
authors.affiliation: College of Life Science, Luoyang Normal University , Luoyang , China.
authors.forename: Hui-Min
authors.initials: HM
authors.lastname: Geng
authors.affiliation: Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences , Xining , China.
authors.forename: Shi-Long
authors.initials: SL
authors.lastname: Chen
keywords: Chloroplast genome; Gentiana lawrencei var. farreri; Qinghai-Tibetan Plateau