title: Comparative analysis of the complete sequence of the plastid genome of Parthenium argentatum and identification of DNA barcodes to differentiate Parthenium species and lines.
abstract: BACKGROUND
  Parthenium argentatum (guayule) is an industrial crop that produces latex, which was recently commercialized as a source of latex rubber safe for people with Type I latex allergy. The complete plastid genome of P. argentatum was sequenced. The sequence provides important information useful for genetic engineering strategies. Comparison to the sequences of plastid genomes from three other members of the Asteraceae, Lactuca sativa, Guitozia abyssinica and Helianthus annuus revealed details of the evolution of the four genomes. Chloroplast-specific DNA barcodes were developed for identification of Parthenium species and lines.
  
  
  RESULTS
  The complete plastid genome of P. argentatum is 152,803 bp. Based on the overall comparison of individual protein coding genes with those in L. sativa, G. abyssinica and H. annuus, we demonstrate that the P. argentatum chloroplast genome sequence is most closely related to that of H. annuus. Similar to chloroplast genomes in G. abyssinica, L. sativa and H. annuus, the plastid genome of P. argentatum has a large 23 kb inversion with a smaller 3.4 kb inversion, within the large inversion. Using the matK and psbA-trnH spacer chloroplast DNA barcodes, three of the four Parthenium species tested, P. tomentosum, P. hysterophorus and P. schottii, can be differentiated from P. argentatum. In addition, we identified lines within P. argentatum.
  
  
  CONCLUSIONS
  The genome sequence of the P. argentatum chloroplast will enrich the sequence resources of plastid genomes in commercial crops. The availability of the complete plastid genome sequence may facilitate transformation efficiency by using the precise sequence of endogenous flanking sequences and regulatory elements in chloroplast transformation vectors. The DNA barcoding study forms the foundation for genetic identification of commercially significant lines of P. argentatum that are important for producing latex.
authors.affiliation: Crop Improvement and Utilization Research Unit, Western Regional Research Center, ARS, USDA, Albany, CA 94710, USA. shashi.kumar@ars.usda.gov
authors.forename: Shashi
authors.initials: S
authors.lastname: Kumar
authors.forename: Frederick M
authors.initials: FM
authors.lastname: Hahn
authors.forename: Colleen M
authors.initials: CM
authors.lastname: McMahan
authors.forename: Katrina
authors.initials: K
authors.lastname: Cornish
authors.forename: Maureen C
authors.initials: MC
authors.lastname: Whalen
mesh_terms: D019659:Asteraceae / Q000145:classification / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D018742:DNA, Chloroplast / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D054628:Genome, Chloroplast; D018745:Genome, Plant; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018742:DNA, Chloroplast; D018744:DNA, Plant