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

BackgroundParthenium 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.ResultsThe 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.ConclusionThe 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.

A rapid screening for adulterants in olive oil using DNA barcodes

“…The application of DNA barcode technology has been found very interesting in our previous research work and to generate uniform guayule plants used for latex production (Kumar, Hahn, McMahan, Cornish, & Whalen, 2009). Here our objective was to establish the authenticity of olive oil based on species-specific plastid DNA markers present in oils in trace amounts.…”

Genomic diversity and phylogenetic relationships in the genus Parthenium (Asteraceae)

“…1). Additionally, we selected for characterization recent wild collections of mariola, the Parthenium species most closely related to guayule (Rollins, 1950;Kumar et al, 2009) and a common guayule interspecific hybridization partner in the wild (Rollins, 1950). Contemporary nursery material of wild quinine, a Parthenium species distantly related to guayule (Rollins, 1950;Kumar et al, 2009), was selected as the outgroup for phylogenetic analysis.…”

“…Additionally, we selected for characterization recent wild collections of mariola, the Parthenium species most closely related to guayule (Rollins, 1950;Kumar et al, 2009) and a common guayule interspecific hybridization partner in the wild (Rollins, 1950). Contemporary nursery material of wild quinine, a Parthenium species distantly related to guayule (Rollins, 1950;Kumar et al, 2009), was selected as the outgroup for phylogenetic analysis. A subset of these accessions has been previously analyzed for ploidy, chromosome number, and nuclear genome size (Gore et al, 2011;Sanchez et al, 2014) and this study expands those analyses to a further five accessions, providing ploidy, chromosome number, and nuclear genome size information for the accessions that were genetically characterized with SNP markers (Table 1).…”

“…ncbi.nlm.nih.gov/tools/vecscreen/univec), which among other vector sequences contains entries for the specific PCR vectors used in the GBS library preparation protocol (UniVec identifiers 'gnl|uv|NGB00362.1:1-61' and 'gnl|uv|NGB00360.1:1-58'). They were further screened against the NCBI artificial vector sequence dataset (taxon id 29278; http://www.ncbi.nlm.nih.gov/Taxonomy/ Browser/wwwtax.cgi?mode=Info&id=29278), the guayule chloroplast sequence (NCBI gi 281190713; Kumar et al, 2009), and the "Representative Genomes" subset of the NCBI Microbial Genomes database (build of May 28, 2014; ftp://ftp.ncbi.nlm.nih. gov/blast/db/Representative Genomes.*tar.gz).…”

Genetic stability analysis of chrysanthemum (Chrysanthemum x morifolium Ramat) after different stages of an encapsulation–dehydration cryopreservation protocol

“…Other sections of the same fragment showed homology (e-value ranging between e −28 and e −9 ) with cpDNA from diverse species (Fig. 4b), with the homology being higher with those species belonging to the Asteraceae family, as for example, the identities found with cpDNA of Parthenium argentatum (Kumar et al, 2009). …”