AUTHOR=Wang Aisuo , Wu Hanwen , Zhu Xiaocheng , Lin Jianmin 

TITLE=Species Identification of Conyza bonariensis Assisted by Chloroplast Genome Sequencing

JOURNAL=Frontiers in Genetics

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2018.00374

DOI=10.3389/fgene.2018.00374

ISSN=1664-8021

ABSTRACT=<p>Flaxleaf fleabane (<italic>Conyza bonariensis</italic> [L.] Cronquist) is one of the most difficult weeds to control worldwide. There are more than 150 <italic>Conyza</italic> species in the world and eight species in Australia. Correct identification of these species can be problematic due to their morphological similarities especially at seedling stage. Developing a robust genetics – based species identification method to distinguish <italic>C. bonariensis</italic> from other closely related species is important for early control of weeds. We thus examined the chloroplast (cp) genome of <italic>C. bonariensis</italic>, aiming to identify novel DNA barcodes from the genome sequences, and use the entire cp genome as a super-barcode for molecular identification. The <italic>C. bonariensis</italic> chloroplast genome is 152,076 bp in size, encodes 133 genes including 88 protein-coding genes, 37 tRNA genes and 8 ribosomal RNA genes. A total of 151 intergenic regions and 19 simple sequence repeats were identified in the cp genome of <italic>C. bonariensis</italic>, which provides a useful genetic resource to develop robust markers for the genetic diversity studies of <italic>Conyza</italic> species. The sequence information was used to design a robust DNA barcode <italic>rps</italic>16 and <italic>trnQ-UUG</italic> which successfully separated three predominant <italic>Conyza</italic> species (<italic>C. bonariensis</italic>, <italic>C. canadensis</italic>, and <italic>C. sumatrensis</italic>). Phylogenetic analyses based on the cp genomes of <italic>C. bonariensis</italic>, <italic>C. canadensis</italic> and 18 other Asteraceae species revealed the potential of using entire cp genome as a plant super-barcode to distinguish closely-related weed species.</p>