With over 20,000 species, Asteraceae is the second largest plant family. In the last decade the advent of Next Generation Sequencing (NGS) allowed insights directly on the nuclear, chloroplastic and mithocondrial genomes giving the opportunity to better understand the evolutionary relationships within this family. Cynara cardunculus is a complex species including two crops (globe artichoke and cardoon) and a wild taxon (wild cardoon). We isolated chloroplast Illumina reads as a contamination of nuclear genome sequencing for an artichoke and a wild cardoon sample. After mapping all the reads on Lactuca sativa chloroplast (cp) genome , the closest cp genome present in public databases, we obtained a very reliable coverage (about 130x). Contigs and supercontigs generated by assembling the raw sequencing data were aligned onto the reference genome showing a 98% coverage of the full cp sequence, with five gaps which were filled by Sanger sequencing. The typical cp quadripartite architecture comprising a large single copy (LSC), a small single copy (SSC) and two inverted repeats (IR1 and IR2) was checked by Sanger sequencing of the relative junctions in order to avoid contingently assembling artifacts. The full sequence was then nnotated with bioinformatic softwares whose errors were corrected by hand. Gene content and order showed to be well conserved within the Asteraceae family and promising regions were used for further investigations in molecular phylogeny of Asteraceae. Moreover, sequencing of various taxa within Cynara provide useful informations to develop molecular markers suitable for performing evolutionary studiesand barcoding applications within this genus.
DISCOVERING ARTICHOKE CHLOROPLAST GENOME: A POWERFUL RESOURCE FOR PHYLOGENETIC STUDIES AND BARCODING APPLICATIONS
Curci PL;De Paola D;Danzi D;Sonnante G
2013
Abstract
With over 20,000 species, Asteraceae is the second largest plant family. In the last decade the advent of Next Generation Sequencing (NGS) allowed insights directly on the nuclear, chloroplastic and mithocondrial genomes giving the opportunity to better understand the evolutionary relationships within this family. Cynara cardunculus is a complex species including two crops (globe artichoke and cardoon) and a wild taxon (wild cardoon). We isolated chloroplast Illumina reads as a contamination of nuclear genome sequencing for an artichoke and a wild cardoon sample. After mapping all the reads on Lactuca sativa chloroplast (cp) genome , the closest cp genome present in public databases, we obtained a very reliable coverage (about 130x). Contigs and supercontigs generated by assembling the raw sequencing data were aligned onto the reference genome showing a 98% coverage of the full cp sequence, with five gaps which were filled by Sanger sequencing. The typical cp quadripartite architecture comprising a large single copy (LSC), a small single copy (SSC) and two inverted repeats (IR1 and IR2) was checked by Sanger sequencing of the relative junctions in order to avoid contingently assembling artifacts. The full sequence was then nnotated with bioinformatic softwares whose errors were corrected by hand. Gene content and order showed to be well conserved within the Asteraceae family and promising regions were used for further investigations in molecular phylogeny of Asteraceae. Moreover, sequencing of various taxa within Cynara provide useful informations to develop molecular markers suitable for performing evolutionary studiesand barcoding applications within this genus.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
