Development of chloroplast genomic resources for Cynara

Abstract

In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.

Characterization of Complete Chloroplast Genome of Allium victorialis and Its Application for Barcode Markers

“…In the study of the Vicia species, no allelic polymorphism were detected in matK region (Raveendar et al 2015), suggesting the high level of conservation of standard barcode locus among the Vicia species. In the chloroplast genome analysis of 20 genotypes belonging to genus Cynara, a total of 73 InDels were identified with 39 polymorphic simple sequence repeats (SSRs) and 34 other InDels (Curci et al 2016), exhibiting the level of quantity of InDels within genus. In this analysis, we compared Allium victorialis chloroplast genome with those of Veratrum patulum and identified five potential regions for future DNA markers.…”

“…These five regions carry multiple InDels ranged from 1-63 bp in size. InDels in chloroplast genome serve as a useful marker system and outperforms SNPs because PCR products are easily discriminated by size (Melodelima et al 2013;Chaney et al 2016;Curci et al 2016;Daniell et al 2016). Intergenic regions are useful sources for InDels, because these regions underwent relatively rapid mutation due to the less evolutionary constraint.…”

Genotyping-by-sequencing highlights patterns of genetic structure and domestication in artichoke and cardoon

“…For the artichoke samples, the four main morpho-agronomic groups were considered: the small headed early types (˝Catanesi˝), the spiny early types (˝Spinosi˝), the violet late types (˝Violetti˝), and the large headed late types (˝Romaneschi˝) [ 23 ]. Several other accessions, belonging to none of the above typologies, were analysed [ 12 , 31 ]. The cultivated cardoon germplasm included material originating from the main regions where this vegetable is grown, i.e.…”

The Chloroplast Genome Sequence of Scutellaria baicalensis Provides Insight into Intraspecific and Interspecific Chloroplast Genome Diversity in Scutellaria

“…Most studies have shown that chloroplast genome mutations are not random but cluster at “hotspots” [ 16 , 19 , 20 , 21 ], and this mutational dynamic has resulted in highly variable regions in the genome. Chloroplast genome single nucleotide polymorphism (SNP), SSR, and indel markers have been developed in recent studies, as they show high abundance in the genome and improve population resolution [ 22 , 23 , 24 , 25 ].…”