Abstract

With over 20,000 species, Asteraceae is the second largest plant family. High-throughput sequencing of nuclear and chloroplast genomes has allowed for a better understanding of the evolutionary relationships within large plant families. Here, the globe artichoke chloroplast (cp) genome was obtained by a combination of whole-genome and BAC clone high-throughput sequencing. The artichoke cp genome is 152,529 bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 25,155 bp, representing the longest IRs found in the Asteraceae family so far. The large (LSC) and the small (SSC) single-copy regions span 83,578 bp and 18,641 bp, respectively. The artichoke cp sequence was compared to the other eight Asteraceae complete cp genomes available, revealing an IR expansion at the SSC/IR boundary. This expansion consists of 17 bp of the ndhF gene generating an overlap between the ndhF and ycf1 genes. A total of 127 cp simple sequence repeats (cpSSRs) were identified in the artichoke cp genome, potentially suitable for future population studies in the Cynara genus. Parsimony-informative regions were evaluated and allowed to place a Cynara species within the Asteraceae family tree. The eight most informative coding regions were also considered and tested for “specific barcode” purpose in the Asteraceae family. Our results highlight the usefulness of cp genome sequencing in exploring plant genome diversity and retrieving reliable molecular resources for phylogenetic and evolutionary studies, as well as for specific barcodes in plants.

Highlights

  • Cynara cardunculus L. is a complex species belonging to the second largest family of plants, Asteraceae, with over 20,000 species [1]

  • Whole genomic DNA was sent to IGA Technology Services (Udine, Italy) in order to perform Illumina sequencing, using the GAIIx platform (200–350 bp library insert size, 75 bp paired-end reads)

  • In order to complete the cp sequence, we screened a BAC library obtained from the same genotype used for nuclear genome sequencing

Read more

Summary

Introduction

Cynara cardunculus L. is a complex species belonging to the second largest family of plants, Asteraceae, with over 20,000 species [1]. It includes two crops, the globe artichoke [C. cardunculus L. var. Scolymus (L.) Fiori] and the cultivated or leafy cardoon The wild perennial cardoon has been recognized as the ancestor of both cultigens [2,3]. 191/2009, and by the project BiodiverSO – PSR Puglia 2007-2013 Mis. 214/4 subaz. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Methods
Results
Conclusion
Full Text
Published version (Free)

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call