Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae

PloS One
Pasquale Luca CurciGabriella Sonnante

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 in...Continue Reading

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Citations

Mar 27, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Pasquale Luca Curci, Gabriella Sonnante
Sep 12, 2015·Molecular Ecology Resources·Pasquale L CurciGabriella Sonnante
Oct 30, 2016·Molecular Ecology Resources·Alex D Twyford, Rob W Ness
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Dec 19, 2019·Frontiers in Pharmacology·Zhonglian ZhangXiaojun Ma
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Jul 24, 2018·Frontiers in Pharmacology·Xinlian ChenHui Yao
May 30, 2020·International Journal of Molecular Sciences·Zhou HongDaping Xu
Feb 3, 2017·Mitochondrial DNA. Part B, Resources·Tianrun ZhengHui Chen

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Datasets Mentioned

BETA
SRP049578
SRR1648410
KM035764

Methods Mentioned

BETA
PCR
Illumina partial sequencing
Tandem Repeat Finder

Software Mentioned

SE
IMEx
DOGMA ( Dual Organellar GenoMe Annotator )
Primer
tRNAscan
Fast Statistical Alignment ( FSA )
PAUP
REPuter
Acua
CLC Genomics Workbench

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