Limited variation across two chloroplast genomes with finishing chloroplast genome of Capsella grandiflora

Mitochondrial DNA A DNA Mapp Seq Anal. 2016 Sep;27(5):3460-1. doi: 10.3109/19401736.2015.1066347. Epub 2015 Jul 17.


The complete chloroplast genome of Capsella grandiflora is finished in this study, which consists of 154 638 base pairs (bp) in size containing a pair of inverted repeats (IRa and IRb) of 26 462 bp each and a small and large single-copies (SSC and LSC) of 17 835 and 83 879 bp, respectively. The overall GC content is 36.54% and the GC contents of LSC, IRs, and SSC are 34.34%, 42.38%, and 29.61% separately. The gene contents and numbers are the same with other two published species in genus Capsella with 112 annotated unique genes including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among these, 16 are duplicated in the inverted repeat regions, 15 genes contained one intron, and three genes (rps12, clpP, and ycf3) comprising two introns. Based on the whole genome comparison, only 28 SNPs and 16 Indels (insertion and deletion) are detected between two closed relatives' chloroplast genomes.

Keywords: Capsella grandiflora; Indel; SNP; chloroplast genome; next-generation sequencing.

Publication types

  • Comparative Study

MeSH terms

  • Base Composition
  • Capsella / classification
  • Capsella / genetics*
  • Chloroplasts / genetics*
  • DNA, Ribosomal / genetics
  • Evolution, Molecular
  • Gene Duplication
  • Gene Order
  • Genome Size
  • Phylogeny
  • RNA, Transfer / genetics
  • Sequence Analysis, DNA / methods*


  • DNA, Ribosomal
  • RNA, Transfer