The Complete Chloroplast Genome of Capsicum annuum var. glabriusculum Using Illumina Sequencing

Abstract

Chloroplast (cp) genome sequences provide a valuable source for DNA barcoding. Molecular phylogenetic studies have concentrated on DNA sequencing of conserved gene loci. However, this approach is time consuming and more difficult to implement when gene organization differs among species. Here we report the complete re-sequencing of the cp genome of Capsicum pepper (Capsicum annuum var. glabriusculum) using the Illumina platform. The total length of the cp genome is 156,817 bp with a 37.7% overall GC content. A pair of inverted repeats (IRs) of 50,284 bp were separated by a small single copy (SSC; 18,948 bp) and a large single copy (LSC; 87,446 bp). The number of cp genes in C. annuum var. glabriusculum is the same as that in other Capsicum species. Variations in the lengths of LSC; SSC and IR regions were the main contributors to the size variation in the cp genome of this species. A total of 125 simple sequence repeat (SSR) and 48 insertions or deletions variants were found by sequence alignment of Capsicum cp genome. These findings provide a foundation for further investigation of cp genome evolution in Capsicum and other higher plants.

Peer Review #1 of "The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene (v0.1)"

“…Moreover, chloroplast simple sequence repeats (cpSSRs) have been widely used previously in crossbreeding, biogeography, and population genetics studies (Bayly et al 2013). This is consistent with the chloroplast genomes of most angiosperms (Raveendar et al 2015;Yang et al 2014). In regards to repeat length, most SSR had 10-20 bp, while fewer had less than 10 bp, indicating that the SSR segment of the Jerusalem artichoke chloroplast genome is short.…”

The complete chloroplast genome of the Jerusalem artichoke (Helianthus tuberosus L.) and an adaptive evolutionary analysis of the ycf2 gene

“…Moreover, chloroplast simple sequence repeats (cpSSRs) have been widely used previously in crossbreeding, biogeography, and population genetics studies (Bayly et al 2013). This is consistent with the chloroplast genomes of most angiosperms (Raveendar et al 2015;Yang et al 2014). In regards to repeat length, most SSR had 10-20 bp, while fewer had less than 10 bp, indicating the SSR segment of the Jerusalem artichoke chloroplast genome is short.…”

The complete chloroplast genome of eggplant (Solanum melongena L.)

“…The phylogenetic analysis in this study included the 12 cp genomes of Solanum species (Chung et al 2006;Daniell et al 2006;Wu 2015) and the newly determined cp genome of S. melongena, using Capsicum annuum (Raveendar et al 2015) as outgroup. ML analysis yielded in a phylogenetic tree with most of the nodes (8/11) supported by a bootstrap value of 100, and S. melongena clustered with S. nigrum supported by a bootstrap value of 52 (Figure 1), which was concordant with the previous studies in the genus Solanum (Wu 2015).…”