Genome surveying reveals the complete chloroplast genome and nuclear genomic features of the crocin-producing plant Gardenia jasminoides Ellis

Abstract

Gardenia jasminoides, a well-known traditional Chinese herb, has been extensively utilized for its being as stable pigment in food industry and as rich source of crocin in treatment of various cancers and cardiovascular disease. Nevertheless, molecular data shortage of the organelle and nuclear genome vastly limits further biological research on G. jasminoides. In this study, complete chloroplast (cp) genome and large-scale nuclear genome sequences of G. jasminoides were initially generated by genome survey sequencing, and comprehensive genomic structure and comparison analyses were performed. The results showed that G. jasminoides cp genome displayed a typical quadripartite organization and was sized in 154,921 bp with 37.5% GC content. It contained 132 genes, 18 out of which were duplicated in the inverted repeat regions (IRs). Fifty long repeats (motif > 10 bp) and 27 simple sequence repeats were detected, and 30 usage-biased codons and 58 RNA-editing sites were predicted in G. jasminoides cp genome. The G. jasminoides cp genome was similar to those related species in Rubiaceae in terms of gene order and IR borders and a sister relationship of Gardenia and Coffea is strongly supported. Furthermore, the nuclear genome size of G. jasminoides was estimated to be 562.9 Mb, with heterozygosity rate being of 0.68%, repeat proportion of 51.6% and GC content of 36.44%. Overall, the data resources and findings generated in the present study will shed new light on the molecular and breeding studies on this important crocin-producing plant in the future.