Analysis on the Chloroplast Genome Characteristics of Rubus lambertianus Ser.

PurposeTo analyze the complete chloroplast genome of Rubus lambertianus.

MethodsThe chloroplast genome of R. lambertianus was sequenced by high-throughput sequencing. We analyzed the chloroplast genome structure, gene composition and codon preference after genome assembly and annotation. And the maximum likelihood method was used to establish phylogenetic trees in R. lambertianus, 48 Rubus and two Geun.

ResultsThe chloroplast genome structure of R. lambertianus was a classical four-section structure with a size of 156 266 bp, and a total of GC content was 37.2%. The length of large single-copy region and small single-copy region was 85 849 and 18 855 bp, respectively. The length of reverse complementary repeat region was 25 781 bp. A total of 131 genes were annotated, including 86 protein-coding genes, 37 tRNA genes and eight rRNA genes. And a total of 33 codons in R. lambertianus chloroplast genome ended in A and U, among of these, 18 codons were identified as optimal codons. It was revealed that the codon preference of R. lambertianus chloroplast genome was more influenced by natural selection by using ENC-plot and other plotting analysis methods. The phylogenetic tree showed that R. lambertianus were most closely related to R. rufus, followed by R. cochinchinensis and R. reflexus.

ConclusionThe chloroplast genome of R. lambertianus is large and conserved, and the genome is most closely related to R. rufus. The results of this study can be used to analyze the phylogenetic of chloroplast genome system in R. lambertianus and Rubus genus.