Complete chloroplast genome sequencing of Job’s tears (Coix L.): genome structure, comparative analysis, and phylogenetic relationships

Job’s tears, also known as adlay, is a valuable plant that has commonly been used in traditional Chinese medicine, as well as an edible food. Due to the lack of knowledge of its genetics and gaps in its evolutionary analysis, breeding of adlay has been hindered. Here, we report five complete chloroplast genomes of various species and varieties in the genus by Illumina sequencing, while their genome structure, comparative analysis, and phylogenetic relationships were conducted. Genome sizes ranged from 140,860 to 140,864 bp in length, GC contents were 38.43%, and genome architecture was of a typical quadripartite structure. We annotated 82～83 protein-coding genes and 46～47 non-coding RNA genes in each genome and they functionally associated with self-replication, photosynthesis, cytochrome synthesis and other unknown functions. Three codons that encoded tryptophan, arginine and leucine were used frequently at rates of 41.42, 37.98, and 32.28% respectively. The preferred codons consistently ended with A or T. A total of 146 simple sequence repeats (SSR), 9 insertions and deletions (InDels) and 143 single nucleotide polymorphisms (SNPs) were observed among genomes. The InDel and SNP variations were mostly distributed in intergenic regions. It confirmed that Coix, Sorghum, Saccharum, Zea, Tripsacum and Saccharum were closely genera and the genetic distance of Sorghum to Coix was closer than Zea to Coix. These results give us more insight into the evolution of Coix in a wide range of evolutionary studies.