Regardless of the duplicate genes, the chloroplast genome of P. wilsonii contained 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Among them, six protein-coding genes, seven tRNAs, and all the four rRNAs were completely duplicated within IRs (Figure 1). The rps12 gene was found to be trans-spliced in chloroplast genomes. It had two duplicates in IRs and one of its exons located in the LSC region (Figure 1). A total of 18 genes, including 12 protein-coding genes and six tRNA genes, had introns. It was noted that 16 genes among them had only one intron while the other two genes had two introns. The comparisons between the genome of P. wilsoniiand the other Primula chloroplasts are shown in Table 1. The results indicated that the gene contents were similar among thePrimula species, excluding the loss of the ycf15 gene in the P. wilsonii chloroplast genome. The chloroplast genomes of P. poissonii and P. wilsonii possessed the infA gene, whereas the others did not have it. Moreover, the trnG -GCC sequence only appeared in the chloroplast genome of P. wilsonii .
3.2. Repeat sequences and SSRs analysis
Except for the largest repeat in each genome (IR regions), a total of 111 repeat pairs no more than 60 bp in length were identified in the five Primula chloroplast genomes. Only two types of repeat sequences, forward and palindromic repeats, were detected (Figure 2). There were 22 (nine forward, 13 palindrome), 22 (nine forward, 13 palindrome), 27 (12 forward, 15 palindrome), 13 (13 forward), and 27 (12 forward, 15 palindrome) repeats in P. wilsonii , P. anisodora , P. miyabeana , P. poissonii , and P. secundiflora , respectively. Among them, the chloroplast genomes ofP. miyabeana and P. secundiflora had the largest number of repeats, whereas P. poissonii had the fewest. The results indicated that forward repeats were more common, accounting for 54.47% (67 of 123 repeats). In these five genomes, the length of the repeats was mainly in the range of 30-39 bp, with a percentage of 61.26% (68 of 111 repeats), followed by 40-49 bp, contributing 29.73% (33 of 111 repeats).