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).