Camellia huana is an endangered species with a narrow distribution in limestone hills of northern Guangxi and southern Guizhou provinces, China. We used one chloroplast DNA (cpDNA) fragment and 12 pairs of microsatellite (simple sequence repeat; SSR) markers to assess the genetic diversity and structure of 12 C. huana populations. A total of 99 alleles were detected for 12 polymorphic loci, and eight haplotypes and nine polymorphic sites were detected within 5200 bp of cpDNA. C. huana populations showed a low level of genetic diversity ( n = 8, Hd = 0.759, Pi = 0.00042 for cpDNA, N A = 3.931, H E = 0.466 for SSRs), but high genetic differentiation between populations ( F ST = 0.2159 for SSRs, F ST = 0.9318 for cpDNA). This can be attributed to the narrow distribution and limestone habitat of C. huana . STRUCTURE analysis divided natural C. huana populations into two groups, consistent with their geographical distribution. Thus, we suggest that five natural C. huana populations should be split into two units to be managed effectively.

In this study, we report on the complete chloroplast genomes of Camellia perpetua and Camellia indochinensis for the first time. The complete chloroplast genome of C. perpetua is 156,804 bp in length and is comprised of two inverted repeat (IR) regions (25,996 bp each), a large single copy (LSC) region (86,570 bp), and a small single copy (SSC) region (18,242 bp). The chloroplast genome of C. perpetua harbors 86 protein-coding genes, 28 tRNA genes, and eight rRNA genes, with an overall GC content of 37.32%. The chloroplast genome of C. indochinensis showed similar characteristics as that of C. perpetua. The total length of C. indochinensis chloroplast genome is 156,571 bp, which includes 26,053 bp each of the two IR regions, 86,246 bp of the LSC region, and 18,219 bp of the SSC region. C. indochinensis chloroplast genome contains 85 protein-coding genes, 28 tRNA genes, and eight rRNA genes, with an overall GC content of 37.34%. Furthermore, a phylogenetic tree was constructed using the chloroplast genome sequences of the two species, and their phylogenetic positions were determined.

Camellia nitidissima is an endangered species. This species contains two varieties. Here, we report on the chloroplast genomes of C. nitidissima var. nitidissima from Fangcheng (GenBank accession MT157617) and Nanning (MT157618), as well as one sample of C . nitidissima var. microcarpa (MT157619) from Nanning. The total chloroplast genomes of C. nitidissima var. nitidissima Fangcheng and Nanning samples are 156,596 bp and 157,567 bp in length, respectively. C. nitidissima var. microcarpa (MT157619) genome is 157,407 bp in length. The three samples possess GC contents of 37.3%, 128 genes, comprising 86 protein-coding genes, 34 tRNA genes, and 8 rRNA genes.