Characterization of the complete chloroplast genome of 'Yunning No.1' lemon (Citrus limon).

'Yunning No.1' lemon, a mutant of Eureka lemon, is originally found in Yunnan province of China and is the main cultivated lemon variety there. In this study, we assembled and annotated its chloroplast genome using Illumina Hiseq-2500 whole genome re-sequencing data. Its chloroplast genome is 160,141 bp in size, containing a 87,754 bp large single copy region, a 18,385 bp small single copy region and a pair of 27,001 bp inverted repeat region. Like many citrus species, 114 unique genes (including 80 protein-coding genes, 30 tRNAs and 4 rRNAs) could be identified from the chloroplast genome of 'Yunning No.1'. Phylogenetic analysis revealed that the 'Yunning No.1' chloroplast genome was closest to Citrus maxima.

Identification of pummelo cultivars by using a panel of 25 selected SNPs and 12 DNA segments.

Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.