ABSTRACT
Citrus hongheensis is a key protected wild plant endemic to the Honghe river region in southeastern Yunnan, China. In the present study, its chloroplast genome was successfully assembled and annotated based on the Illumina Hiseq-2500 whole genome re-sequencing data. The chloroplast genome is 160,275 bp in size. Its large single copy region, small single copy region and inverted repeat region is 87,886 bp, 18,387 bp and 27,001 bp, respectively. Totally, 114 unique genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs, were identified from the C. hongheensis chloroplast genome. According to the phylogenetic analysis result, the relationship between the chloroplast genome of C. hongheensis and C. maxima was found to be the closest.
ABSTRACT
Hongkong qumquat (Fortunella hindsii Swingle) is a wild citrus species native to China. In this study, we firstly reporteded its complete chloroplast genome using BGISEQ-500 sequencing. The chloroplast genome is 160,145 bp in size, containing a large single copy region (87,467 bp), a small single copy region (18,730 bp), and a pair of IR regions (26,974 bp). The chloroplast genome contains 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and 4 rRNAs. Phylogenetic maximum-likelihood analysis indicated that F. hindsii is closely related to Citrus species. The complete chloroplast genome would be subsequently used for citrus species researches.
ABSTRACT
In this study, we reported the complete chloroplast genome of Fortunella crassifolia Swingle using the HiSeq-4000 sequencing. The chloroplast genome size is 160,229 bp, which consists of a large single-copy region (87,774 bp), a small single-copy region (18,721 bp), and a pair of IR regions (26,867 bp). The chloroplast genome contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs. Phylogenetic maximum likelihood analysis showed that F. crassifolia was closest to Hongkong kumquat (F. hindsii). The complete chloroplast genome would be subsequently used for citrus species researches.
ABSTRACT
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.
