Characterization of the complete chloroplast genome of Citrus hongheensis, a key protected wild plant in Yunnan province of China

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.

Bayesian phylodynamic analysis reveals the evolutionary history and the dispersal patterns of citrus tristeza virus in China based on the p25 gene

“…The genus Citrus and related genera ( Fortunella , Poncirus , Eremocitrus , and Microcitrus ) belong to Rutaceae family and subfamily Aurantioideae, which comprise some of the most widely cultivated fruit crops worldwide [ 1 ]. Citrus fruits are rich in various bioactives such as flavonoids, essential oils, carotenoids, limonoids, and synephrines [ 2 , 3 ]. These natural nutrients have been reported effective in protecting human from various ailments, including cancer and inflammation, digestive, and cardiovascular diseases.…”

“…Increasing by 27.68% from 2016, by 2022, Chinese citrus cultivated acreage was 45.531 million acres, 1.32 tons/acre for our citrus groves in 2022, orange production in 2022 reached 7.6 million metric tons ( https://www.fas.usda.gov/data/china-citrus-annual-5 ). Meanwhile, there are abundant wild citrus resources in China, such as Citrus mangshanensis , Citrus cavaleriei and Citrus medica et al [ 3 , 4 ]. But there are still many factors that limit the growth of the citrus cultivation area and production, such as diseases, drought, frigidity, soil salinization, among which citrus tristeza caused by CTV presents as one of the most damaging disasters [ 5 – 7 ].…”

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

“…The whole genomic DNA resequencing was performed on the Illumina Hiseq-2500 platform to generate 125 bp pair end reads (BIG, Shenzhen, CA, CHN). Totally, we obtained about 15.58 Gbp high quality clean reads, which were aligned to chloroplast genomes of six citrus species, including C. maxima (NC_034290.1), C. sinensis (DQ864733.1), C. aurantiifolia (KJ865401.1), C. platymamma (NC_030194.4), Citrus limon (KY085897.1), C. depressa (LC147381.1) and C. reticulata (NC_034671.1), assembled into chloroplast genome and annotated according to our previous studies (Zhang et al 2020a(Zhang et al , 2020b. The annotated chloroplast genome has been deposited in Genbank with the accession number MT880608.…”