Characterization of the complete chloroplast genome of Yuanjiang wild Ichang papeda (Citrus cavaleriei) in China

Abstract

Ichang papeda (Citrus cavaleriei) is an endemic perennial plant in China. In this study, we assembled and annotated the complete chloroplast genome of Yuanjiang wild Ichang papeda using Illumina Hiseq-2500 sequencing data. The chloroplast genome is constituted of 160,996 bp, containing a 87,634 bp large single-copy region, a 18,762 bp small single-copy region, and a pair of 27,300 bp inverted repeat regions. The chloroplast genome contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and 4 rRNAs. Phylogenetic analysis showed that the relationship between the chloroplast gennomes of C. cavaleriei and C. reticulata is the closest, which consistently support their chloroplast relationships.

Identification of Putative Parental Species of Yuzu (Citrus junos Sieb. Ex Tanaka) by Comparative Analyses of Variations in Chloroplast Genomes and Nuclear Single-copy Genes of Citrus

“…Later on, complete chloroplast genome sequences of 34 Citrus species have been assembled by mapping raw sequences to sweet orange sequences as a reference, and five hypervariable regions on citrus chloroplast genomes have been identified (Carbonell-Caballero et al, 2015). Recently, the complete chloroplast genome sequence of Ichang papeda has been reported (Zhang et al, 2020). Swingle and Reece (1967) have proposed that Ichang papeda is a seed parent of yuzu.…”

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.…”

“…Sequence annotation identified 114 unique genes (including 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes) from the chloroplast genome of 'Yunning No.1'. Similar to the Citrus cavaleriei chloroplast genome (Zhang et al 2020a), nine protein coding genes (i.e. ndhB, rpl2, rpl22, rpl23, rps7, rps12, rps19, ycf2 and ycf15), seven tRNA genes (i.e.…”

“…Similar to the Citrus cavaleriei chloroplast genome (Zhang et al. 2020a ), nine protein coding genes (i.e. ndhB , rpl2 , rpl22 , rpl23 , rps7 , rps12 , rps19 , ycf2 and ycf15 ), seven tRNA genes (i.e.…”