Characterisation of the complete chloroplast genome of Fortunella Crassifolia Swingle and phylogenetic relationships

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 singlecopy 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.

Comparative Analysis and Phylogenetic Implications of Plastomes of Five Genera in Subfamily Amyridoideae (Rutaceae)

“…The proteincoding genes of the 36 sequences were also extracted to construct phylogenetic trees using the same methods as the complete chloroplast genome sequences. (Table 1), which were similar to or slightly smaller than the reported plastomes of some genera of subfamily Aurantioideae, Rutaceae [39][40][41].…”

Characterization of the complete chloroplast genome of Houttuynia cordata Thunb and phylogenetic relationships

“…Sequence alignment analysis was performed using chloroplast genome sequences of three plant species belonging to Piperaceae, four plant species from Chloranthaceae and the H. cordata chloroplast genome using HomBlocks pipeline (Bi et al 2018). Maximum likelihood tree was constructed according to the method described by Wu et al (2019). Phylogenetic maximum likelihood analysis indicated that H. cordata Thunb is closest to P. cenocladum (Figure 1).…”

“…Maximum likelihood tree was constructed according to the method described by Wu et al. ( 2019 ). Phylogenetic maximum likelihood analysis indicated that H. cordata Thunb is closest to P. cenocladum ( Figure 1 ).…”

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

“…The whole genomic DNA re-sequencing was performed on the Illumina Hiseq-2500 platform to generate 125 bp pair-end reads (BIG, Shenzhen, CA, CHN). Totally, we obtained about 7 G high quality reads, which were aligned to chloroplast genomes of six Citrus species according to Wu et al (2019) and Xu et al (2019). Chloroplast genome assembly and annotation were performed according to the method described by Xu et al (2019), and the annotated chloroplast genome has been deposited in Genbank with the accession number MT880606.…”

“…Totally, we obtained about 7 G high quality reads, which were aligned to chloroplast genomes of six Citrus species according to Wu et al. ( 2019 ) and Xu et al. ( 2019 ).…”