Analyses on chloroplast genome characteristics and phylogeny of Camellia cordifolia
To clarify the structural characteristics of chloroplast genome and phylogenetic relationships of Camellia cordifolia(Metc.)Nakai,the chloroplast genome of C.cordifolia was sequenced for the first time by using the high-throughput sequencing technology based on the Illumina NovaSeq sequencing platform,assembly,annotation,mapping,and sequence characteristic analysis of this genome were performed by using bioinformatics-related softwares,and a phylogenetic tree of 16 species in Camellia Linn.was constructed based on their chloroplast genomes.The results show that the chloroplast genome of C.cordifolia exhibits a typical quadripartite structure,its total length is 156 745 bp,and its total GC content is 37.3％;the genome has 135 genes,including 90 protein-coding genes,37 tRNA genes,and 8 rRNA genes.The codon usage bias analysis shows that the codons of chloroplast genes of C.cordifolia prefer to end with A or U,but the codon usage bias is relatively weak in general.A total of 57 long repeated sequences and 73 simple sequence repeat(SSR)loci are detected in the repeated sequence analysis.The boundary structure analysis of the inverted repeat(IR)region reveals that the gene length and distance from the boundary of rps19,ndhF,and ycfl(pseudogene)are different in different species.The phylogenetic analysis suggests that C.cordifolia has a relatively close genetic relationship with Camellia cuspidata(Kochs)Wright ex Gard.Chron.in the Sect.Theopsis Coh.St.(the bootstrap support rate is 100％).The comprehensive study results show that the length,structure,and arrangement order of chloroplast genome of C.cordifolia are highly conserved,the boundary of IR region has contracted to a certain extent during evolution process,the most frequently used codon is AUU,which encodes isoleucine(Ile),SSR loci dominated by mononucleotide A/T repeats are relatively rich,and the base composition of the chloroplast genome prefers to use A or T;the viewpoint of merging Sect.Eriandria Coh.St.and Sect.Theopsis is supported in terms of molecular phylogeny.
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