Abstract:
Objective To reveal the structural characteristics and phylogenetic relationships of the chloroplast genomes of Zanthoxylum armatum ‘Jiuyeqing’, and provide reference for identifying germplasm resources, breeding new varieties and the genetic analysis among varieties of the genus Zanthoxylum.
Method The total DNA of Z. armatum ‘Jiuyeqing’ was extracted using a modified CTAB method. High-throughput sequencing was performed using the BGISeq-500 platform, the chloroplast genome was assembled by SPAdes v3.13.0 software, the whole chloroplast genome information of Z. armatum ‘Jiuyeqing’ was annotated by GeSeq software, and the structural characteristics, repetitive sequences, codon preference and phylogenetic relationship were analyzed.
Result Z. armatum ‘Jiuyeqing’ was a typical tetrad structure with a full-length sequence of 158 579 bp, encoding 133 genes. 19 tandem repeats were detected, 49 long repeat sequences, 70 simple sequence repeat (SSR) were detected. A total of 26 398 codons (excluding stop codons) were detected in the protein-coding gene of the chloroplast genome of Z. armatum ‘Jiuyeqing’, and there was a strong A/T base preference at the third base of the codon.
Conclusion The complete chloroplast genome sequences of Z. armatum 'Jiuyeqing' was firstly assembled for the study. The results of phylogenetic analysis show that the genus Zanthoxylum is a monophyletic group, and the Z. armatum 'Jiuyeqing' is closely related to Z. simulans. The results of the study enrich the genetic information of Zanthoxylum and improve important references for Zanthoxylum germplasm resource evaluation, molecular breeding, development of cpSSR molecular markers, and genetic diversity research.
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