Chloroplast genomic characteristics and molecular markers of Prunus conradinae
[Objective]To assemble the chloroplast genome of Prunus conradinae and carry out sequence analysis and preliminary identification of molecular markers.[Method]SPAdes,prodigal v2.6.3,hmmer v3.1b2 and aragorn v1.2.38 software were used to assemble the chloroplast genome,annotate the gene coding region,and predict rRNA and tRNA.The genome map of chloroplast was drawn by OGDRAW.Multiple alignment of chloroplast genome sequences of P.conradinae and 26 subgenus Cerasus species was carried out using DNAMAN software,and the SNP and InDel sites unique to P.conradinae were manually retrieved.Codon W1.4.2 and EMBOSS cusp software were used to analyze the relative synonymous codon usage of genes in chloroplast genome.[Result]The chloroplast genome size of P.conradinae was 158 019 bp,including small single copy(SSC),large single copy(LSC)and inverted repeat(IR),which were 19 247 bp,85 910 bp and 52 862 bp,respectively,and the total GC content was 36.7%.The chloroplast genome of P.conradinae encodes 130 genes,including 8 ribosomal RNA genes,37 transport RNA genes and 85 protein-coding genes.There were 240 SSR sites in the sequence,including 153 single nucleotide repeat sites,12 dinucleotide repeat sites,63 trinucleotide repeat sites,11 tetranucleotide repeat sites,and 1 six-nucleotide repeat site.Through multiple alignment with the chloroplast genome sequences of 26 other subgenus Cerasus species,29 potential species-specific SNP sites and 8 InDel markers were identified.According to the statistics of codons,66 codons of this species encode 21 amino acids,of which 32 codons with RSCU＞1,29 codons end with A/U,and these codons end with A/U preference.[Conclusion]The chloroplast genome of P.conradinae is a typical ring tetrad structure,which is similar in size to the chloroplast genome of other Rosaceae plants.A number of SSR,SNP and InDel markers have been excavated to provide references for the study of lineage geography,population genetics and interspecific hybrid identification of P.conradinae.
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