Chloroplast genome characteristics and codon usage preference of Solanum tuberosum var.cormosus'Huaiyushan'
[Objective]This study aims to analyze the chloroplast genome characteristics and codon usage preference of Solanum tuberosum var.cormosus'Huaiyushan',so as to provide a reference and theoretical basis for future research on chloroplast genome codon optimization,chloroplast genome modification,exploration of species evolution,and increased expression of exogenous genes.[Method]The chloroplast genome of S.tuberosum var.cormosus'Huaiyushan'was sequenced by high-throughput sequencing technology.The structure,gene composition and codon preference of the assembled and annotated chloroplast genome were analyzed using bioinformatics analysis software.[Result]The chloroplast genome size of S.tuberosum var.cormosus'Huaiyushan'was 155 296 bp,which was a classical 4-segment structure.The length of large single copy region(LSC),small single copy region(SSC)and inverted repeat region(IR)was 85 737,18 373 and 25 593 bp respectively,and the proportion of total guanine and cytosine(GC ratio)was 37.88％.A total of 133 genes were released,including 87 CDS genes,37 tRNA genes,8 rRNA genes and 1 pseudogene.A total of 38 simple sequence repeat(SSR)loci(36 single base repeats and 2 double base repeats)and 32 long repeat sequences(16 forward repeats and 16 palindrome repeats)were detected in the chloroplast genome of SS.tuberosum var.cormosus'Huaiyushan'.The variation range of nucleotide diversity of chloroplast genome of S.tuberosum var.cormosus'Huaiyushan'was 0-0.139 27.The hypervariable regions were mainly distributed in LSC and SSC regions.LSC region had the highest mutation rates of trnL-UAA-trnF-GAA,cemA,rps12-exon1-clpP1 and clpP1 genes,while SSC region had the highest mutation rates of rpl32-trnL-UAG andycfl genes.The average effective number of codon(ENC)value of 87 CDS genes in the chloroplast genome of S.tuberosum var.cormosus'Huaiyushan'was 47.29,and there were 60 genes with ENC value larger than 45,indicating weak codon preference.The preference for codons ending with A and U in the chloroplast genome of S.tuberosum var.cormosus'Huaiyushan'was largely affected by natural selection,and less affected by mutation pressure.CGU,AAA,CUU,GUU,GGA,GUA,GGU,UCA,GCU,and CCU were the 10 best codons in the chloroplast genome of S.tuberosum var.cormosus'Huaiyushan'.[Conclusion]S.tuberosum var.cormosus'Huaiyushan'has a close genetic relationship with S.tuberosum'Desiree'.[Ch,5 fig.3 tab.41 ref.]
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