Identification of the Complete Chloroplast Genome of Malus zhaojiaoensis Jiang and Its Comparison and Evolutionary Analysis with Other Malus Species

Abstract

The genus <i>Malus</i> is rich in species and many of its plastid genomes have been released. However, limited resources and few markers are not conducive to the comparison of differences among species and resource identification and evaluation. In this study, the complete chloroplast genome of <i>Malus zhaojiaoensis</i> was studied by NGS sequencing, with a total length of 159998 bp. It consists of four regions, LSC (88,070 bp), IRB (26,359 bp), SSC (19,210 bp) and IRA (26,359 bp). <i>M. zhaojiaoensis</i> cp genome contained a total of 111 genes made up of three classes: 78 coding sequences, 29 tRNA genes, and four rRNA genes. In addition, a total of 91 SSRs and 43 INEs were found in the <i>M. zhaojiaoensis</i> cp genome, which was slightly different from <i>M. baccata</i> and <i>M. hupehensis</i> in number. The analysis of codon usage and RNA editing showed that high-frequency codons tended to end at A/U bases and RNA editing mainly occurred at the second codon. Comparative genome analysis suggested that the cp genomes of eight <i>Malus</i> species had higher overall similarity, but there were more variation hotspots (<i>rps16_trnK-UUU</i>, <i>trnG-UCC_atpA</i>, <i>atpH_atpF</i>, <i>trnT-GGU_psbD</i>, etc.) in the LSC region. By building evolutionary trees, it can be clearly observed that <i>M. zhaojiaoensis</i> formed a large group with eight species of <i>Malus</i>, but was relatively independent in differentiation. In conclusion, this study provides high-quality chloroplast genome resources of <i>M. zhaojiaoensis</i> and discusses the genetic variation characteristics of <i>Malus</i> genus. The findings of this study will provide a good reference for plastid genome assembly and interspecific comparison in the future.