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Background  Lima bean ( Phaseolus lunatus  L.) is a member of subfamily Phaseolinae belonging to the family Leguminosae and an important source of plant proteins for the human diet. As we all know, lima beans have important economic value and great diversity. However, our knowledge of the chloroplast genome level of lima beans is limited.    Results  The chloroplast genome of lima bean was obtained by Illumina sequencing technology for the first time. The Cp genome with a length of 150,902 bp, including a pair of inverted repeats (IRA and IRB 26543 bp each), a large single-copy (LSC 80218 bp) and a small single-copy region (SSC 17598 bp). In total, 124 unique genes including 82 protein-coding genes, 34 tRNA genes, and 8 rRNA genes were identified in the  P. lunatus  Cp genome. A total of 61 long repeats and 290 SSRs were detected in the lima bean Cp genome. It has a typical 50 kb inversion of the Leguminosae family and an 70 kb inversion to subtribe Phaseolinae.  rpl16 ,  accD ,  petB ,  rsp16 ,  clpP ,  ndhA ,  ndhF  and  ycf1  genes in coding regions was found significant variation, the intergenic regions of  trnk - rbcL ,  rbcL - atpB ,  ndhJ - rps4 ,  psbD - rpoB ,  atpI - atpA ,  atpA - accD ,  accD - psbJ ,  psbE - psbB ,  rsp11 - rsp19 ,  ndhF - ccsA  was found in a high degree of divergence. A phylogenetic analysis showed that  P. lunatus  appears to be more closely related to  P. vulgaris ,  V.unguiculata  and  V. radiata .    Conclusions  The characteristics of the lima bean Cp genome was identified for the first time, these results will provide useful insights for species identification, evolutionary studies and molecular biology research.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07467-8.

Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes