Genome wide identification of MADS box gene family in Musa balbisiana and their divergence during evolution

•Identification of 97 MADS box genes in Musa balbisiana by analysing the whole genome. Using HMM search and Blast search the whole genome of Musa balbisiana was analysed and initially 119 MADS-box genes were identified.. Subsequent to domain analysis by Pfam and SMART, only 97 genes from Musa balbisiana respectively were considered as MADS-box encoding genes.•Study of evolutionary divergence of MADS gene between Musa balbisiana and Musa acuminate The expansion of the MADS box genes in Musa sp can be attributed to the αβ whole genome duplication which occurred around 65 mya (Ks median of 0.6). It can clearly be seen that the MADS box genes in Musa acuminata diverged more than in Musa balbisiana.•Structural differences in ripening related MADS - RIN genes in Musa balbisiana and Musa acuminata. Out of 11 MADS-RIN genes from Musa acuminata, orthologs for only 2 genes were identified in Musa balbisiana. The structural analysis revealed that there proteins are structurally very divergent. There were gaps in the alignments and the protein structures did not overlap.•Neofunctionalization of duplicated MADS genes in Musa acuminata with reference to fruit development and ripening. Many of the MADS box genes in Musa acuminata had more than one duplicated genes due to the multiple rounds of whole genome duplications and also had differential functions. The functional differences between the expression of duplicated gene pairs also explains the reason for the retention of these genes during the course of evolution.•The MADS box genes of Musa balbisiana behaved liked the MADS genes of non-climacteric fruits and hence the fruit ripening in Musa balbisiana is slow. The coexpression networks of MADS box genes from Musa acumiata showed interactions with many ripening related genes with two MADS box genes MADS8 and MADS10 being the hub genes. However no ripening related genes were identified in the co-expression networks of MADS box genes in Musa balbisiana, showing that these genes were not involved during the ripening of the fruit. Hence the ripening pattern of Musa balbisiana is like non-climacteric fruits. MADS box gene family is transcription factor gene family that is involved in growth and development of eukaryotes. In plants the MADS box gene family is mainly associated with floral meristem identity and flower development, apart from being involved in nearly all the phases of plant growth. The MADS box gene family has also been shown to be involved during fruit devel