β-carotene is an important nutritious content in banana. However, its lifetime depends on the enzymes controlling its conversion into strigolactone. To understand the involved enzymes’ activity, which are β-carotene isomerase (D27), carotenoid cleavage dioxygenase 7 (CCD7), and CCD8, would be the key to manipulate the rate of β-carotene degradation. In this research, we characterized the structure of genes and proteins of the D27, CCD7, and CCD8 from Musa acuminata ‘DH-Pahang’ and Musa balbisiana ‘Pisang Klutuk Wulung’ (PKW). We aligned the corresponding sequence of genes from both species to determine similarity and intron/exon positions. We also identified domains and motifs in the sequences of putative proteins of D27, CCD7, and CCD8. We found that D27, CCD7, and CCD8 genes in DH-Pahang and PKW comprise of various nucleotide sequence length, putative proteins, and numbers and length of exons and introns. However, the putative proteins possess the same domains: DUF4033 (domain of unknown function) in D27 and RPE65 (retinal pigment epithelium) in CCD7 and CCD8. Phylogenetic trees showed that D27, CCD7, and CCD8 proteins from DH-Pahang and PKW are conserved and clustered in the same clades with the same proteins of monocot plants. Hence, the results could be useful for future research in optimizing β-carotene content in banana.

• Ahrazem, O., Gómez-Gómez, L., Rodrigo, M. J., Avalos, J., & Limón, M. C. (2016). Carotenoid cleavage oxygenases from microbes and photosynthetic organisms: Features and functions. International Journal of Molecular Sciences, 17(11), 1781. https://doi.org/10.3390/ijms17111781

• Alder, A., Jamil, M., Marzorati, M., Bruno, M., Vermathen, M., Bigler, P., Ghisla, S., Bouwmeester, H., Beyer, P., & Al-Babili, S. (2012). The path from β-carotene to carlactone, a strigolactone-like plant hormone. Science, 335(6074), 1348–1351. https://doi.org/10.1126/science.1218094

• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

• Bailey, T. L., & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings International Conference on Intelligent Systems for Molecular Biology, 2, 28–36.

• Batra, R., Agarwal, P., Tyagi, S., Saini, D. K., Kumar, V., Kumar, A., Kumar, S., Balyan, H. S., Pandey, R., & Gupta, P. K. (2019). A study of CCD8 genes/proteins in seven monocots and eight dicots. PLOS One, 14(3), 1–21. https://doi.org/10.1371/journal.pone.0213531

• Buah, S. (2015). Regulation of carotenoid biosynthesis in banana fruit (Doctoral thesis, Queensland University of Technology, Australia). Queensland University of Technology ePrints. https://eprints.qut.edu.au/82719/

• Calberto, G., Staver, G. C., & Siles, P. (2015). An assessment of global banana production and suitability under climate change scenarios. In A. Elbehri (Ed.), Climate change and food systems: Global assessments and implications for food security and trade (pp. 266-291). Food Agriculture Organization of the United Nations (FAO).

• Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2016). GenBank. Nucleic Acids Research, 44(D1), D67-D72. https://doi.org/10.1093/nar/gkv1276

• D’Hont, A., Denoeud, F., Aury, J.-M., Baurens, F.-C., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengellé, J., Rodier-Goud, M., … Wincker, P. (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410), 213–217. https://doi.org/10.1038/nature11241

• Davey, M. W., Gudimella, R., Harikrishna, J. A., Sin, L. W., Khalid, N., & Keulemans, J. (2013). “A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”. BMC Genomics, 14(1), 683. https://doi.org/10.1186/1471-2164-14-683

• Englberger, L., Wills, R. B. H., Blades, B., Dufficy, L., Daniells, J. W., & Coyne, T. (2006). Carotenoid content and flesh color of selected banana cultivars growing in Australia. Food and Nutrition Bulletin, 27(4), 281–291. https://doi.org/10.1177/156482650602700401

• Florea, L., Hartzell, G., Zhang, Z., Rubin, G. M., & Miller, W. (1998). A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Research, 8(9), 967–974. https://doi.org/10.1101/gr.8.9.967

• Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.

• Häuser, R., Pech, M., Kijek, J., Yamamoto, H., Titz, B., Naeve, F., Tovchigrechko, A., Yamamoto, K., Szaflarski, W., Takeuchi, N., Stellberger, T., Diefenbacher, M. E., Nierhaus, K. H., & Uetz, P. (2012). RsfA (YbeB) proteins are conserved ribosomal silencing factors. PLOS Genetics, 8(7), e1002815. https://doi.org/10.1371/journal.pgen.1002815

• Huelsenbeck, J. P., & Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England), 17(8), 754–755. https://doi.org/10.1093/bioinformatics/17.8.754

• Jones, P., Binns, D., Chang, H.-Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador-Vegas, A., Scheremetjew, M., Yong, S.-Y., Lopez, R., & Hunter, S. (2014). InterProScan 5: Genome-scale protein function classification. Bioinformatics, 30(9), 1236–1240. https://doi.org/10.1093/bioinformatics/btu031

• Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., & Lopez, R. (2019). The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research, 47(W1), W636–W641. https://doi.org/10.1093/nar/gkz268

• Marchler-Bauer, A., Bo, Y., Han, L., He, J., Lanczycki, C. J., Lu, S., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Lu, F., Marchler, G. H., Song, J. S., Thanki, N., Wang, Z., Yamashita, R. A., Zhang, D., … Bryant, S. H. (2017). CDD/SPARCLE: Functional classification of proteins via subfamily domain architectures. Nucleic Acids Research, 45(D1), D200–D203. https://doi.org/10.1093/nar/gkw1129

• Mathew, D., & Muhammed, T. A. (2015). Nutritional studies on lesser known wild edible bananas from Western Ghats, India. Global Journal of Research on Medical Plants and Indigenous Medicine, 3(4), 127–133.

• Mishra, S., Upadhyay, S., & Shukla, R. K. (2017). The role of strigolactones and their potential cross-talk under hostile ecological conditions in plants. Frontiers in Physiology, 7, 691. https://doi.org/10.3389/fphys.2016.00691

• Notredame, C., Higgins, D. G., & Heringa, J. (2000). T-coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1), 205–217. https://doi.org/10.1006/jmbi.2000.4042

• Page, R. D. (1996). Tree View: An application to display phylogenetic trees on personal computers. Bioinformatics, 12(4), 357–358. https://doi.org/10.1093/bioinformatics/12.4.357

• Ronquist, F., & Huelsenbeck, J. P. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19(12), 1572–1574. https://doi.org/10.1093/bioinformatics/btg180

• Solovyev, V., Kosarev, P., Seledsov, I., & Vorobyev, D. (2006). Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biology, 7(Suppl 1), S10. https://doi.org/10.1186/gb-2006-7-s1-s10

• Wang, Y., Ding, G., Gu, T., Ding, J., & Li, Y. (2017). Bioinformatic and expression analyses on carotenoid dioxygenase genes in fruit development and abiotic stress responses in Fragaria vesca. Molecular Genetics and Genomics, 292(4), 895–907. https://doi.org/10.1007/s00438-017-1321-5

• Waters, M. T., Brewer, P. B., Bussell, J. D., Smith, S. M., & Beveridge, C. A. (2012). The Arabidopsis ortholog of rice DWARF27 acts upstream of MAX1 in the control of plant development by strigolactones. Plant Physiology, 159(3), 1073–1085. https://doi.org/10.1104/pp.112.196253