Genome-wide identification and characterization of DTX family genes highlighting their locations, functions, and regulatory factors in banana (Musa acuminata)

Abstract

The detoxification efflux carriers (DTX) are a significant group of multidrug efflux transporter family members that play diverse functions in all kingdoms of living organisms. However, genome-wide identification and characterization of DTX family transporters have not yet been performed in banana, despite its importance as an economic fruit plant. Therefore, a detailed genome-wide analysis of DTX family transporters in banana (Musa acuminata) was conducted using integrated bioinformatics and systems biology approaches. In this study, a total of 37 DTX transporters were identified in the banana genome and divided into four groups (I, II, III, and IV) based on phylogenetic analysis. The gene structures, as well as their proteins' domains and motifs, were found to be significantly conserved. Gene ontology (GO) annotation revealed that the predicted DTX genes might play a vital role in protecting cells and membrane-bound organelles through detoxification mechanisms and the removal of drug molecules from banana cells. Gene regulatory analyses identified key transcription factors (TFs), cis-acting elements, and post-transcriptional regulators (miRNAs) of DTX genes, suggesting their potential roles in banana. Furthermore, the changes in gene expression levels due to pathogenic infections and non-living factor indicate that banana DTX genes play a role in responses to both biotic and abiotic stresses. The results of this study could serve as valuable tools to improve banana quality by protecting them from a range of environmental stresses.

Fig 1. The procedural diagram outlining the operations conducted in this study.

Fig 2. The neighbor-joining (NJ) phylogenetic tree of banana and Arabidopsis DTX proteins.

Different groups are indicated by the different colors (Group I in green, Group II in orange, Group III in blue and Group IV in red). ‘MaDTX’ denotes DTX members from banana, ‘AtDTX’ denotes DTX members from Arabidopsis.

Fig 3. The conserved domains of the DTX family proteins in M. acuminata and A. thaliana were drawn using Pfam database information.

(A) Group I, (B) Group II, (C) Group IV, (D) Group III.

Fig 4. The conserved motif composition of the DTX family proteins in M. acuminata and A. thaliana.

Different colors indicated different motifs, where top 12 motifs are displayed. (A) Group I, (B) Group II, (C) Group IV, (D) Group III.

Fig 5. Exon-intron structure of the DTX family genes in M. acuminata and A. thaliana.

The rounded rectangle boxes represent CDS, lines represent introns. The scale at the bottom can be used to estimate the length of genes. (A) Group I, (B) Group II, (C) Group IV, (D) Group III.

Fig 6. Sub-cellular localization of the predicted MaDTX proteins in M. acuminata.

The numbers roughly indicate the number of nearest neighbors to the query predicted protein sequences which localize to each site. Here, plasma membrane (Plas), nucleus (Nucl), cytoplasm (Cyto), mitochondria (Mito), vacuole (Vacu), cytoskeleton (Cysk), chloroplast (Chlo), endoplasmic reticulum (E.R), golgi apparatus (Golg), peroxisome (Pero), and extracellular (Extra). The numbers roughly indicate the number of nearest neighbors to the query predicted protein sequences which localize to each site.

Fig 7. The heatmap for the predicted GO terms corresponding to the predicted MaDTX genes in banana.

The pink, blue and sky blue color represent presence and white color indicate absent of the genes.

Fig 8. The regulatory network among the TFs and MaDTX proteins.

The nodes of the network were colored based on DTX genes and TFs. DTX genes were represented by orange color and the TALE, ERF and pink, blue and green color stand in for other TFs.

Fig 9. The regulatory network among the predicted miRNA and MaDTX genes.

The square and round boxes represent the targeted MaDTX genes and miRNA. The cyan circle represent the miRNAs related to growth, development and protection of banana plant.

Fig 10. The cis-regulatory elements in 1.5 kb upstream region of the identified MaDTX genes.

The deep color with circular rectangle shapes represent the presence of that elements alongside their respective genes.

Fig 11. The heatmap of the MaDTX genes in response to F. oxysporum (race 1 & 4) and low-nitrogen stress.

TPM and FPKM values were transformed by log2.