Genome-wide characterization of 2OGD superfamily for mining of susceptibility factors responding to various biotic stresses in Musa spp.

Bananas are an important staple food and cash crop, but they are vulnerable to a variety of pests and diseases that substantially reduce yield and quality. Banana diseases are challenging to control and necessitate an integrated strategy, and development of resistant cultivars is one of the effective ways of managing diseases. Lasting disease resistance is the main goal in crop improvement and resistance mediated by a single resistant (R) gene mostly lack durability. However, long-term resistance can be obtained by inactivating susceptibility factors (S), which facilitate pathogen infection and proliferation. Identification and inactivation of susceptibility factors against the major pathogens like Fusarium oxysporum f. sp. cubense (Foc), Pseudocercospora eumusae and Pratylenchus coffeae in banana will be an effective way in developing banana varieties with more durable resistance. Downy mildew resistance 6 (DMR6) and DMR-like oxygenases (DLO1) are one such susceptibility factors and they belong to 2-oxoglutarate Fe(II) dependent oxygenases (2OGD) superfamily. 2OGDs are known to catalyze a plethora of reactions and also confer resistance to different pathogens in various crops, but not much is known about the 2OGD in Musa species. Through a comprehensive genome-wide analysis, 133 and 122 potential 2OGDs were systematically identified and categorized from the A and B genomes of banana, respectively. Real time expression of dmr6 and dlo1 genes showed positive correlation with transcriptome data upon Foc race1 and TR4 infection and examination of expression pattern of Macma4_04_g22670 (Ma04_g20880) and Macma4_02_g13590 (Ma02_g12040) genes revealed their involvement in Foc race1 and TR4 infections, respectively. Further the expression profile of 2OGDs, specifically Macma4_04_g25310 (Ma04_g23390), Macma4_08_g11980 (Ma08_g12090) and Macma4_04_g38910 (Ma04_g36640) shows that they may play a significant role as a susceptibility factor, particularly against P. eumusae and P. coffeae, implying that they can be exploited as a candidate gene for editing in developing resistant cultivars against these diseases. In summary, our findings contribute to a deeper comprehension of the evolutionary and functional aspects of 2OGDs in Musa spp. Furthermore, they highlight the substantial functions of these family constituents in the progression of diseases. These insights hold significance in the context of enhancing the genetic makeup of bananas to attain extended and more durable resistance against pathogens. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01380-y.

Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp.

Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.

A Systematic Phylogenomic Classification of the Multidrug and Toxic Compound Extrusion Transporter Gene Family in Plants.

Multidrug and toxic compound extrusion (MATE) transporters comprise a multigene family that mediates multiple functions in plants through the efflux of diverse substrates including organic molecules, specialized metabolites, hormones, and xenobiotics. MATE classification based on genome-wide studies remains ambiguous, likely due to a lack of large-scale phylogenomic studies and/or reference sequence datasets. To resolve this, we established a phylogeny of the plant MATE gene family using a comprehensive kingdom-wide phylogenomic analysis of 74 diverse plant species. We identified more than 4,000 MATEs, which were classified into 14 subgroups based on a systematic bioinformatics pipeline using USEARCH, blast+ and synteny network tools. Our classification was performed using a four-step process, whereby MATEs sharing ≥ 60% protein sequence identity with a ≤ 1E-05 threshold at different sequence lengths (either full-length, ≥ 60% length, or ≥ 150 amino acids) or retaining in the similar synteny blocks were assigned to the same subgroup. In this way, we assigned subgroups to 95.8% of the identified MATEs, which we substantiated using synteny network clustering analysis. The subgroups were clustered under four major phylogenetic groups and named according to their clockwise appearance within each group. We then generated a reference sequence dataset, the usefulness of which was demonstrated in the classification of MATEs in additional species not included in the original analysis. Approximately 74% of the plant MATEs exhibited synteny relationships with angiosperm-wide or lineage-, order/family-, and species-specific conservation. Most subgroups evolved independently, and their distinct evolutionary trends were likely associated with the development of functional novelties or the maintenance of conserved functions. Together with the systematic classification and synteny network profiling analyses, we identified all the major evolutionary events experienced by the MATE gene family in plants. We believe that our findings and the reference dataset provide a valuable resource to guide future functional studies aiming to explore the key roles of MATEs in different aspects of plant physiology. Our classification framework can also be readily extendable to other (super) families.

Phylogenomic classification and synteny network analyses deciphered the evolutionary landscape of aldo-keto reductase (AKR) gene superfamily in the plant kingdom.

Aldo-keto reductase-domain (PF00248) containing proteins (AKRs) are NAD(P)(H)-dependent oxidoreductases of a multigene superfamily that mediate versatile functions in plants ranging from detoxification, metal chelation, potassium ion efflux to specialized metabolism. To uncover the complete repertoire of AKR gene superfamily in plants, a systematic kingdom-wide identification, phylogeny reconstruction, classification and synteny network clustering analyses were performed in this study using 74 diverse plant genomes. Plant AKRs were omnipresent, legitimately classified into 4 groups (based on phylogeny) and 14 subgroups (based on the ≥ 60% of protein sequence identity). Species composition of AKR subgroups highlights their distinct emergence during plant evolution. Loss of AKR subgroups among plants was apparent and that various lineage-, order/family- and species-specific losses were observed. The subgroups IA, IVB and IVF were flourished and diversified well during plant evolution, likely related to the complexity of plant's specialized metabolism and environmental adaptation. About 65% of AKRs were in genomic synteny regions across the plant kingdom and the AKRs relevant to important functions (e.g. vitamin B6 metabolism) were in profoundly conserved angiosperm-wide synteny communities. This study underscores the evolutionary landscape of plant AKRs and provides a comprehensive resource to facilitate the functional characterization of them.

Influence of food hydrocolloids on the structural, textural and chemical characteristics of low-fat banana chips.

Banana chips are gaining popularity as a deep-fried product for its unique taste and flavour. This study is aimed to investigate the effect of hydrocolloids on oil absorption, physico-chemical and sensory properties of banana chips from two different varieties (var. Popoulu and var. Nendran), when fried at 180 °C for 3 min. The reduction in oil content was about 15%-35% and 19%-30% for hydrocolloid treated Popoulu and Nendran chips, respectively. The Free fatty acid content (FFA) of hydrocolloid treated banana chips was lower than that of untreated chips. The peroxide value (PV) values of all samples fell below 2 meq oxygen kg-1. CMC pre-treated banana chips were crispier than other formulations on both the varieties. Microscopic analysis showed the improved cellular integrity without large void spaces in hydrocolloid treated banana chips. PCA analyses elucidated that variables such as physical appearance, colour, crispiness, after taste, overall acceptability contributed positively, whereas hardness and sogginess contributed negatively to the correlation among the variables. From the chemical and sensory attributes, 0.5% CMC treated Popoulu chips and 1% CMC treated Nendran chips is recommended to produce chips with lower oil content.

Genome-scale analyses of polyketide synthases in banana: Phylogenetics and expression profiling forecast their candidacy in specialized metabolism.

Plant type III polyketide synthases (PKSs) are associated with various functions in plant growth, development and defense by providing a multitude of polyketide scaffolds for diverse specialized metabolic pathways (SMPs). To decipher banana PKSs involved in specialized metabolism, genome-wide comparative analyses were conducted with A (Musa acuminata) and B (Musa balbisiana) genomes of banana. Both genomes retained eight chalcone synthases (CHSs), seven curcumin synthases (CURSs), three diketidyl-CoA synthases (DCSs) and one anther specific CHS (ASC). Segmental (42%) and tandem (37%) duplication events majorly flourished the banana PKS family. Six of 19 PKSs of A genome (designated as MaPKSs) showed relatively a higher expression in the root, corm, sheath, leaf and embryogenic cell suspension (ECS) of banana. To determine the defense response of MaPKSs and to highlight their candidacy in various SMPs, expression profiling was conducted by qPCR in ECSs treated with 100/200 µM of jasmonic acid (JA) and salicylic acid (SA) at 24/48 h. Maximum and subordinate expression induction of MaPKSs was apparent respectively against JA and SA treatments. Notably, most MaPKSs achieved their peak expression within 24 h of JA and the total flavonoid content was reached maximum within 24 h of JA/SA elicitations. Considering the homology, phylogeny, and expression levels in each analyzed sample (n = 13), three CHSs, three DCSs along with three CURSs and one ASC were selected as most promising candidates respectively for flavonoids, phenylphenalenones and sporopollenin biosynthesis in banana. Our findings provide a first-line resource to disclose the functions of banana PKSs involved in distinct SMPs.

Molecular analysis of somatic embryogenesis through proteomic approach and optimization of protocol in recalcitrant Musa spp.

Somatic embryogenesis (SE) is a complex stress related process regulated by numerous biological factors. SE is mainly applicable to mass propagation and genetic improvement of plants through gene transfer technology and induced mutations. In banana, SE is highly genome dependent as the efficiency varies with cultivars. To understand the molecular mechanism of SE, a proteomics approach was carried out to identify proteins expressed during embryogenic calli (EC) induction, regeneration and germination of somatic embryos in the banana cultivar cv. Rasthali (AAB). In total, 70 spots were differentially expressed in various developmental stages of SE, of which 16 were uniquely expressed and 17 were highly abundant in EC compared to non-embryogenic calli and explants. Also, four spots were uniquely expressed in germinating somatic embryos. The functional annotation of identified proteins revealed that calcium signaling along with stress and endogenous hormones related proteins played a vital role in EC induction and germination of somatic embryos. Thus, based on this outcome, the callus induction media was modified and tested in five cultivars. Among them, cultivars Grand Naine (AAA), Monthan (ABB) and Ney Poovan (AB) showed a better response in tryptophan added media, whereas Red Banana (AAA) and Karpuravalli (ABB) showed maximum EC induction in kinetin and CaCl2 supplemented media respectively. Simultaneously, germination media were modified to induce proteins responsible for germination. In cv. Rasthali, media supplemented with 10 mM CaCl2 showed a maximum increase in germination (51.79%) over control plants. Thus, the present study revealed that media modification based on proteomic analysis can induce SE in recalcitrant cultivars and also enhance germination in cultivars amenable for SE.

Comparison of two different electrophoretic methods in studying the genetic diversity among plantains (Musa spp.) using ISSR markers.

Inter simple sequence repeat markers were employed for the genotyping of 16 plantain ecotypes. Two different electrophoretic systems namely conventional gel electrophoresis (CVGE) and fully automated high-resolution CGE were used to evaluate the genetic diversity. Comparative analysis indicated that all parameters related to marker informativeness were higher in CGE except polymorphic information content. But genetic diversity parameters like effective number of alleles, Nei's gene diversity (1973) and Shannon's information index showed higher values (1.52 ± 0.12, 0.34 ± 0.05 and 0.52 ± 0.05, respectively) in CVGE as against CGE (1.29 ± 0.04, 0.22 ± 0.02 and 0.38 ± 0.03, respectively) system. The unweighed pair group method with arithmetic averages was used to obtain the dendrogram for both analyses. The results of dendrogram and principal component analysis were found to be consistent in both systems except for some minor disagreements. The clone-specific bands could be used in the identification and development of SCAR markers. Inter simple sequence repeat markers used in this study provided sufficient polymorphism and reproducible banding pattern for evaluating the genetic diversity of different plantain ecotypes. Lack of accuracy and consistency of the CVGE warrants the employment of high-throughput CGE for diversity analysis as it provided better separation of bands with higher resolution.

Evolutionary Expansion of WRKY Gene Family in Banana and Its Expression Profile during the Infection of Root Lesion Nematode, Pratylenchus coffeae.

The WRKY family of transcription factors orchestrate the reprogrammed expression of the complex network of defense genes at various biotic and abiotic stresses. Within the last 96 million years, three rounds of Musa polyploidization events had occurred from selective pressure causing duplication of MusaWRKYs with new activities. Here, we identified a total of 153 WRKY transcription factors available from the DH Pahang genome. Based on their phylogenetic relationship, the MusaWRKYs available with complete gene sequence were classified into the seven common WRKY sub-groups. Synteny analyses data revealed paralogous relationships, with 17 MusaWRKY gene pairs originating from the duplication events that had occurred within the Musa lineage. We also found 15 other MusaWRKY gene pairs originating from much older duplication events that had occurred along Arecales and Poales lineage of commelinids. Based on the synonymous and nonsynonymous substitution rates, the fate of duplicated MusaWRKY genes was predicted to have undergone sub-functionalization in which the duplicated gene copies retain a subset of the ancestral gene function. Also, to understand the regulatory roles of MusaWRKY during a biotic stress, Illumina sequencing was performed on resistant and susceptible cultivars during the infection of root lesion nematode, Pratylenchus coffeae. The differential WRKY gene expression analysis in nematode resistant and susceptible cultivars during challenged and unchallenged conditions had distinguished: 1) MusaWRKYs participating in general banana defense mechanism against P.coffeae common to both susceptible and resistant cultivars, 2) MusaWRKYs that may aid in the pathogen survival as suppressors of plant triggered immunity, 3) MusaWRKYs that may aid in the host defense as activators of plant triggered immunity and 4) cultivar specific MusaWRKY regulation. Mainly, MusaWRKY52, -69 and -92 are found to be P.coffeae specific and can act as activators or repressors in a defense pathway. Overall, this preliminary study in Musa provides the basis for understanding the evolution and regulatory mechanism of MusaWRKY during nematode stress.