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Genome-wide identification, characterization of expansin gene family of banana and their expression pattern under various stresses

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Abstract

Expansin, a cell wall-modifying gene family, has been well characterized and its role in biotic and abiotic stress resistance has been proven in many monocots, but not yet studied in banana, a unique model crop. Banana is one of the staple food crops in developing countries and its production is highly influenced by various biotic and abiotic factors. Characterizing the expansin genes of the ancestor genome (M. acuminata and M. balbisiana) of present day cultivated banana will enlighten their role in growth and development, and stress responses. In the present study, 58 (MaEXPs) and 55 (MbaEXPs) putative expansin genes were identified in A and B genome, respectively, and were grouped in four subfamilies based on phylogenetic analysis. Gene structure and its duplications revealed that EXPA genes are highly conserved and are under negative selection whereas the presence of more number of introns in other subfamilies revealed that they are diversifying. Expression profiling of expansin genes showed a distinct expression pattern for biotic and abiotic stress conditions. This study revealed that among the expansin subfamilies, EXPAs contributed significantly towards stress-resistant mechanism. The differential expression of MaEXPA18 and MaEXPA26 under drought stress conditions in the contrasting cultivar suggested their role in drought-tolerant mechanism. Most of the MaEXPA genes are differentially expressed in the root lesion nematode contrasting cultivars which speculated that this expansin subfamily might be the susceptible factor. The downregulation of MaEXPLA6 in resistant cultivar during Sigatoka leaf spot infection suggested that by suppressing this gene, resistance may be enhanced in susceptible cultivar. Further, in-depth studies of these genes will lead to gain insight into their role in various stress conditions in banana.

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Abbreviations

EXP:

Expansin

qRT-PCR:

Quantitative real-time polymerase chain reaction

FAO:

Food and Agriculture Organization

HMM:

Hidden Markov model

PPI:

Protein–protein interaction

MEME:

Multiple Em for motif elucidation

MEGA:

Molecular evolutionary genetics analysis

MeJA:

Methyl jasmonate

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Acknowledgements

This study was supported by Indian Council of Agricultural Research (ICAR), India under the project NPFGGM-Functional Genomics (3020). We express our sincere gratitude to Director, ICAR-National Research Centre for Banana, India for the facilities provided for this project.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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Author notes

  1. Suthanthiram Backiyarani, Chelliah Anuradha and Arumugam chandrasekar have contributed equally to this work.

Authors and Affiliations

  1. ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchchirappalli, Tamil Nadu, 620 102, India

    Suthanthiram Backiyarani, Chelliah Anuradha, Raman Thangavelu, Arumugam Chandrasekar, Baratvaj Renganathan, Parasuraman Subeshkumar, Palaniappan Giribabu & Subbaraya Uma

  2. Department of Agricultural Biotechnology, National Institute of Agricultural Sciences (NAS), RDA, Jeonju, 54874, Korea

    Muthusamy Muthusamy

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  1. Suthanthiram Backiyarani
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  2. Chelliah Anuradha
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Contributions

Conceptualization, resources, writing, and overall monitoring: SBR. Draft preparation, review and editing: CA. Sample preparation and analysis: RT, PG, and MM. Methodology, in silico analysis, work design, and formatting: ACS. qRT-PCR work and data analysis: BR and PSK. Supervision, conceptualization, and project administration: SU.

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Correspondence to Suthanthiram Backiyarani.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 Supplementary file 1 Expansin gene family in banana A & B genome (XLSX 27 KB)

Supplementary file2 Supplementary file 2 Nomenclature of expansin genes in Musa A & B genome (XLSX 13 KB)

Supplementary file3 Supplementary file 3 Motif analysis for Expansin genes in Musa A & B genome (XLSX 14 KB)

Supplementary file4 Supplementary file 4 Synonymous and nonsynonymous substitution of MbEXPs (XLSX 14 KB)

13205_2021_3106_MOESM5_ESM.xlsx

Supplementary file5 Supplementary file 5 Cis acting elements from Expansin gene family promoters of banana A & B genome (XLSX 58 KB)

13205_2021_3106_MOESM6_ESM.xlsx

Supplementary file6 Supplementary file 6 Digital Gene Expression details of MaEXPs between resistant and susceptible cultivars under Sigatoka & Nematode and Drought stress. (XLSX 19 KB)

Supplementary file7 Table S1 Number of expansin genes in five plant species (DOCX 13 KB)

Supplementary file8 Table S2 Synteny relationship between Musa acuminate and Arabidopsis thaliana. (DOCX 21 KB)

Supplementary file9 Table S3 qRT-PCR Primers for the validation of MaEXPs in biotic and abiotic stresses (DOCX 14 KB)

Supplementary file10 Table S4 Expression details of Expansin gene in other crops (DOCX 19 KB)

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Backiyarani, S., Anuradha, C., Thangavelu, R. et al. Genome-wide identification, characterization of expansin gene family of banana and their expression pattern under various stresses. 3 Biotech 12, 101 (2022). https://doi.org/10.1007/s13205-021-03106-x

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