Genome-wide identification and expression analysis of orphan genes in twelve Musa (sub)species

Qingwen Ren; Yat-Yuen Lim; Chee How Teo

doi:10.1007/s13205-025-04213-9

Genome-wide identification and expression analysis of orphan genes in twelve Musa (sub)species

3 Biotech. 2025 Feb;15(2):41. doi: 10.1007/s13205-025-04213-9. Epub 2025 Jan 14.

Authors

Qingwen Ren¹, Yat-Yuen Lim², Chee How Teo¹

Affiliations

¹ Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
² Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.

PMID: 39822754
PMCID: PMC11732818 (available on 2026-02-01)
DOI: 10.1007/s13205-025-04213-9

Abstract

Orphan genes (OGs), also known as lineage-specific genes, are species-specific genes that play a crucial role in species-specific adaptations to various stresses. Although OGs have been identified in several plant species, there is no information on OGs in banana genomes. This study aimed to systematically identify OGs in twelve banana (sub)species using comparative genomics. The results showed that OG content varied widely among these (sub)species, from 0.4% in Musa itinerans to 7.3% in Ensete glaucum. Genetic structure analysis showed that banana OGs have significantly shorter protein lengths, smaller molecular weight, fewer exons, and shorter exon lengths than non-orphan genes (NOGs). Subcellular localization predictions showed that banana OGs are mainly found in the chloroplast, nucleus, and cytosol, and are evenly distributed across chromosomes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested that OGs may be involved in cellular processes, metabolic processes, and molecular transport. The transcriptome analysis of 9 AAA cultivars against 4 M. acuminata subspecies genomes showed the OGs content. Analysis of gene expression in M. acuminata subsp. malaccensis showed 75 differentially expressed (DE) OGs in response to abiotic stresses and 46 DE OGs related to biotic stresses, indicating that these OGs might play important roles in response to abiotic and biotic stresses. This study provides a foundation for further in-depth research into the functions of OGs in bananas.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-025-04213-9.

Keywords: Musa; banana; lineage-specific genes; orphan genes; transcriptome.

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