Comparative RNA-seq analysis of resistant and susceptible banana genotypes reveals molecular mechanisms in response to Banana bunchy top virus (BBTV)

Lantican, D. V.; Nocum, J. D. L.; Manohar, A. N. C.; Mendoza, J.-V. S.; Gardoce, R. R.; Lachica, G. C.; Gueco, L. S.; Dela Cueva, F. M.

doi:10.1101/2022.09.08.507103

bioRxiv · 10.1101/2022.09.08.507103

Comparative RNA-seq analysis of resistant and susceptible banana genotypes reveals molecular mechanisms in response to Banana bunchy top virus (BBTV)

Lantican, D. V.·Nocum, J. D. L.·Manohar, A. N. C.·Mendoza, J.-V. S.·Gardoce, R. R.·Lachica, G. C.·Gueco, L. S.·Dela Cueva, F. M.

View original source ↗Export metadata ↓

Abstract

Banana is a major fruit crop in the Philippines and remains to be a large contributor to the countrys dollar reserve. Among the main hindrances in global banana production, diseases such as Banana bunchy top disease (BBTD) caused by BBTV can bring catastrophic loss to any banana plantation. To elucidate the resistance mechanism and understand the interplay of host factors in the presence of the invading pathogen, we implemented RNA-seq-based comparative transcriptomics analyses of mock- and BBTV-inoculated resistant (wild M. balbisiana) and susceptible (M. acuminata Lakatan) banana genotypes. Similar patterns of expression for 119 differentially expressed genes (DEGs) were observed on both genotypes, representing the typical defense response of banana to BBTV. A set of 173 DEGs specific to the susceptible Lakatan banana cultivar revealed potential host factors and susceptibility mechanisms involved in successful BBTV infection. Further, differential transcriptomic analysis revealed 268 DEGs exclusive to the resistant wild M. balbisiana, unraveling insights into the complex resistance mechanisms involved in BBTV defense such as pathogen perception, phytohormone action, reactive oxygen species (ROS), hypersensitive response (HR), production of secondary metabolites and cell wall modification. The DEGs identified in this study will aid in the design of foreground markers for the precise integration of resistance genes during marker-assisted breeding programs. Furthermore, the application of these results will also enable the foreseen deployment of genome-edited banana cultivars targeting the resistance and host factor genes towards a future-proof banana industry.

Source connections

Published article ↗

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Lantican, D. V., Nocum, J. D. L., Manohar, A. N. C., Mendoza, J.-V. S., Gardoce, R. R., Lachica, G. C., Gueco, L. S., Dela Cueva, F. M.. 2022-09-12. Comparative RNA-seq analysis of resistant and susceptible banana genotypes reveals molecular mechanisms in response to Banana bunchy top virus (BBTV). https://doi.org/10.1101/2022.09.08.507103

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗

bioRxiv2026

Targeted CRISPRi screening reveals unexpected resilience across the RNA polymerase III transcriptome

Increased RNA polymerase III (Pol III) activity and tRNA abundance are widely linked to cancer cell growth, yet the functional requirement for individual Pol III genes and core components remains unclear, in part due to the difficulty of achieving gene-specific perturbation of highly conserved loci. Here, we developed an inducible CRISPR interference platform and a custom single-guide RNA (sgRNA) library enabling gene-specific targeting of Pol III-transcribed genes and Pol III machinery. Genome-wide screening identified several Pol III dependencies in diploid fibroblasts and HEK293T cells, including multiple initiator methionine tRNA genes among the strongest fitness dependencies. Unexpectedly, glioblastoma models remained largely insensitive to repression of both individual Pol III genes and core Pol III components, despite efficient target repression. These findings establish a general strategy for gene-specific interrogation of conserved Pol III genes and indicate that glioblastoma models tolerate extensive perturbation of Pol III genes and machinery.

genomics↗