Hybrid Assembly-Based Genomic Analysis for the Identification and Characterisation of Flowering Genes in Musa acuminata subsp. sumatrana (Becc.) Ahmad, Volkaert, Sulist. & Poerba

¹ Biochemistry Department, Faculty of Mathematics and Natural Science, 16680, Indonesia
² Research Center for Applied Botany, Organization for Research on Life Sciences and the Environment, BRIN, Indonesia

^* Corresponding author: imart@apps.ipb.ac.id

Abstract

Musa acuminata subsp. sumatrana exhibits rare productivity advantages (± 20 hands/bunch, 35% > Cavendish). This research aims to characterize the genome of Musa acuminata subsp. sumatrana through Whole Genome Sequencing (WGS) by comparing long-read PromethION data and short-read Illumina data for in silico identification of flowering genes. The hybrid assembly method integrated PromethION ONT and Illumina (N50 4,097 bp; 13.9 Gb), followed by gene annotation using BRAKER3 and FunAnnotate. The results identified 51,358 genes, including 12 significant genes: MADS-box (AGL11, SOC1, AGL12), Myb (RS1, RS2, NUCT14, PLAT1, PUB13), AP2/ERF (RAV2, LOGL3), and QUIRKY (FTIP7, CNOT9). Two new genes (RAV2 and LOGL3) from the AP2/ERF domain were identified to be associated with flowering in bananas for the first time, but their functional roles still need to be validated. High expression of AGL11 correlates with increased seed formation, while the adaptive divergence of SOC1 (NJ:0.59) reflects tropical photoperiod selection. GO enrichment confirms the dominance of the "flower development" process (FDR < 1.0e⁻⁷), with the regulatory mechanism: environmental stimulus → CO/QUIRKY → phase transition → flower differentiation and fruit initiation by MADS-box and AP2/ERF-Myb. This study concludes that the subspecies has the potential to be a source of superior alleles for high-yield banana breeding.