Biology subjects

Wicaksono, A.

Publications and source records attributed to Wicaksono, A..

3 recordsLinked to original sources

bioRxiv2026

Reference-guided comparative genomics of seven Indonesian rice cultivars identifies conserved gene space and trait-associated sequence candidates

Indonesian rice cultivars represent valuable genetic resources, yet many remain poorly characterized at the genomic level. Here, we generated 95.40 Gb of PacBio HiFi sequence data from seven Indonesian rice cultivars and constructed cultivar-specific consensus genomes using the telomere-to-telomere Nipponbare reference AGIS1.0. Sequencing coverage ranged from 27.92x to 41.58x, and the resulting consensus genomes spanned 387.93-390.54 Mb, with BUSCO completeness of approximately 98.3-98.5%. OrthoFinder assigned 99.1% of predicted proteins to 40,737 orthogroups, including 27,514 core orthogroups represented across all seven cultivars, indicating a highly conserved predicted gene space within the reference-guided framework. Targeted analysis recovered 278 of 280 cultivar-by-locus combinations representing 40 genes or gene family entries associated with grain pigmentation, nitrogen and amino-acid metabolism, and starch properties. Comparative predicted protein analysis prioritized ANS1, SBE2b, SSIIa/ALK, Wx/GBSSI, OsAAP6/qPC1, and SSI as candidates for further investigation. Among 269 completed AGIS1.0-anchored promoter comparisons, 159 passed quality-control criteria, whereas 110 were flagged for gene-model, boundary, synteny, or structural concerns. Notably, these flagged comparisons accounted for more than 90% of the alignment-derived sequence variation, emphasizing the importance of rigorous quality control when interpreting apparent promoter divergence. Collectively, these reference-guided genomic resources provide a standardized framework for investigating sequence variation in Indonesian rice germplasm and prioritize testable coding and regulatory candidates for functional validation and future genomics-assisted crop improvement.

genomics↗

bioRxiv2026

Untargeted metabolomics reveals host responses and metabolites linked to host compatibility in Rafflesiaceae parasitism

Rafflesiaceae, including Rafflesia, Sapria, and Rhizanthes, are some of the rarest flowering plants in the world, known for producing the largest blooms on Earth. These holoparasites depend exclusively on Tetrastigma (Vitaceae) vines, yet the chemical basis for this host specificity is poorly understood, complicating conservation efforts. Untargeted negative-ion LC- MS metabolomics was used to profile Rafflesiaceae buds and seeds, infected Tetrastigma hosts associated with Rafflesia lagascae, R. speciosa, and Sapria himalayana, uninfected Tetrastigma hosts, and corresponding non-host species from the Philippines and Thailand. Python scripts used for data processing and visualization were developed with generative AI assistance and validated by the authors. Principal component analysis revealed distinct metabolomic profiles across samples, with significant shifts in host metabolites upon infection. Infected Tetrastigma tissues showed nominal enrichment in phenylpropanoid and gibberellin-related metabolites, suggestive of defense and hormonal pathway activation during Rafflesia infection, as well as citric acid, suggesting increased energy demand to support the parasite. Non-host Tetrastigma species showed nominal enrichment in metabolites putatively annotated as stilbenoids, resveratrol diglucosides, and condensed tannins such as procyanidin B2, compounds broadly associated with plant defense. Rafflesia seeds harbored fatty acids/oxylipins, while Rafflesia buds accumulated gallic acid derivatives, compounds also reported in galls. These findings support a chemically mediated model of host compatibility and parasitism, with implications for the ex-situ conservation of these endangered plants.

plant biology↗

bioRxiv2026

Deciphering Parasitic Strategies: Dual Transcriptomics Reveal Distinct Infection Mechanisms and Gall-like Traits in Rafflesiaceae

Rafflesiaceae, known for producing the largest flowers in the world, are obligate parasites that exclusively infect Tetrastigma sp. (Vitaceae). Despite their unique biology, the interactions between parasitic tissues and host roots remain poorly understood, particularly during the flower morphogenesis phase, where parasitic tissue erupts through the host root. Here, we performed dual transcriptome analyses of two Rafflesiaceae species and their respective Tetrastigma hosts: Sapria himalayana with T. cauliflorum and Rafflesia speciosa with T. magnum. Our findings reveal species-specific transcriptional responses in Tetrastigma, suggesting divergent parasitism strategies between Rafflesia and Sapria. Moreover, we identify molecular signatures of parasitism that parallel plant gall formation, particularly in genes governing cell wall modification and host tissue reorganization. Unlike bacterial or insect-induced galls, these mechanisms may involve fungal symbionts, highlighting the unique nature of these interactions. Together, our results demonstrate that Rafflesiaceae parasitism represents a complex tripartite relationship among host, holoparasite, and associated microbes, offering new insights into the hidden biology of these remarkable parasitic plants.

plant biology↗