Biology subjects

Paleni, C.

Publications and source records attributed to Paleni, C..

3 recordsLinked to original sources

bioRxiv2026

Population-scalable genotyping from low-coverage sequencing data using pangenome graphs

Pangenome-based genotyping of structurally complex loci remains challenging at low sequencing depths, particularly when samples are of low quality, such as in ancient DNA. We present COSIGT (COsine SImilarity-based GenoTyper), a method that infers structural genotypes by matching short-read coverage patterns to pangenome haplotypes using cosine similarity. COSIGT maintains robust accuracy at low coverage (1-2X), outperforming existing methods where depth-sensitive approaches degrade. We demonstrate scalability to thousands of modern and ancient genomes, enabling population-scale analyses of complex variation from low-coverage data.

bioinformatics↗

bioRxiv2024

Co-cultivation with Azolla affects the metabolome of whole rice plant beyond canonical inorganic nitrogen fertilization

Azolla spp. are floating ferns used for centuries as biofertilizers to enrich the soil with inorganic nitrogen and improve rice yields. In this study, rice plants were grown together with Azolla by maintaining a low and constant concentration of inorganic nitrogen. We employed a combination of non-targeted metabolomics, chemometrics, and molecular networking to dissect the impact of Azolla co-cultivation on the metabolome of rice roots-and leaves. Our analyses revealed that Azolla releases a broad range of metabolites in the culture medium, mainly comprising small peptides and flavonoids. Moreover, in rice co-cultivated with Azolla, we observed a systematic response in the upregulation of metabolites that started from the roots and, over time, shifted to the leaves. During the early stages of co-cultivation, Azolla led to the accumulation of small peptides, lipids, and carbohydrates in roots, and flavonoid glycosides and carbohydrates in leaves of rice. Consistent with these results, transcriptomics analysis of rice roots indicated significant changes in the expression of genes coding for small peptide and lipid transporters, and genes involved in amino acid salvage and biosynthesis. Overall, our study highlights novel growth-promoting effects of Azolla on rice which could facilitate the development of sustainable techniques to increase yields. HighlightsThe aquatic fern Azolla synthesizes and releases a broad range of growth promoting metabolites (i.e. small peptides) that can be absorbed by the roots of co-cultivated rice plants

plant biology↗

bioRxiv2024

Co-cultivating rice plants with Azolla filiculoides modifies root architecture and timing of developmental stages

Strategies for increasing the yield of rice, the staple food for more than half of the global population, are needed to keep pace with the expected worldwide population increase, and sustainably forefront the challenges posed by climate change. In Southern-East Asian countries, rice farming benefits from the use of Azolla spp. for nitrogen supply. In virtue of the symbiosis with the nitrogen-fixing cyanobacterium Trichormus azollae, Azolla spp. are ferns that release nitrogen into the environment upon decomposition of their biomass. However, if and to what extent actively growing Azolla plants impact on the development of co-cultivated rice plantlets remains to be understood. Here, we show that actively growing Azolla filiculoides plants alter the architecture of the roots and accelerates the differentiation and proliferation of leaves and tillers in co-cultivated rice plants. These changes result from an intimate cross-talk between rice and A. filiculoides, in which hormones and other metabolites released by the fern in the growth medium trigger an alteration in the rice root transcriptome and the hormonal profiles of both roots and leaves. Overall, the present data let us argue that co-cultivation with A. filiculoides might prime rice plants to better deal with both abiotic and biotic stress. HighlightAzolla filiculoides alters the root transcriptome and hormonal balance in both roots and leaves of co-cultivated rice plantlets, thereby interfering with the progression of their developmental programs

plant biology↗