Munoz Perez, J. M. | bioRxiv Science

bioRxiv2025

Identifying associations between maize leaf transcriptome and bacteriome during different diurnal periods

O_LIBacterial communities play important roles in the plant phyllosphere. Both microbial communities and their hosts have circadian rhythms and are subject to diurnal environmental changes. However, the interaction between the host and microbiome is still poorly understood. Here, we exploit paired sequencing data of host transcriptome and microbiome derived maize genotypes in field conditions and under two contrasting diurnal periods. C_LIO_LIGene expression patterns of circadian cycle genes confirmed expected diurnal dynamics. Groups of co-expressed genes that responded to diurnal periods were associated with nucleic acid-binding, heat stress responses, and photosynthesis. C_LIO_LIMicrobiome analysis revealed only modest differences in alpha diversity between midday and midnight samples. However, beta diversity indicated a significant shift in community composition. Co-occurrence network analysis identified keystone taxa specific to each time point, suggesting time-dependent ecological roles within the phyllosphere microbiome. C_LIO_LICross-correlation analyses between host gene expression and bacterial taxon abundance revealed a greater number of host-microbe associations during the night. Several maize genes involved in circadian regulation significantly correlated with microbial taxa. Our findings provide initial evidence for diurnal-associated relationships between host gene expression and leaf-associated bacteriome, suggesting that maize circadian regulation may play a role in shaping the composition and functional potential of the phyllosphere microbiome. C_LI

bioinformatics↗

bioRxiv2019

Genome-wide diversity of northern South America cultivated Coconut (Cocus nucifera L.) uncovers diversification times and targets of domestication of coconut globally

Coconut palms (Cocos nucifera) are a combination of wild admixed populations and perennial crops with a worldwide distribution. Here we develop single nucleotide polymorphisms (SNPs) along the coconut genome based on Genotyping by Sequencing (GBS) for at least four different commercially important and widely cultivated coconut varieties and hybrids growing in northern South America. We present a comprehensive catalog of approximately 27K SNPs to conduct genetic diversity, population structure and linkage disequilibrium analysis. A relatively fast LD decay for the Atlantic accessions within ~250Kb was observed in comparison to the Pacific accessions ~ 1500 Kb. The complete SNPs sampling showed a strong population structure at K = 2, separating accessions from the Pacific and Atlantic coasts as it has been found in previous studies. At higher K values, one non-admixed group was observed for the Atlantic while further substructures emerged for the Pacific accessions, where three non-admixed groups were found. Population structure analysis also showed a great degree of admixture between the Atlantic and Pacific populations, and SNPs of the Pacific non-admixed genetic groups were mostly introgressed into the Atlantic individuals but the contrary was rarely observed. The results of principal component analysis and Neighbor-Joining Hierarchical Clustering were consistent with the results from Structure and provided a measure of genetic relationships among individual genotypes. The Pacific group has a lower genetic diversity and a higher rate of inbreeding than the Atlantic group. These results suggest that the Pacific coconuts of Colombia belong to the pre-Columbian population found on the Pacific coast of Panama and Peru. If it had been introduced after Columbus (as in Mexico), genetic diversity would have been higher than on the Atlantic coast.

genomics↗