Biology subjects

Ranaweera, T.

Publications and source records attributed to Ranaweera, T..

4 recordsLinked to original sources

bioRxiv2026

Spatial expression evolution of duplicated genes post-whole genome duplication in cultivated tomato

The mechanisms by which whole genome duplication contributes to expression divergence of duplicate genes, which can impact the evolution of form and function, has been a long-standing question in evolutionary biology. We compared expression patterns of paralogs derived from the most recent Solanaceae-specific genome triplication event across 23 tissues and inferred ancestral expression states to investigate patterns of expression evolution. While the partitioning of ancestral expression states is traditionally considered the second most common (after the gene loss) trajectory of duplicate expression evolution, we found that the ancestral expression states tended to be retained by most (~66%) duplicates, with ~6% of gene lineages experiencing expression gain events and ~20% experiencing expression losses. The genes that gained expression in fruit tissues are significantly enriched with functions associated with fruit quality. Notably, asymmetrical expression divergence is prevalent among duplicates, especially when ancestral genes were either not expressed or were highly expressed. Our study demonstrates the utility of integrating paralog expression comparisons with phylogenetic analyses to document the potential evolutionary history of spatial expression patterns and gain insight into how expression divergence contributes to the evolution of function across tissues.

plant biology↗

bioRxiv2024

CLAVATA signalling shapes barley inflorescence architecture by controlling activity and determinacy of shoot apical and rachilla meristems

Grasses exhibit a large variety of diverse inflorescence architectures, from complex branched inflorescences in Oryzeae (rice) to simple spike-type inflorescences in Triticeae (e.g. barley, wheat). Inflorescence architecture depends on shape, longevity and determinacy of meristems that direct growth of the main rachis and lateral branches, but how individual meristem activities are determined and integrated within complex inflorescences is not yet understood. We found that activity of distinct meristems in the barley inflorescence is coordinated by a signalling pathway comprising the receptor like kinase Hordeum vulgare CLAVATA1 (HvCLV1) and the secreted CLAVATA3/ENDOSPERM SURROUNDING REGION (CLE)-family peptide FON2- LIKE CLE PROTEIN1 (HvFCP1). HvFCP1 interacts with HvCLV1 to promote spikelet formation but restricts inflorescence meristem and rachilla meristem proliferation. Hvfcp1 or Hvclv1 mutants generate branched inflorescences with additional rows of spikelets and supernumerary florets. Transcriptome analysis reveals that HvFCP1/HvCLV1 signalling controls inflorescence branching through the regulation of trehalose-6-phosphate synthesis and sugar transport. Our discoveries reveal the potential to engineer barley inflorescence architecture by manipulating regulation of distinct meristem activities.

plant biology↗

bioRxiv2022

Temporal Regulation of Cold Transcriptional Response in Switchgrass

Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis-regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k-mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k-mers, referred to as putative cis-regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies.

plant biology↗

bioRxiv2020

Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves

Premise of studyLeaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. We measured leaf morphology from over 200 vines over four years, and modeled changes in leaf shape along the shoot to determine if a composite "shape of shapes" can better capture variation and predict species identity compared to individual leaves. MethodsUsing homologous universal landmarks found in grapevine leaves, we modeled various morphological features as a polynomial function of leaf node. The resulting functions are used to reconstruct modeled leaf shapes across shoots, generating composite leaves that comprehensively capture the spectrum of possible leaf morphologies. ResultsWe found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict species identity of previously unassigned vines, which were verified with genotyping. DiscussionObservations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape--an assemblage of modeled leaf snapshots across the shoot--is a better representation of the dynamic and essential shapes of leaves, as well as serving as a better predictor of species identity than individual leaves.

plant biology↗