Biology subjects

Mathew, L. S.

Publications and source records attributed to Mathew, L. S..

8 recordsLinked to original sources

bioRxiv2025

Genomic Analysis of Date Palm Fruit Size Trait and Identification of Candidate Genes through GWAS

The commercial value of economically significant fruits, including date palm fruit (dates), is influenced by various factors, such as biochemical composition and morphological features like size, shape, and visual appearance, which are key determinants of their quality and market value. Dates are typically consumed at the dry stage (Tamar), during which they exhibit a wide range of physical characteristics, such as color, length, weight, and skin appearance. Understanding the genetic basis of these traits is crucial for improving crop quality and breeding new cultivars. In this study, we integrated a genome dataset from highly diverse date cultivars with phenotypes of dry fruit such as length, width, area, and weight, identifying multiple significant genetic loci (SNPs) associated with these traits. We also identified candidate genes located near the associated SNPs that are involved in biological processes such as cell differentiation, proliferation, growth, and the regulation of signalling pathways for growth regulators like auxin and abscisic acid, as observed in other plants. Gene expression analysis reveals that many of these genes are highly expressed in the early stage of fruit development when the fruit attains its maximum size and weight. These findings will enhance our understanding of genetic determinants of fruit size particularly at the commercially important Tamar stage.

genomics↗

bioRxiv2025

Temporal Dynamics of Transcriptional Responses to Repeated mRNA Vaccination: Insights from Third Dose Profiling

mRNA vaccines have played a crucial role in combating the COVID-19 pandemic, but the long-term dynamics of immune responses to repeated vaccination remain poorly understood. In this study, we extend our previous work on first and second dose responses by characterizing the immune signatures elicited by a third dose of COVID-19 mRNA vaccines using high-resolution temporal profiling of blood transcriptomes collected daily for 9 days post-vaccination. We observed distinct patterns of gene expression related to interferon responses, inflammation, erythroid cell signatures, and plasmablast activity across the three doses. While the first dose elicited a modest response primarily characterized by interferon signaling, the second dose induced a robust, polyfunctional response. The third dose, administered approximately nine months later, maintained this polyfunctional character and matched the second dose in magnitude, though with distinct temporal dynamics. The interferon component peaked on day 2 (similar to the first dose) rather than day 1 (as seen in the second dose), while the erythroid signature showed a markedly different trajectory, with sustained elevation rather than decrease over the following week. Notably, we observed a progressive amplification of the plasmablast response across the three doses, with an earlier peak (day 4) compared to other vaccines, potentially a unique feature of mRNA vaccines. These findings demonstrate that the heightened, polyfunctional responsiveness induced by the second dose is robustly maintained even after a prolonged interval, suggesting effective immune memory. Our results contribute to understanding mRNA vaccine-induced immunity, with implications for optimizing booster strategies and developing next-generation vaccines.

immunology↗

bioRxiv2024

The genetics of fruit skin separation in date palm

The physical appearance of date palm (Phoenix dactylifera) fruit (dates) is important for its market value. Many date-producing countries experience significant financial losses due to the poor appearance of the fruit, skin separation or puffiness being a major reason. Previous research showed evidence linking the skin separation phenotype to environmental conditions. In this study, we show that there is both an environmental and genetic contribution to the fruit skin separation phenotype. We show that beyond environmental factors, genetics is a strong contributor to the most extreme skin separation in some cultivars. A genome-wide association study was conducted using genome data of 199 samples collected from 14 countries that identified nine genetic loci associated with this phenotype and investigated genes in these regions that may contribute to the phenotype overall. Identifying the genetic factors may help better understand the biology and pathways that lead to the environmental effects on skin separation and improve commercial date production. In conclusion, our key finding is that both environmental and genetic factors contribute to skin separation variation, and improvements in environmental factors alone cannot overcome the extreme level of variation observed in some cultivars.

bioinformatics↗

bioRxiv2022

Genome-wide analysis of dry (Tamar) Date palm fruit color

Date palm (Phoenix dactylifera) fruit are an economically and culturally significant crop in the Middle East and North Africa. There are hundreds of different commercial cultivars producing dates with distinctive shapes, colors, and sizes. Genetic studies of some Date palm traits have been performed, including for date palm sex-determination, sugar content and fresh fruit colour. In this study, we used genome sequences and image data of 199 dry date fruit (Tamar) samples collected from 14 countries to identify genetic loci associated with the color of this fruit stage. Here, we find loci across multiple linkage groups (LG) associated with dry fruit color phenotype. We recover the previously identified VIR genotype associated with fresh fruit yellow or red color and new associations with the lightness and darkness of dry fruit. This study will add resolution to our understanding of the date palm fruit color phenotype especially at the most commercially important tamar stage.

bioinformatics↗

bioRxiv2021

The anatomical logic of smell

The sense of smell helps us navigate the environment, but its molecular architecture and underlying logic remain unknown. The spatial location of odorant receptor genes (Olfrs) in the nose is widely thought to be independent of the structural diversity of the odorants they detect. Using spatial transcriptomics, we created a genome-wide 3D atlas of the mouse olfactory mucosa (OM). Topographic maps of genes differentially expressed in space reveal that both Olfrs and non-Olfrs are distributed in a continuous and overlapping fashion over five broad zones in the OM. The spatial locations of Olfrs correlate with the mucus solubility of the odorants they recognize, providing direct evidence for the chromatographic theory of olfaction. This resource resolved the molecular architecture of the mouse OM, and will inform future studies on mechanisms underlying Olfr gene choice, axonal pathfinding, patterning of the nervous system, and basic logic for the peripheral representation of smell.

neuroscience↗

bioRxiv2020

Multi-organ transcriptomic profiling reveals differential regulation of the immune system among the brain-liver-fats organ network of short-term fasted mice

Different fasting regimens are known to promote health, mitigate chronic immunological disorders, and improve age-related pathophysiological parameters in animals and humans. Indeed, several clinical trials are currently ongoing using fasting as a potential therapy for a wide range of conditions. Fasting alters metabolism by acting as a reset for energy homeostasis. However, the molecular mechanisms underlying the beneficial effects of short-term fasting (STF) are still not well understood, particularly at the systems or multi-organ level. Here, we investigated the dynamic gene expression patterns associated with six periods of STF in nine different mouse organs. We cataloged the transcriptional dynamics within and between organs during STF and discovered differential temporal effects of STF among organs. Using gene ontology enrichment analysis, we identified an organ network sharing 37 common biological pathways perturbed by STF. This network incorporates the brain, liver, interscapular brown adipose tissue, and posterior-subcutaneous white adipose tissue, hence we named it the brain-liver-fats organ network. Using Reactome pathways analysis, we identified the immune system, dominated by T cell regulation processes, as a central and prominent target of systemic modulations during STF in this organ network. The changes we identified in specific immune components point to the priming of adaptive immunity and parallel the fine-tuning of innate immune signaling. Our study provides a comprehensive multi-organ transcriptomic profiling of mice subjected to multiple periods of STF, and adds new insights into the molecular modulators involved in the systemic immuno-transcriptomic changes that occur during short-term energy loss.

systems biology↗

bioRxiv2019

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content we analyzed date fruit metabolomics for association with genotype data from 121 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the beta-fructofuranosidase (invertase) gene in the reference Khalas genome, a low sucrose fruit. High sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains the all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end-point sucrose content in date fruit may be used in selective breeding in the future.

plant biology↗

bioRxiv2018

Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix

The date palm tree is a commercially important member of the genus Phoenix whose 14 species are all dioecious with separate male and female individuals. Previous studies identified a multi-megabase region of the date palm genome linked to sex and showed that dioecy likely developed in Phoenix prior to speciation. To identify genes critical to sex determination we sequenced the genomes of 28 Phoenix trees representing all 14 species. Male-specific sequences were identified and extended using phased single molecule sequencing or BAC clones to distinguish X and Y alleles.\n\nHere we show that only four genes contain sequences conserved in all analyzed males, likely identifying the changes foundational to dioecy in Phoenix. The majority of these sequences show similarity to a single genomic locus in the closely related oil palm. CYP703 and GPAT3, two genes critical to male flower development in other monocots, appear fully deleted in females while maintained as single copy in males. A LOG-like gene appears translocated into the Y chromosome and a cytidine deaminase-like appears at the border of a chromosomal rearrangement. Our data supports a two-mutation model for the evolution from hermaphroditism to dioecy through a gynodioecious intermediate.

genomics↗