Biology subjects

Martinez, C. C.

Publications and source records attributed to Martinez, C. C..

4 recordsLinked to original sources

bioRxiv2026

Disentangling blade and vasculature shape in grapevine leaves

The leaf blade and vasculature develop together within a shared morphological space. Despite shared molecular patterning pathways, it is unknown if developmental and evolutionary variation affect these tissues separately or together in a coordinated way. Grapevine leaves have a morphometric history and abundant data measuring the shape of the blade and vasculature together. Using a combination of topological data analysis and deep learning, we perform reciprocal semantic segmentation of leaf blade and vasculature. Each tissue contains sufficient information to predict the other. We hypothesize that this is due to a one-to-one relationship between blade and vein. Using thin plate splines to swap and warp different combinations of blade and vein shapes, we show that a set of leaves with a many-to-one relationship of blade and vein are distinguishable from true leaves. We also swap blade and vein across the developmental series and between species and show that only reversing the developmental series disrupts the relationship between blade and vasculature. We end by discussing the evolutionary and developmental implications that there is a unique, one-to-one mapping between blade and vein that allows each to be predicted from the other. Author summaryLeaves are made of two closely connected parts: the flat blade that captures light and the network of veins that transports water, nutrients, and developmental signals. Although these tissues grow together and share common molecular patterning pathways, it has remained unclear whether a particular blade shape is uniquely linked to a specific vein pattern. In this study, we use grapevine leaves as a model system and combine mathematical shape analysis with deep learning to examine this relationship. We show that the shape of the blade alone can accurately predict the vein network, and that the vein network can likewise predict the blade. This finding suggests a near one-to-one relationship between these two tissues. To test this idea, we created artificial leaves in which blade and vein shapes were deliberately mismatched. Although these synthetic leaves appeared realistic at a global level, a neural network was able to distinguish them from real leaves based on subtle differences. We further show that this tight coupling is maintained by the developmental sequence of leaf growth rather than by species identity, revealing a conserved constraint linking leaf form and internal structure.

plant biology↗

bioRxiv2023

The importance of habitat type and historical fire regimes in arthropod community response following large-scale wildfires

Wildfires are increasingly altering ecosystems, posing significant challenges for biodiversity conservation and ecosystem management. In this study, we used DNA metabarcoding to assess the response of arthropod communities to large-scale wildfires across diverse habitat types. We sampled six reserves within the University of California Natural Reserve System (UCNRS), each which was partially burned in the 2020 Lightning Complex wildfires in California. Using yellow pan traps to target pollinators, we collected arthropods from burned and unburned sites across multiple habitat types including oak woodland, redwood, scrub, chamise, grassland, forest, and serpentine habitats. We found no significant difference in alpha diversity values between burned and unburned sites; instead, seasonal variations played a significant role in arthropod community dynamics, with the emergence of plant species in Spring promoting increased pollinator richness at all sites. Compositional similarity analysis revealed that burn status was not a significant grouping factor when comparing all sites. Instead, community composition primarily varied across reserves, indicating distinct pools of arthropods structured geographically. Habitat type played a crucial role in determining the response of arthropod communities to fire. While communities in grasslands and oak woodlands exhibited recovery following burn, scrublands experienced substantial changes in community composition. Our study highlights the importance of examining community responses to wildfires across broad spatial scales and diverse habitat types. By understanding the nuanced dynamics of arthropod communities in response to fire disturbances, we can develop effective conservation strategies that promote resilience and maintain biodiversity in the face of increasing wildfire frequency and intensity driven by climate change.

ecology↗

bioRxiv2019

Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): A resource for testing evolutionary hypotheses

Large groups of species with well-defined phylogenies are excellent systems for testing evolutionary hypotheses. In this paper, we describe the creation of a comparative genomic resource consisting of 23 genomes from the species-rich Drosophila montium species group, 22 of which are presented here for the first time. The montium group is uniquely positioned for comparative studies. Within the montium clade, evolutionary distances are such that large numbers of sequences can be accurately aligned while also recovering strong signals of divergence; and the distance between the montium group and D. melanogaster is short enough so that orthologous sequence can be readily identified. All genomes were assembled from a single, small-insert library using MaSuRCA, before going through an extensive post-assembly pipeline. Estimated genome sizes within the montium group range from 155 Mb to 223 Mb (mean=196 Mb). The absence of long-distance information during the assembly process resulted in fragmented assemblies, with the scaffold NG50s varying widely based on repeat content and sample heterozygosity (min=18 kb, max=390 kb, mean=74 kb). The total scaffold length for most assemblies is also shorter than the estimated genome size, typically by 5 - 15 %. However, subsequent analysis showed that our assemblies are highly complete. Despite large differences in contiguity, all assemblies contain at least 96 % of known single-copy Dipteran genes (BUSCOs, n=2,799). Similarly, by aligning our assemblies to the D. melanogaster genome and remapping coordinates for a large set of transcriptional enhancers (n=3,457), we showed that each montium assembly contains orthologs for at least 91 % of D. melanogaster enhancers. Importantly, the genic and enhancer contents of our assemblies are comparable to that of far more contiguous Drosophila assemblies. The alignment of our own D. serrata assembly to a previously published PacBio D. serrata assembly also showed that our longest scaffolds (up to 1 Mb) are free of large-scale misassemblies. Our genome assemblies are a valuable resource that can be used to further resolve the montium group phylogeny; study the evolution of protein-coding genes and cis-regulatory sequences; and determine the genetic basis of ecological and behavioral adaptations.

genomics↗

bioRxiv2019

Spatial transcriptional signatures define margin morphogenesis along the proximal-distal and medio-lateral axes in complex leaf species Solanum lycopersicum (tomato)

Leaf morphogenesis involves cell division, expansion, and differentiation in the developing leaf, cells at different positions along the medio-lateral and proximal-distal leaf axes divide, expand, and differentiate at different rates. The gene expression changes that control cell fate along these axes remain elusive due to difficulties in precisely isolating tissues. Here, we combined rigorous early leaf characterization, laser capture microdissection, and transcriptomic sequencing to ask how gene expression patterns regulate early leaf morphogenesis in wild-type tomato (Solanum lycopersicum) and the leaf morphogenesis mutant trifoliate. We observed transcriptional regulation of cell differentiation along the proximal-distal axis and identified molecular signatures delineating the classically defined marginal meristem/blastozone region during early leaf development. We describe the importance of endoreduplication during leaf development, when and where leaf cells first achieve photosynthetic competency, and the regulation of auxin transport and signaling along the leaf axes. Knockout mutants of BLADE-ON-PETIOLE2 exhibited ectopic shoot apical meristem formation on leaves, highlighting the role of this gene in regulating margin tissue identity. We mapped gene expression signatures in specific leaf domains and evaluated the role of each domain in conferring indeterminacy and permitting blade outgrowth. Finally, we generated a global gene expression atlas of the early developing compound leaf. One-sentence summaryRigorous structural characterization, laser capture microdissection, and transcriptomic sequencing reveal how gene expression patterns regulate early morphogenesis of the compound tomato leaf. The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is Ciera C. Martinez (ccmartinez@berkeley.edu).

plant biology↗