Biology subjects

Acosta, K.

Publications and source records attributed to Acosta, K..

3 recordsLinked to original sources

bioRxiv2023

The genomes and epigenomes of aquatic plants (Lemnaceae) promote triploid hybridization and clonal reproduction

The Lemnaceae (duckweeds) are the worlds smallest but fastest growing flowering plants. Prolific clonal propagation facilitates continuous micro-cropping for plant-based protein and starch production, and holds tremendous promise for sequestration of atmospheric CO2. Here, we present chromosomal assemblies, annotations, and phylogenomic analysis of Lemna genomes that uncover candidate genes responsible for the metabolic and developmental traits of the family, such as anatomical reduction, adaxial stomata, lack of stomatal closure, and carbon sequestration via crystalline calcium oxalate. Lemnaceae have selectively lost genes required for RNA interference, including Argonaute genes required for reproductive isolation (the triploid block) and haploid gamete formation. Triploid hybrids arise commonly among Lemna, and we have found mutations in highly-conserved meiotic crossover genes that could support polyploid meiosis. Syntenic comparisons with Wolffia and Spirodela reveal that diversification of these genera coincided with the "Azolla event" in the mid-Eocene, during which aquatic macrophytes reduced high atmospheric CO2 levels to those of the current ice age. Facile regeneration of transgenic fronds from tissue culture, aided by reduced epigenetic silencing, makes Lemna a powerful biotechnological platform, as exemplified by recent engineering of high-oil Lemna that outperforms oil seed crops.

plant biology↗

bioRxiv2023

Optimization of molecular methods for detection and quantification of specific duckweed-bacteria interactions

Bacterial colonization dynamics of plants can differ between phylogenetically similar bacterial strains as well as in the context of complex bacterial communities. Quantitative studies that can resolve closely related bacteria within complex communities can lead to a better understanding of plant-microbe interactions. However, current methods lack the specificity to differentiate phylogenetically similar bacterial strains. In this study, we describe molecular strategies to study specific duckweed-bacteria interactions. We first systematically optimized a bead-beating protocol to co-isolate nucleic acids simultaneously from duckweed and bacteria. We then developed a generic fingerprinting assay to detect bacteria present in duckweed samples. To detect specific duckweed-bacteria interactions, we developed a genomics-based computational pipeline to generate bacterial strain-specific primers. These strain-specific primers differentiated bacterial strains from the same genus and enabled the detection of specific duckweed-bacteria interactions present in a community context. Moreover, we used these strain-specific primers to quantify the bacterial colonization of duckweed by normalization to a plant reference gene and revealed differences in colonization levels between strains from the same genus. Lastly, confocal microscopy of inoculated duckweed further supported our PCR results and showed bacterial colonization of the duckweed root-frond interface and root interior. The molecular methods introduced in this work should enable the tracking and quantification of specific plant-microbe interactions within plant-microbial communities.

ecology↗

bioRxiv2022

Genomics of turions from the Greater Duckweed reveal its pathways for dormancy and reemergence strategy

O_LIOver 15 families of aquatic plants are known to use a strategy of developmental switching upon environmental stress to produce dormant propagules called turions. However, few molecular details for turion biology have been elucidated due to the difficulties in isolating high-quality nucleic acids from this tissue. We successfully developed a new protocol to isolate high-quality transcripts and carried out RNA-seq analysis of mature turions from the Greater Duckweed Spirodela polyrhiza. Comparison of turion transcriptome to that of fronds, the actively growing leaf-like tissue, were carried out. C_LIO_LIBioinformatic analysis of high confidence, differentially expressed transcripts between frond and mature turion tissues revealed major pathways related to stress tolerance, starch and lipid metabolism, and dormancy that are mobilized to reprogram frond meristems for turion differentiation. C_LIO_LIWe identified the key genes that are likely to drive starch and lipid accumulation during turion formation, as well as in pathways for starch and lipid utilization upon turion germination. Comparison of genome-wide cytosine methylation levels also revealed evidence for epigenetic changes in the formation of turion tissues. C_LIO_LISimilarities between turions and seeds provided evidence that key regulators for seed maturation and germination have been retooled for their function in turion biology. C_LI

plant biology↗