Merlin, I. | Search bioRxiv

bioRxiv2023

DASH-CAM: Dynamic Approximate SearcH Content Addressable Memory for genome classification

We propose a novel dynamic storage-based approximate search content addressable memory (DASH-CAM) for computational genomics applications, particularly for identification and classification of viral pathogens of epidemic significance. DASH-CAM provides 5.5x better density compared to state-of-the-art SRAM-based approximate search CAM. This allows using DASH-CAM as a portable classifier that can be applied to pathogen surveillance in low-quality field settings during pandemics, as well as to pathogen diagnostics at points of care. DASH-CAM approximate search capabilities allow a high level of flexibility when dealing with a variety of industrial sequencers with different error profiles. DASH-CAM achieves up to 30% and 20% higher F1 score when classifying DNA reads with 10% error rate, compared to state-of-the-art DNA classification tools MetaCache-GPU and Kraken2 respectively. Simulated at 1GHz, DASH-CAM provides 1, 178x and 1, 040x average speedup over MetaCache-GPU and Kraken2 respectively. CCS CONCEPTS*Hardware [->] Bio-embedded electronics.

genomics↗

bioRxiv2020

VviMYB41 orthologs contribute to the water deficit induced suberization of grapevine fine roots

The permeability of roots to water and nutrients is controlled through a variety of mechanisms and one of the most conspicuous is the presence of structures such as the Casparian strips and suberin lamellae. Roots actively regulate the creation of these structures developmentally, along the length of the root, and in response to the environment, including abiotic stresses such as drought. In the current study, we characterized the suberin composition along the length of grapevine fine roots during development and in response to water deficit. In parallel samples we quantified changes in expression of suberin biosynthesis- and deposition-related gene families (via RNAseq) allowing the identification of drought-responsive suberin-related genes. Grapevine suberin composition did not differ between primary and lateral roots, and was similar to that of other species. Under water deficit there was a global upregulation of suberin biosynthesis which resulted in an increase of suberin specific monomers, but without changes in their relative abundances, and this upregulation took place across all the developmental stages of fine roots. These changes corresponded to the upregulation of numerous suberin biosynthesis- and deposition-related genes which included orthologs of the previously characterized AtMYB41 transcriptional factor. Functional validation of two grapevine MYB41 orthologs, VviMYB41 and VviMYB41-like, confirmed their ability to globally upregulate suberin biosynthesis and deposition. This study provides a detailed characterization of the developmental and water deficit induced suberization of grapevine fine roots and identifies important orthologs responsible for suberin biosynthesis, deposition, and its regulation in grape. One sentence summaryOur study details the biochemical changes and molecular regulation of how grapevines decrease their root permeability during drought.

plant biology↗