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Volume 14, Issue 11, November 2024
Investigation
Genetic characterization of candidate ecdysteroid kinases in Drosophila melanogaster
Remote sensing for estimating genetic parameters of biomass accumulation and modeling stability of growth curves in alfalfa
Random regression models were utilized to estimate parameters of alfalfa growth curves using vegetation indices derived from multispectral images. The vegetation indices had moderate to high heritability and genetic correlations with harvest biomass. Results showed correspondence between plasticity in growth curves and stability in harvest biomass across years and environments. Findings indicate that vegetation indices can be used to estimate heritable growth parameters that could be used to phenotyping efficiency and model temporally dynamic interactions between cultivars and environment.
Comparative genome analysis and the genome-shaping role of long terminal repeat retrotransposons in the evolutionary divergence of fungal pathogens Blastomyces dermatitidis and Blastomyces gilchristii
Disentangling cobionts and contamination in long-read genomic data using sequence composition
Samples collected for genomic sequencing often contain genetic material from several organisms. Determining if a given sequence represents contamination can be difficult without suitable reference data. However, sequence composition can differ vastly between genomes. This work explores how 2D representations of composition can help separate genomic long reads from different sources. A Variational Autoencoder (a generative model based on a neural network) provides an effective framework for embedding millions of reads and identifying sequences from parasites, symbionts, and contaminants.
Prediction of additive genetic variances of descendants for complex families based on Mendelian sampling variances
The N terminus-only (trans) function of the adhesion G protein-coupled receptor latrophilin-1 controls multiple processes in reproduction of Caenorhabditis elegans
Genomic factors shaping codon usage across the Saccharomycotina subphylum
Local adaptation can cause both peaks and troughs in nucleotide diversity within populations
Linear poly-ubiquitin remodels the proteome and influences hundreds of regulators in Drosophila
The epistatic relationship of Drosophila melanogaster CtIP and Rif1 in homology-directed repair of DNA double-strand breaks
Y and mitochondrial chromosomes in the heterogeneous stock rat population
Evaluating cellular roles and phenotypes associated with trehalose degradation genes in Saccharomyces cerevisiae
Flynotyper 2.0: an updated tool for rapid quantitative assessment of Drosophila eye phenotypes
Sub-sampling graph neural networks for genomic prediction of quantitative phenotypes
Characterization of BioID tagging systems in budding yeast and exploring the interactome of the Ccr4-Not complex
Regulation of Drosophila brain development and organ growth by the Minibrain/Rala signaling network
Induced and natural variation affect traits independently in hybrid Populus
Both environmental and genetic variation can affect plant growth. Within the genetic factors, both DNA sequence and dosage (gene copy number) can change and affect plant function. Here, Guo et al. use a population of poplar trees to investigate if these two types of changes affect plants similarly, and whether or not they interact with each other. This helps create a broader understanding of what matters most to proper plant function and what is most likely to affect it.
A role for the circadian photoreceptor CRYPTOCHROME in regulating triglyceride metabolism in Drosophila
Cross potential selection: a proposal for optimizing crossing combinations in recurrent selection using the usefulness criterion of future inbred lines
Genome Report
Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness
The Gongora gibba genome assembly provides new insights into the evolution of floral scent in male euglossine bee–pollinated orchids
Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar
The genome sequence for the drought tolerant peanut variety "Line8" is the most complete peanut genome resource available. The Line8 genome allows for improved evaluation of genome variation among peanut genotypes. Using the Line8 genome, patterns emerge relating chromosomal structural differences and genetic exchange between chromosomes. Line8 contains an introgression from a wild relative of peanut that is an important donor of disease resistance alleles, providing an additional resource for peanut crop improvement efforts.
