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A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus) provide evidence of haplotype diversity.
Gigascience
January 2025
Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, 53113 Bonn, Germany.
Background: In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).
Results: We achieved a haploid size of 940 megabase pairs (Mbp) for haplome 1 and 929 Mbp for haplome 2 with high scaffold N50 values of 36.
Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.
Cell Genom
January 2025
Department of Cell and Molecular Biology, Karolinska Institute, 171 65 Stockholm, Sweden. Electronic address:
Newts have large genomes harboring many repeat elements. How these elements shape the genome and relate to newts' unique regeneration ability remains unknown. We present here the chromosome-scale assembly of the 20.
View Article and Find Full Text PDFA network-enabled pipeline for gene discovery and validation in non-model plant species.
Cell Rep Methods
January 2025
MSU-DOE Plant Research Lab, Michigan State University, East Lansing, MI 48824, USA; Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA. Electronic address:
Identifying key regulators of important genes in non-model crop species is challenging due to limited multi-omics resources. To address this, we introduce the network-enabled gene discovery pipeline NEEDLE, a user-friendly tool that systematically generates coexpression gene network modules, measures gene connectivity, and establishes network hierarchy to pinpoint key transcriptional regulators from dynamic transcriptome datasets. After validating its accuracy with two independent datasets, we applied NEEDLE to identify transcription factors (TFs) regulating the expression of cellulose synthase-like F6 (CSLF6), a crucial cell wall biosynthetic gene, in Brachypodium and sorghum.
View Article and Find Full Text PDFEnzymes in a human cytoplasm model organize into submetabolon complexes.
Proc Natl Acad Sci U S A
February 2025
Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801.
Enzyme-enzyme interactions are fundamental to the function of cells. Their atomistic mechanisms remain elusive mainly due to limitations of in-cell measurements. We address this challenge by atomistically modeling, for a total of ≈80 μs, a slice of the human cell cytoplasm that includes three successive enzymes along the glycolytic pathway: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), and phosphoglycerate mutase (PGM).
View Article and Find Full Text PDFThe Developmental Origin of Novel Complex Morphological Traits in Lepidoptera.
Annu Rev Entomol
January 2025
Department of Biology and Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico.
Novel traits in the order Lepidoptera include prolegs in the abdomen of larvae, scales, and eyespot and band color patterns in the wings of adults. We review recent work that investigates the developmental origin and diversification of these four traits from a gene-regulatory network (GRN) perspective. While prolegs and eyespots appear to derive from distinct ancestral GRNs co-opted to novel body regions, scales derive from in situ modifications of a sensory bristle GRN.
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