Gene duplication and evolutionary plasticity of lin-12/Notch gene function in Caenorhabditis

Genetics, Journal Year: 2024, Volume and Issue: 227(3)

Published: May 29, 2024

Abstract Gene duplication is an important substrate for the evolution of new gene functions, but impacts duplicates on their own activities and developmental networks in which they act are poorly understood. Here, we use a natural experiment lin-12/Notch within nematode genus Caenorhabditis, combined with characterization loss- gain-of-function mutations, to uncover functional distinctions between duplicate genes 1 species (Caenorhabditis briggsae) single-copy ortholog Caenorhabditis elegans. First, using improved genomic sequence model characterization, confirm that C. briggsae genome includes 2 complete lin-12 genes, whereas most other encoding proteins participate LIN-12 signaling pathway retain one-to-one orthology We CRISPR-mediated editing introduce alleles predicted cause (gf) or loss-of-function (lf) into each find gf mutations not apparent from lf alleles. Specifically, Cbr-lin-12.1(gf), Cbr-lin-12.2(gf), causes defects similar those observed Cel-lin-12(gf). In contrast Cel-lin-12(gf), however, Cbr-lin-12.1(gf) do dominant phenotypes as compared wild type, mutant phenotype only when present. Our results demonstrate can exhibit differential capacities compensate interfere normal development, coincident sensitivity LIN-12/Notch activity.

Language: Английский

Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 7, 2023

Abstract The advancement of sequencing technologies results in the rapid release hundreds new genome assemblies a year providing unprecedented resources for study evolution. Within this context, significance in-depth analyses repetitive elements, transposable elements (TEs) particular, is increasingly recognized understanding Despite plethora available bioinformatic tools identifying and annotating TEs, phylogenetic distance target species from curated classified database element sequences constrains any automated annotation effort. Manual curation raw repeat libraries deemed essential due to frequent incompleteness automatically generated consensus sequences. However, manual classification are time-consuming processes that offer limited short-term academic rewards typically confined few research groups where methods taught through hands-on experience. Crowd sourcing efforts could significant opportunity bridge gap between learning effectively empowering scientific community with high-quality, reusable libraries. Here, we present an example such crowd effort developed both in-person online courses built around collaborative peer-reviewed teaching process can be used as reference guide similar projects. TEs two tardigrade species, which there were no TE available, resulted successful characterization diverse TEs: A hidden treasure awaits discovery within non-model organisms.

Language: Английский