Cover image
Volume 15, Issue 1, January 2025
Dialogue and Debate
When is it subfunctionalization and when is it not?
New genes arise from duplication followed by divergence. The most common fate of a duplication is one copy is deleted to return to a single copy. But if divergence occurs, the function of the gene can be split between the two copies, which is called subfunctionalization, or a new function can arise, which is called neofunctionalization. Changes in expression between the two copies does not necessarily suggest that subfunctionalization has occurred. In this commentary, the caveats and criteria for subfunctionalization are discussed.
Investigation
myh9b is a critical non-muscle myosin II encoding gene that interacts with myh9a and myh10 during zebrafish development in both compensatory and redundant pathways
Glial peroxisome dysfunction induces axonal swelling and neuroinflammation in Drosophila
Testis- and ovary-expressed polo-like kinase transcripts and gene duplications affect male fertility when expressed in the Drosophila melanogaster germline
Comparative genomics reveals putative copper tolerance genes in a Fusarium oxysporum strain
New mutations in the core Schizosaccharomyces pombe spindle pole body scaffold Ppc89 reveal separable functions in regulating cell division
Wild yeast isolation by middle-school students reveals features of populations residing on North American oaks
Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola
Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa)
Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions
Loss- of-function mutant alleles were characterized for 22 maize transcription factors to test the functional relevance of prior gene regulatory network predictions. The transcriptome and phenolic metabolome of these mutants were profiled to document the functional roles of these transcription factors. A subset of the prior gene regulatory network predictions were supported but had limited overall power in predicting changes in gene expression or phenolic compounds. The limitations of testing transcription factor-target predictions with single TF knockouts are discussed.
Bellymount-pulsed tracking: a novel approach for real-time in vivo imaging of Drosophila abdominal tissues
Optimization of breeding program design through stochastic simulation with evolutionary algorithms
The optimization of a breeding program is a highly complex task with various design options involved. Hassanpour et al. have developed an evolutionary algorithm optimization method to address the resource allocation problems in breeding programs. Evolutionary algorithm involves creating a population of potential solutions and iteratively evolving them over time using different operators. The optimization process with thousands of individual simulations and hundreds of iterations is implemented via the Snakemake workflow to allow for reproducible, flexible, and scalable management of computing dependencies.
Marginal interaction test for detecting interactions between genetic marker sets and environment in genome-wide studies
Establishment of a locally adaptive allele in multidimensional continuous space
Detection and annotation of unique regions in mammalian genomes
Genome Reports
The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki
Chromosome-level reference genome for the Jonah crab, Cancer borealis
Somy evolution in the honey bee infecting trypanosomatid parasite Lotmaria passim
Here Markowitz et al. report the updated sequencing, assembly, and annotation of the BRL type strain (ATCC PRA-422) Lotmaria passim, a trypanosomatid parasite of honey bees within the medically important subfamily Leishmaniinae. The genome has 31 chromosomes that display high levels of aneuploidy attributed to evolutionarily recent chromosomal duplication events. These features mirror the genomic flexibility employed by other trypanosomatids and can provide insights into adaptations employed by bee-specific trypanosomatids, which parallel challenges faced by other Leishmaniinae within insect vectors and mammalian hosts.
