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1. Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana

   https://doi.org/10.1093/g3journal/jkae104  

   Vuruputoor, Vidya S; Starovoitov, Andrew; Cai, Yuqing; Liu, Yang; Rahmatpour, Nasim; Hedderson, Terry A; Wilding, Nicholas; Wegrzyn, Jill L; Goffinet, Bernard (May 2024, G3: Genes, Genomes, Genetics)

   Ingvarsson, P (Ed.)

   Abstract The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events. 

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2. A PhyloFisher utility for nucleotide-based phylogenomic matrix construction; nucl_matrix_constructor.py

   https://doi.org/10.1101/2023.11.30.569490  

   Jones, Robert E; Jones, Erin P; Tice, Alexander K; Brown, Matthew W (December 2023, bioRxiv)

   ABSTRACT Phylogenies built from multiple genes have become a common component of evolutionary biology studies. Molecular phylogenomic matrices used to build multi-gene phylogenies can be built from either nucleotide or protein matrices. Nucleotide-based analyses are often more appropriate for addressing phylogenetic questions in evolutionarily shallow timescales (i.e., less than 100 million years) while protein-based analyses are often more appropriate for addressing deep phylogenetic questions. PhyloFisher is a phylogenomic software package written in Python3. The manually curated PhyloFisher database contains 240 protein-coding genes from 304 eukaryotic taxa. Here we presentnucl_matrix_constructor.py, an expansion of the PhyloFisher starting database, and an update to PhyloFisher that maintains DNA sequences. This combination will allow users the ability to easily build nucleotide phylogenomic matrices while retaining the benefits of protein-based pre-processing used to identify contaminants and paralogy. 

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3. Beyond adaptive gene transfers: a primer on horizontal gene transfer across scales

   https://doi.org/10.1093/icb/icag125  

   Van_Etten, Julia; Johnson, Matthew D (July 2026, Integrative And Comparative Biology)

   Abstract Horizontal gene transfer (HGT) is a fundamental ecological and evolutionary process involving the movement of genetic material across taxa within a single generation. While traditionally studied at the level of individual genes with encoded adaptive functions, recent advances in genomics and metagenomics highlight the need for a broader, integrative framework. Here, we expand the concept of the “ecology of DNA transfer,” which conceptualizes HGT as a multi-layered process spanning the genome, cell, and ecological context. We further explore how the fate and expression of transferred DNA vary over evolutionary timescales, from recently acquired, transcriptionally silenced sequences to ancient, fully integrated genes. Together, this framework underscores HGT as a dynamic, context-dependent process shaped by interactions across biological scales. 

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4. The Genomic Basis of Evolutionary Novelties in a Leafhopper

   https://doi.org/10.1093/molbev/msac184  

   Li, Zheng; Li, Yiyuan; Xue, Allen Z; Dang, Vy; Holmes, V Renee; Johnston, J Spencer; Barrick, Jeffrey E; Moran, Nancy A (September 2022, Molecular Biology and Evolution)

   Parsch, John (Ed.)

   Abstract Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory. 

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5. Gene function predicts divergence across molecular levels

   https://doi.org/10.1038/s41598-026-64001-0  

   Piya, Antara Anika; Macias_Calix, Ksenia; Assis, Raquel (August 2026, Scientific Reports)

   Abstract Genes can evolve through changes at their DNA, RNA, or protein levels. However, because these changes are measured using distinct and often incomparable metrics, their relative contributions to genic evolution remain unclear. Here, we address this challenge by developing a standardized framework for comparing evolutionary divergence in protein-coding sequences, multi-tissue expression profiles, and protein structures. Application of this approach to data from insects, rodents, primates, and plants reveals substantial variation in divergence patterns across taxa, with only sequence divergence matching expectations based on evolutionary theory. Moreover, sequences evolve slowest and protein structures fastest in all taxa, consistent with the idea that higher levels of biological organization are closer proxies for the functions on which selection acts. Yet, weak correlations among divergence measures suggest that targets of selection vary across genes, perhaps depending on their functions. Indeed, few genes exhibit similar evolutionary patterns across all three levels, and different functions are enriched in genes with low or high divergence in protein-coding sequences, gene expression profiles, and protein structures. Together, these findings support the hypothesis that evolutionary targets of genes depend on their functions, shedding light on how selection shapes different levels of biological organization across taxa. 

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