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1. Distinct patterns of genome size evolution in each bryophyte lineage are not correlated with whole genome duplication

   https://doi.org/10.1093/aob/mcaf012  

   Patel, Nikisha; Budke, Jessica M; Bainard, Jillian D (January 2025, Annals of botany)

   Abstract Background and AimsGenome size varies by orders of magnitude across land plants, and the factors driving evolutionary increases and decreases in genome size vary across lineages. Bryophytes have the smallest genomes relative to other land plants, and there is growing evidence for frequent whole genome duplication (WGD) across the lineage. However, the broad patterns of genome size, chromosome number and WGD have yet to be characterized across bryophytes in a phylogenetic context. MethodsIn the present study, we adopt a phylogenetic comparative approach and leverage previously published data on genome size, chromosome number and WGD to reconstruct the evolutionary history of these traits across the three major bryophyte lineages: hornworts, liverworts and mosses. We infer ancestral haploid chromosome numbers for each lineage and introduce a novel metric for assessing polyploidy using chromosome counts. Key ResultsEach lineage of bryophytes exhibits a distinct pattern of genome size evolution and prevalence of WGD, with mosses having the most dynamic genome sizes and highest propensity for WGD. We found that 21.3 % of mosses and 13 % of liverworts species have naturally occurring polyploids. In addition, haploid genome size (1C) is most dynamic in the mosses, which includes at least 15 transitions to larger genomes and nine reversals, largely in the orders Dicranales and Hypnales. ConclusionsThere is no correlation between genome size and WGD or between genome size and chromosome number, potentially suggesting rapid genome downsizing following WGD. Given that bryophytes are poikilohydric (desiccation-tolerant) plants, having large genomes might be physiologically prohibitive given the cost to growth and metabolism associated with them. These findings emphasize the unique evolution of the bryophytes broadly and of the hornworts, liverworts and mosses individually, and should therefore serve as impetus for more in-depth experimental studies of genome size evolution and WGD in bryophytes. 

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2. Chromosome‐scale reference genome of Pectocarya recurvata , the species with the smallest reported genome size in Boraginaceae

   https://doi.org/10.1002/aps3.70008  

   Northing, Poppy C; Pelosi, Jessie A; Venable, D Lawrence; Dlugosch, Katrina M (May 2025, Applications in Plant Sciences)

   Abstract PremisePectocarya recurvata(Boraginaceae, subfamily Cynoglossoideae), a species native to the Sonoran Desert (North America), has served as a model system for a suite of ecological and evolutionary studies. However, no reference genomes are currently available in Cynoglossoideae. A high‐quality reference genome forP. recurvatawould be valuable for addressing questions in this system and across broader taxonomic scales. MethodsUsing PacBio HiFi sequencing, we assembled a reference genome forP. recurvataand annotated coding regions with full‐length transcripts from an Iso‐Seq library. We assessed genome completeness with BUSCO andk‐mer analysis, and estimated the genome size of six individuals using flow cytometry. ResultsThe chromosome‐scale genome assembly forP. recurvatawas 216.0 Mbp long (N50 = 12.1 Mbp). Previous observations indicatedP. recurvatais 2n = 24. Our assembly included 12 primary contigs (158.3 Mbp) containing 30,655 genes with telomeres at 23 out of 24 ends. Flow cytometry measurements from the same population included two plants with 1C = 196.9 Mbp, the smallest measured for Boraginaceae, and four with 1C = 385.8 Mbp, which is consistent with tetraploidy in this population. DiscussionTheP. recurvatagenome assembly and annotation provide a high‐quality genomic resource in a sparsely represented area of the angiosperm phylogeny. This new reference genome will facilitate answering open questions in ecophysiology, biogeography, and systematics. 

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3. Anuran genome size evolution is driven by relatively recent retrotransposon activity and by life history

   https://doi.org/10.1186/s12864-025-12414-y  

   Rubio, Andrew O; Neddermeyer, John H; James, Aakash; Janz, Nicholas; Rader, Jonathan A; Tollis, Marc; Stuckert, Adam_M M (December 2026, BMC Genomics)

   Abstract BackgroundTransposable elements (TEs), often referred to as ‘selfish genetic elements’, hijack their host’s genetic machinery to replicate themselves within the host genome, and are primary contributors to genome size in vertebrates. In particular, frogs and toads (Order: Anura) are well known for not only having large genomes, but for having genomes with drastic variation in size (e.g.,Scaphiopus couchii: 0.48 Gbp,Rana muscosa10 Gbp). This discrepancy in size is due in part to relative differences in the proliferation and success of TEs across anuran genomes. In this study, we ask: do specific TE families drive genome size variation and are these patterns phylogenetically-constrained? To answer this, we use 61 publicly available anuran reference genome assemblies, comprising 22 anuran families, to investigate the effects of TEs on the evolution of anuran genome size. In addition, we used repeat landscapes to analyze TE activity in the context of anuran evolutionary history, in order to understand how lineage-specific TE activity affects genome size variation in anurans. Finally, we examined how life history traits that have been predicted to be constrained by genome size, larval period and clutch size, are associated with TEs. ResultsOur results suggest that copy number of elements and total content of several TEs families (L1/CIN4, Ty1/Copia, Ty3/DIRS1, hobo-Activator) are associated with increased genome size across anurans. We further found that the copy numbers of recently active Ty3 retrotransposons are correlated with increased genome size, suggesting that expansions of this family of TE have had a distinct effect on the size of the anuran genome across evolutionary time. Finally, we found interactions between several TE families (hobo-Activator, PiggyBac, L2/CR1/Rex, and SINEs) and larval period, indicating that developmental time may be a major constraint on genome size and species with additional constraints may more effectively purge TEs. ConclusionOur findings underscore the pivotal roles of both the activity of specific TE families (L1/CIN4, Ty1/Copia, Ty3/DIRS1, hobo-Activator) and developmental constraints in amphibian genome size evolution. 

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4. The Genome Explorer genome browser

   https://doi.org/10.1128/msystems.00267-24  

   Herson, James; Krummenacker, Markus; Spaulding, Aaron; O'Maille, Paul; Karp, Peter D (July 2024, mSystems)

   Fodor, Anthony (Ed.)

   ABSTRACT <p>Are two adjacent genes in the same operon? What are the order and spacing between several transcription factor binding sites? Genome browsers are software data visualization and exploration tools that enable biologists to answer questions such as these. In this paper, we report on a major update to our browser, Genome Explorer, that provides nearly instantaneous scaling and traversing of a genome, enabling users to quickly and easily zoom into an area of interest. The user can rapidly move between scales that depict the entire genome, individual genes, and the sequence; Genome Explorer presents the most relevant detail and context for each scale. By downloading the data for the entire genome to the user’s web browser and dynamically generating visualizations locally, we enable fine control of zoom and pan functions and real-time redrawing of the visualization, resulting in smoother and more intuitive exploration of a genome than is possible with other browsers. Further, genome features are presented together, in-line, using familiar graphical depictions. In contrast, many other browsers depict genome features using data tracks, which have low information density and can visually obscure the relative positions of features. Genome Explorer diagrams have a high information density that provides larger amounts of genome context and sequence information to be presented in a given-sized monitor than for tracks-based browsers. Genome Explorer provides optional data tracks for the analysis of large-scale data sets and a unique comparative mode that aligns genomes at orthologous genes with synchronized zooming.</p></sec> <sec><title>IMPORTANCEGenome browsers provide graphical depictions of genome information to speed the uptake of complex genome data by scientists. They provide search operations to help scientists find information and zoom operations to enable scientists to view genome features at different resolutions. We introduce the Genome Explorer browser, which provides extremely fast zooming and panning of genome visualizations and displays with high information density. 

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5. Welcome to the big leaves: Best practices for improving genome annotation in non‐model plant genomes

   https://doi.org/10.1002/aps3.11533  

   Vuruputoor, Vidya S.; Monyak, Daniel; Fetter, Karl C.; Webster, Cynthia; Bhattarai, Akriti; Shrestha, Bikash; Zaman, Sumaira; Bennett, Jeremy; McEvoy, Susan L.; Caballero, Madison; et al (July 2023, Applications in Plant Sciences)

   Abstract PremiseRobust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein‐coding gene predictions. MethodsThe impact of repeat masking, long‐read and short‐read inputs, and de novo and genome‐guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. ResultsBenchmarks that reflect gene structures, reciprocal similarity search alignments, and mono‐exonic/multi‐exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA‐read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence‐based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome‐guided transcriptome assemblies, or full‐length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post‐processing with functional and structural filters is highly recommended. DiscussionWhile the annotation of non‐model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions. 

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