The diatom Order Rhopalodiales comprises canal-bearing taxa with nitrogen-fixing cyanobacterial endosymbionts, but its genus-level systematics remains unresolved due to the paraphyly of Rhopalodia. We characterized two Northern California strains of Rhopalodia californica sp. nov. using valve morphology, complete organellar and spheroid body (SB) genomes, and multi-gene phylogenetics. Chloroplast (133,208-133,222 bp), mitochondrial (35,955-36,097 bp), and SB (3.064 Mbp) genomes were all structurally conserved and identical in gene content. Phylogenetic analysis of nuclear (18S, 28S), chloroplast (rbcL, psbC), and mitochondrial (cob) genes placed R. californica with Epithemia sp. GazosCreekCA in a strongly supported ‘californica’ clade, distinct from other clades of Epithemia and Rhopalodia species. Genome-wide nucleotide similarity was high within the clade (>97.6%) but markedly lower (<95%) when compared to other Rhopalodiales, a pattern that aligns with distinctions observed in the SB, chloroplast, and mitochondrial datasets. Evolutionary rate was fastest for the mitochondrion, followed by the SB and then the chloroplast. Synteny analysis revealed that gene order and structure were highly conserved between the two R. californica strains and remained well conserved even in comparison with Epithemia sp. GazosCreekCA. These results demonstrate that the ‘californica’ group is a genetically and morphologically cohesive lineage within Rhopalodia sensu lato, supporting its recognition in future taxonomic studies.

ABSTRACT In sunflower ( Helianthus annuus L.), the composition of fatty acids in the seeds, primarily oleic, linoleic, stearic and palmitic acid, is of utmost importance for oil quality. Despite this, the genetic basis of this trait and its interaction with the environment is poorly understood. Understanding this interaction is critical to improvement of sunflower within the context of climate change. In this work, we incorporated fatty acid composition measurements from the sunflower SAM population and eight environments across an extensive geographic cline into GWAS. The SAM panel consists of 287 varieties representing approximately 90% of sunflower diversity, for which 2.2 million high-quality SNPs with a MAF > 5% are available. For increased power, multivariate GWAS was performed with four different inputs: (i) mean fatty acid composition within each environment, (ii) mean fatty acid composition within each environment omitting high oleic varieties, (iii) trait stability within environments quantified by standard errors among replicate samples (α stability) and (iv) Eberhart and Russell’s β which quantifies trait stabilities across environments (β stability). All four analyses yielded highly significantly associated SNPs. We found that high oleic varieties exhibited high β trait stability, resulting in substantial overlap in markers between analyses (i) and (iv), with signals being fairly consistent between environments in analysis (i). For analyses (ii) and (iii), significant markers tended to vary between trials. For significant SNPs across all analyses, 147 candidate genes were identified, including promising candidates such as 15 fatty acid metabolism genes, 6 heat shock proteins and 22 transcription factors. Lastly, a large introgression consisting of two flanking inverted sequences on Chromosome 5 was found to coincide with α stability in the Georgia trial, suggesting a role in FA composition stability under high heat conditions.

Plant genetics can exert a strong effect on soil rhizosphere microbes. Broad-sense heritability estimates quantify the degree to which plant genotype predicts microbiome composition, enabling characterization of plant genotype effects on rhizosphere microbes. We used 16S rRNA and internal transcribed spacer marker gene sequencing data from rhizosphere soil from 95 field-grown sunflower (Helianthus annuus) inbred lines to test the heritability of archaeal, bacterial, and fungal rhizosphere communities, as well as alpha- and beta-diversity metrics and differences in the relative abundance of microbial zero-radius operational taxonomic units (ZOTUs). The majority of taxa passing prevalence and relative abundance cutoffs of 25 and 0.01% were heritable across all taxonomic levels for both prokaryotes (archaea and bacteria) and fungi, with higher heritabilities at finer taxonomic resolution. Metrics of alpha and beta diversity were also heritable, particularly for prokaryotes. Prokaryotic and fungal communities were both heritable, but there was significantly higher fungal heritability at the ZOTU, genus, and family levels. Prokaryotic richness and fungal richness were only weakly positively correlated, and beta diversity was not correlated, suggesting that sunflower inbred lines affect prokaryotes and fungi in different ways. Our work provides valuable information for crop breeding and provides a general methodological framework for assessing the strength and types of genotype-microbial associations. Because of high heritability for individual microbial taxa, as well as for microbial diversity metrics more broadly, sunflowers are clearly an important species to study the ecology, evolution, and genetics of plant-microbe interactions, and this knowledge can be used to improve sustainability of the crop.Copyright (c) 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Accurate variant calling is critical for identifying the genetic basis of complex traits, yet filters used in variant detection may inadvertently exclude valuable genetic information. In this study, we compare common sequencing depth filters, used to eliminate error-prone variants associated with repetitive regions and technical issues, with a biologically relevant filtering approach that targets expected Mendelian segregation. The resulting variant sets were evaluated in the context of nectar volume quantitative trait loci (QTL) mapping in sunflower (Helianthus annuus L.). Our previous research failed to detect an interval containing a strong candidate gene for nectar production (HaCWINV2). We removed hard filters and implemented a chi-square goodness-of-fit test to retain variants that segregate according to expected genetic ratios. We demonstrate that biologically relevant filtering retains more significant QTL and candidate genes, including HaCWINV2, while removing variants due to technical errors more effectively, and accounted for 48.55% of nectar production phenotypic variation. In finding nine putative homologs of Arabidopsis genes with nectary function within QTL regions, we demonstrate that this filtering strategy has a higher power of true variant detection in QTL mapping than the commonly used variant depth filtering strategy. Future research will adapt the technique to multiple population contexts, such as genomic selection.

We report the complete chloroplast genomes of two closely related taxa, Nitzschia nienhuisii and Epithemia catenata. The plastids share 96.85% nucleotide similarity and exhibit similar genomic structure. The N. nienhuisii plastome is 128,415 bp with 129 protein-coding genes, whereas E. catenata plastome is 140,525 bp with 130 protein-coding genes, including a duplicated psaJ in the inverted repeat. Both genomes encode 30 tRNAs, one tmRNA, six rRNAs, and two pseudogenes (tyrC and ycf42). The larger E. catenata genome likely reflects 12 unique ORFs. Maximum likelihood phylogenetic analysis supports a close relationship between these taxa.

Despite their ecological significance and unique endosymbiotic capabilities, diatoms in the genus Rhopalodia remain poorly represented in genomic databases, particularly with respect to the availability of complete genomes from multiple organellar compartments. This study addresses that gap by presenting, for the first time, the complete chloroplast (133,086 bp), mitochondrial (36,786 bp), and spheroid body (3,024,495 bp) genomes of Rhopalodia sterrenburgii, a nitrogen-fixing diatom with a cyanobacterial endosymbiont. Phylogenetic reconstruction based on five genes from different cellular compartments (18S, 28S, rbcL, psbC, cob) placed R. sterrenburgii as a basal lineage relative to R. gibba (Rhopalodia sensu lato) and the Epithemia sensu stricto species E. argus, E. turgida, and E. sorex, providing new insights into evolutionary relationships within Rhopalodiales. Additionally, pathway analysis revealed the progressive loss of genes involved in vitamin B12 and chlorophyll a biosynthesis in more recently diverged Rhopalodia and Epithemia lineages. Our findings support a pattern of genome reduction in symbiotic diazotrophic diatoms, potentially driven by coevolution with their endosymbionts, and an increasing reliance on integrated metabolic functions between the host and the endosymbiont.

The sunflower (Helianthus annuus) pericarp protects the seed within from both abiotic and biotic stresses. Achenes with stronger pericarps are less susceptible to damage from insect feeding. Complicating the genetic improvement of pericarp strength is the negative correlation between pericarp thickness (a component of strength) and oil content. As breeding efforts have increased oil content, there has been a concomitant decrease in pericarp thickness. One breeding goal is to improve oil content while preserving pericarp strength through genetic mechanisms independent of the tradeoffs with pericarp thickness. To determine the genetic basis of oil content, pericarp strength, and thickness, we identified QTL in two populations: the Sunflower Association Mapping panel (Mandel et al. in Theor Appl Genet 123:693–704, 2011) and a recombinant inbred line (RIL) population derived from a thin pericarp oilseed inbred (HA 467) crossed to a thick pericarp open-pollinated variety from Türkiye (PI 170415). A region on chromosome 15 was associated with neighboring QTL for banded moth resistance, oil content, and pericarp thickness, partially underlying the trade-offs among these traits. Additional QTL on chromosome 5 and 14 for pericarp strength provide fewer trade-offs with oil content. QTL for pericarp strength on chromosome 5 and pericarp thickness on chromosome 16 were associated with large structural variants on chromosome 5 and putative structural variation on chromosome 16, with candidate gene presence/absence variation between the haplotypes on chromosome 5. Understanding the origin and nature of phenotypic tradeoffs is beneficial to plant biologists and sunflower breeders as they seek to understand the origin and genetic architecture of adaptive and maladaptive traits.

The genetic architecture of mating-type loci in lichen-forming fungi has been characterized in very few taxa. Despite the limited data, and in contrast to all other major fungal lineages, arrangements that have both mating-type alleles in a single haploid genome have been hypothesized to be absent from the largest lineage of lichen-forming fungi, the Lecanoromycetes. We report the discovery of both mating-type alleles from the haploid genomes of three species within this group. Our results demonstrate that Lecanoromycetes are not an outlier among Ascomycetes.

Intracellular plant defense against pathogens is mediated by a class of disease resistance genes known as NB-LRRs or NLRs (R genes). Many of the diseases these genes protect against are more prevalent in regions of higher rainfall, which provide better growth conditions for the pathogens. As such, we expect a higher selective pressure for the maintenance and proliferation of R genes in plants adapted to wetter conditions. In this study, we enriched libraries for R genes using RenSeq from baits primarily developed from the common sunflower (Helianthus annuus) reference genome. We sequenced the R gene libraries of Silphium integrifolium Michx, a perennial relative of sunflower, from 12 prairie remnants across a rainfall gradient in the Central Plains of the United States, with both Illumina short-read (n=99) and PacBio long-read (n=10) approaches. We found a positive relationship between the mean effective annual precipitation of a plant’s source prairie remnant and the number of R genes in its genome, consistent with intensity of plant pathogen coevolution increasing with precipitation. We show that RenSeq can be applied to the study of ecological hypotheses in non-model relatives of model organisms.

Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the "true" reindeer lichens, Cladonia subgenus Cladina, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of Cladonia, Pilophorus, and Stereocaulon were consistently larger than those of Lepraria and contained more introns, suggesting a selective pressure in asexual morphology in Lepraria driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from Cladonia ravenelii and Stereocaulon pileatum exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in Lepraria, were diverse and abundant in Cladonia, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with C. rangiferina especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of Cladonia and related genera, allowing future study alongside a wealth of assembled genomes.

Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity and community-scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbours substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co-vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defence in natural and human-altered environments.

The National Institute on Drug Abuse (NIDA) is the sole producer of Cannabis for research purposes in the United States, including medical investigation. Previous research established that cannabinoid profiles in the NIDA varieties lacked diversity and potency relative to the Cannabis produced commercially. Additionally, microsatellite marker analyses have established that the NIDA varieties are genetically divergent form varieties produced in the private legal market. Here, we analyzed the genomes of multiple Cannabis varieties from diverse lineages including two produced by NIDA, and we provide further support that NIDA’s varieties differ from widely available medical, recreational, or industrial Cannabis . Furthermore, our results suggest that NIDA’s varieties lack diversity in the single-copy portion of the genome, the maternally inherited genomes, the cannabinoid genes, and in the repetitive content of the genome. Therefore, results based on NIDA’s varieties are not generalizable regarding the effects of Cannabis after consumption. For medical research to be relevant, material that is more widely used would have to be studied. Clearly, having research to date dominated by a single, non-representative source of Cannabis has hindered scientific investigation.

Data sharing is not applicable to this article as no new data were created or analyzed in this study.

Bacidia depriestiana is described as new to science based on material from the southern Appalachian Mountains of eastern North America. The species has a granular to minutely areolate thallus, with minute, erumpent soralia, produces atranorin and zeorin, and is not known to produce apothecia. The combination of chemistry and thallus type appears to be unique within the genus. Originally identified as Lecanora nothocaesiella, the species was recognized as distinct in conjunction with study of a large metagenomic dataset for lichens from the region. In connection with obtaining molecular loci use for phylogenetic placement of the material, the mitochondrial genome was assembled, found to be 38,546 bp in length, and encoded for the full suite of protein coding genes previously found in lichen fungi, with the exception of atp9.

Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4-7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses.

PREMISE:Lichens are fungi that enter into obligate symbioses with photosynthesizing organisms (algae, cyanobacteria). Traditional narratives of lichens as binary symbiont pairs have given way to their recognition as dynamic metacommunities. Basidiomycete yeasts, particularly of the genus Cyphobasidium, have been inferred to be widespread and important components of lichen metacommunities. Yet, the presence of basidiomycete yeasts across a wide diversity of lichen lineages has not previously been tested.METHODS:We searched for lichen-associated cystobasidiomycete yeasts in newly generated metagenomic data from 413 samples of 339 lichen species spanning 57 families and 25 orders. The data set was generated as part of a large-scale project to study lichen biodiversity gradients in the southern Appalachian Mountains Biodiversity Hotspot of southeastern North America.RESULTS:Our efforts detected cystobasidiomycete yeasts in nine taxa (Bryoria nadvornikiana, Heterodermia leucomelos, Lecidea roseotincta, Opegrapha vulgata, Parmotrema hypotropum, P. subsumptum, Usnea cornuta, U. strigosa, and U. subgracilis), representing 2.7% of all species sampled. Seven of these taxa (78%) are foliose (leaf-like) or fruticose (shrubby) lichens that belong to families where basidiomycete yeasts have been previously detected. In several of the nine cases, cystobasidiomycete rDNA coverage was comparable to, or greater than, that of the primary lichen fungus single-copy nuclear genomic rDNA, suggesting sampling artifacts are unlikely to account for our results.CONCLUSIONS:Studies from diverse areas of the natural sciences have led to the need to reconceptualize lichens as dynamic metacommunities. However, our failure to detect cystobasidiomycetes in 97.3% (330 species) of the sampled species suggests that basidiomycete yeasts are not ubiquitous in lichens.

Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.

In this study we demonstrate the utility of whole genome shotgun (WGS) metagenomics in study organisms with small genomes to improve upon amplicon-based estimates of biodiversity and microbial diversity in environmental samples for the purpose of understanding ecological and evolutionary processes. We generated a database of full-length and near-full-length ribosomal DNA sequence complexes from 273 lichenized fungal species and used this database to facilitate fungal species identification in the southern Appalachian Mountains using low coverage WGS at higher resolution and without the biases of amplicon-based approaches. Using this new database and methods herein developed, we detected between 2.8 and 11 times as many species from lichen fungal propagules by aligning reads from WGS-sequenced environmental samples compared to a traditional amplicon-based approach. We then conducted complete taxonomic diversity inventories of the lichens in each one-hectare plot to assess overlap between standing taxonomic diversity and diversity detected based on propagules present in environmental samples (i.e., the “potential” of diversity). From the environmental samples, we detected 94 species not observed in organism-level sampling in these ecosystems with high confidence using both WGS and amplicon-based methods. This study highlights the utility of WGS sequence-based approaches in detecting hidden species diversity and demonstrates that amplicon-based methods likely miss important components of fungal diversity. We suggest that the adoption of this method will not only improve understanding of biotic constraints on the distributions of biodiversity but will also help to inform important environmental policy.

The mitochondrial genome of the Gunnison's prairie dog, Cynomys gunnisoni gunnisoni, is described and incorporated into a phylogenetic inference of the genus Cynomys based on seven new mitochondrial genomes and published genomes from Cynomys leucurus and Cynomys ludovicianus. The mitochondrial genome from Ictidomys tridecemlineatus, the sister genus, was included as an outgroup. Our results lend further support to published phylogenetic hypotheses.

There is an abundance (currently over 1016 DNA bases) of publicly available genetic sequence data and a dearth of trained genomicists to process and interpret it, necessitating more trained bioinformaticians with biological expertise. For example, thousands of data sets are deposited on NCBI's Sequence Read Archive with plans to use only part of the data generated, though much of this data could be used to address other important biological questions. Course-Based Undergraduate Research Experiences (CUREs) are growing in popularity as a way to engage undergraduates in a project-based learning experience to analyze data that could not otherwise be processed. Through CUREs, students can receive training in the most relevant and up-to-date skill sets used within the field. We present a lesson plan for a CURE centered around teaching genome annotation. This project is suitable as a four week module in an undergraduate/graduate cross-listed course and focuses on annotating streamlined organellar genomes. This module is similar to other programs, such as the Genomics Education Partnership. However, students are additionally provided with the opportunity to publish their annotated genomes to NCBI's GenBank. In addition, many students who have taken this course have gone on to pursue internships and careers using the bioinformatics skills gained.