Biology subjects

Pelosi, J.

Publications and source records attributed to Pelosi, J..

4 recordsLinked to original sources

bioRxiv2026

Near chromosome-level genome assembly for the invasive annual forb Centaurea melitensis

PremiseCentaurea melitensis (Asteraceae) is a problematic invader of grasslands globally, but little is known about its genetic makeup. Here we develop a reference genome to facilitate studies of its invasion history, genetic variation, and evolution. MethodsInbred offspring of a single individual of C. melitensis from its invasion of California, USA were used for flow cytometry to estimate genome size, and for genomic DNA extraction. DNA was sequenced with PacBio HiFi technology (yield = 85.7Gb). The genome was assembled with Hifiasm and annotated with BRAKER3. GENESPACE was used to compare gene order (synteny) with three other species within the subfamily Cichorioideae. ResultsWe estimated a mean genome size of 795.0 Mbp for C. melitensis, and our assembly totaled 696.6 Mbp in 48 contigs (N50 = 55.6 Mbp; BUSCO = 98%), with annotation of 25,157 protein-encoding genes. This included four telomere-to-telomere putative chromosomes, nine additional chromosome arms terminated by telomeric repeats, and a complete chloroplast genome. Synteny varied markedly across the genus and subfamily, suggesting a dynamic history of structural variation in the lineage of C. melitensis. DiscussionWe provide a highly complete and contiguous genome assembly to facilitate the further study of genomic variation in C. melitensis.

genomics↗

bioRxiv2026

Testing fundamental hypotheses of colonization success in the ferns

Background and AimsNon-native species are now ubiquitous members of regional floras. The factors that lead to establishment and dominance of non-native species are continuously debated. Fundamental hypotheses about drivers of invasion success include the role of phylogeny, polyploidy, genome size, and rapid niche evolution. These hypotheses have been tested in the seed plants, but ferns, the second largest group of vascular plants, have rarely been considered in these analyses, despite making up a non-trivial portion of non-native floras. MethodsWe compiled a dataset of global non-native ferns and categorized them along the invasion spectrum using descriptions from the literature and natural history collections. Using this dataset, we assessed I) the taxonomic diversity and phylogenetic clustering of non-native ferns, II) the geographic distribution of fern introductions, testing for shifts in climatic niches, and III) test for the association of invader traits across the invasion continuum, including smaller genome sizes and higher ploidal levels. Key ResultsWe generated a dataset that includes 83 taxa; of these, we classified 18 as casual, 35 as naturalized (but not invasive), and 30 as invasive. Using this dataset, we found I) weak or no phylogenetic clustering of non-native ferns, II) some regions are overrepresented as sources and recipients of introductions, III) climatic niches are often conserved between native and introduced ranges, but can differ between introductions, IV) naturalized ferns have smaller genomes, and V) invaders have higher ploidal levels. ConclusionsWe integrated regional floras, occurrence and climate data, phylogeny, and cytology to test fundamental hypotheses regarding the colonization success of ferns. This study provides insights into the ecological, genomic, and phylogenetic features associated with the colonization of new habitats by non-native ferns, a largely overlooked portion of non-native plant taxa.

evolutionary biology↗

bioRxiv2025

Near chromosome-level genome assembly of Neomusotima conspurcatalis gives insights into the evolution of moth genome architecture and fern-insect interactions

Plant-insect interactions are the foundation of ecosystems globally, yet we are still determining the underlying mechanisms through which these relationships evolve. The co-evolution between insects and their host plants should shape the genomes of both partners, and genes involved in interaction specificity should show unique genomic signatures (e.g., rapid evolution, gene family expansions). Biological control programs are an excellent system for disentangling the genomics and molecular biology of the establishment of an insect and its host plant specificity. Fern-insect relationships are among the most poorly understood, and ferns have long been thought to have few interactions with insects, although recent evidence suggests that these relationships are under-sampled and studied. Here, we present a near-chromosome genome assembly of the crambid moth Neomusotima conspurcatalis, a biological control agent employed in the management of the invasive vining fern Lygodium microphyllum. We use this novel genomic resource to explore the evolution of genome architecture across the Crambidae, revealing highly conserved genome structure across this family of moths. We also examine gene family evolution across the phylogeny and identify expansions in odorant receptor gene families that may be involved in the highly specific interaction of N. conspurcatalis with L. microphyllum. This work highlights the utility of genomics in biological control, and the utility of biological control in informing fundamental understanding of plant-insect interactions. SummaryPlant-insect interactions form the basis of ecological communities and can be highly specific through long lasting co-evolution. Classical biological control provides excellent opportunities to investigate how insect and host genomes are shaped by co-evolutionary processes. We sequenced the genome of Neomusotima conspurcatalis, a biological control moth used to manage the invasive fern Lygodium microphyllum. We analyzed how the structure of the genome has evolved over time relative to other crambid moths and how expansions in gene families involved in odorant reception may be involved in co-evolution with its host. This work provides insight into herbivore interactions in seed-free vascular plants.

evolutionary biology↗

bioRxiv2025

The genome of the vining fern Lygodium microphyllum highlights genomic and functional differences between life phases of an invasive plant

Functional and genomic studies on the differences between gametophyte and sporophyte life phases remain scarce, yet unraveling these dynamics is crucial to understanding the biology of plants and the success of each phase under different environments. Here, we provide a novel reference genome for the highly invasive fern Lygodium microphyllum and compare the transcriptomic and epigenomic landscapes of the gametophyte and sporophyte life phases. We found differential regulation of developmental genes (homeobox and MADS-box clades) and usage of alternative isoforms that may play a role in the genomic determination of the haploid and diploid life stages. We further generated the first base pair-resolution methylome of a fern gametophyte, and determined that methylation patterns are remarkably similar between vegetative tissues despite their morphological and functional differences. By examining the physiological and transcriptomic responses of gametophytes and sporophytes to freezing stress, the most likely abiotic factor preventing further expansion of this invasive species, we show that life phases and tissues use alternative molecular pathways to respond to this stressor, underscoring the need to incorporate both life phases when developing effective mitigation strategies. These new genomic resources fill a gap in our understanding of fundamental plant biology and inform invasive species research. SIGNIFICANCEAll land plants undergo an alternation of generations between haploid gametophyte and diploid sporophyte life phases. How these disparate life phases are generated from a single genome, and the functional implications of these differences for plant success, is largely unknown. Moreover, understanding life-phase-specific differences in rapidly evolving populations, such as invasive species, is critical to developing effective management strategies. We assembled a chromosome-level genome and generated epigenomic and transcriptomic resources from gametophyte and sporophyte phases of the invasive fern Lygodium microphyllum, which is estimated to cost the U.S. more than $2 million annually. We highlight transcriptomic, epigenomic, and physiological variation between life phases and find support for the crucial role of the often overlooked gametophyte in the invasion process.

plant biology↗