Biology subjects

Jacobs, S. J.

Publications and source records attributed to Jacobs, S. J..

3 recordsLinked to original sources

bioRxiv2026

Phased Chromosome-level Genome and Organellar Assemblies of Castilleja foliolosa Provide Vital Resource for Orobanchaceae Genomics

Castilleja (Orobanchaceae) is a diverse, facultatively hemiparasitic plant genus characterized by a complex evolutionary history of reticulate evolution and significant taxonomic ambiguity. High-quality genomic resources have historically been limited, hindering robust macro-evolutionary and macro-ecological inquiries. Here, we present the first high-quality, phased, chromosome-level reference genome for the diploid species Castilleja foliolosa. Utilizing a hybrid assembly strategy, we integrated long-read PacBio HiFi sequencing with Omni-C proximity ligation data to generate a highly contiguous nuclear assembly, complemented by reconstructed mitochondrial and chloroplastic genomes. The primary nuclear haplotype spans approximately 510 Mbp, containing 39,417 predicted genes and a substantial repetitive landscape covering ~66% of the genome. Our organellar assemblies reveal notable structural complexity: the chloroplast maintains heteroplasmy via two primary structural haplotypes, while the 611 kbp mitogenome adopts a circular master topology existing in two isomeric forms. Comparative genomic analyses demonstrate a largely conserved chromosomal architecture relative to the closely related Pedicularis cranolopha, punctuated by the presence of lineage-specific genes. Functional enrichment of Castilleja-specific orthogroups identifies a consistent association with telomere maintenance, DNA integration, and zinc ion binding, likely stemming from the substantial repeat content. This reference genome provides a robust framework for dissecting the genomic drivers of taxonomic diversification and adaptation within the Orobanchaceae family. This resource significantly enhances our capacity to untangle reticulate evolutionary patterns, offering a definitive foundation for future comparative studies of genome evolution in the Orobanchaceae lineage of parasitic plants.

plant biology↗

bioRxiv2026

Painting the evolutionary history of a multicompartmentalized syngameon in North American Castilleja (Orobanchaceae)

Understanding the evolutionary history of recent rapidly radiating groups remains a major challenge in systematics, especially when incomplete reproductive isolation and rampant interspecific gene flow obscure phylogenetic signal. Here, we present a comprehensive phylogenomic study of the genus Castilleja (the paintbrushes, Orobanchaceae), integrating nuclear and chloroplast data to investigate patterns of diversification, hybridization, and geographic structure across its range. Our results provide the first evidence that Castilleja functions as a multicompartmentalized syngameon-a network of closely related species with ongoing or historical gene flow among non-sister lineages within and between geographically structured compartments. High nuclear gene tree discordance, coupled with strong cpDNA geographic compartment structuring and nuclear network analysis, supports the hypothesis that recent rapid radiation and Plio-Pleistocene climatic fluctuations created alternating periods of range expansion and contraction. These dynamics likely promoted localized hybridization within isolated compartments during contraction and further introgression between compartments during range expansion. Our findings not only clarify the evolutionary relationships within Castilleja but also demonstrate the importance of genome-scale data and syngameon theory in understanding diversification in lineages where hybridization is rampant.

evolutionary biology↗

bioRxiv2022

Global phylogenomic assessment of Leptoseris and Agaricia reveals substantial undescribed diversity at mesophotic depths

Mesophotic coral communities are increasingly gaining attention for the unique biological species they host, exemplified by the numerous mesophotic fish species that continue to be discovered. In contrast, many of the photosynthetic scleractinian corals observed at mesophotic depths are assumed to be depth-generalists, with very few species characterised as mesophotic-specialists. This presumed lack of a specialised community remains largely untested, as phylogenetic studies rarely include mesophotic samples and have long suffered from resolution issues associated with traditional sequence markers. Here, we used reduced-representation genome sequencing to provide a phylogenomic assessment of the two dominant mesophotic genera of plating corals in the Indo-Pacific and Western Atlantic, respectively, Leptoseris and Agaricia. While these genome-wide phylogenies broadly corroborated the morphological taxonomy, they also exposed substantial undescribed diversity (at least 24 molecular clades across the 8 species), including deep divergences within genera and current taxonomic species. Five of the eight focal species consisted of at least two sympatrically-occurring, genetically distinct clades, which were consistently detected across different methods. The repeated observation of genetically divergent clades associated with mesophotic depths highlights that there are many more mesophotic-specialist coral species than currently acknowledged, and that an urgent assessment of this largely unstudied biological diversity is warranted.

evolutionary biology↗