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1. Comparison of Conservation Strategies for California Channel Island Oak ( Quercus tomentella ) Using Climate Suitability Predicted From Genomic Data

   https://doi.org/10.1111/eva.70057  

   Mead, Alayna; Fitz‐Gibbon, Sorel; Knapp, John; Sork, Victoria L (December 2024, Evolutionary Applications)

   ABSTRACT Management strategies, such as assisted gene flow, can increase resilience to climate change in tree populations. Knowledge of evolutionary history and genetic structure of species are needed to assess the risks and benefits of different strategies.Quercus tomentella, or Island Oak, is a rare oak restricted to six Channel Islands in California, United States, and Baja California, Mexico. Previous work has shown that Island Oaks on each island are genetically differentiated, but it is unclear whether assisted gene flow could enable populations to tolerate future climates. We performed whole‐genome sequencing on Island Oak individuals andQ. chrysolepis, a closely related species that hybridizes with Island Oak (127 total), to characterize genetic structure and introgression across its range and assess the relationship between genomic variation and climate. We introduce and assess three potential management strategies with different trade‐offs between conserving historic genetic structure and enabling populations to survive changing climates: the status quo approach; ecosystem preservation approach, which conserves the trees and their associated biodiversity; and species preservation approach, which conserves the species. We compare the impact of these approaches on predicted maladaptation to climate using Gradient Forest. We also introduce a climate suitability index to identify optimal pairs of seed sources and planting sites for approaches involving assisted gene flow. We found one island (Santa Rosa) that could benefit from the ecosystem preservation approach and also serve as a species preservation site. Overall, we find that both the ecosystem and species preservation approaches will do better than the status quo approach. If preserving Island Oak ecosystems is the goal, assisted dispersal into multiple sites could produce adapted populations. If the goal is to preserve a species, the Santa Rosa population would be suitable. This case study both illustrates viable conservation strategies for Island Oak and introduces a framework for tree conservation. 

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2. Complete Chloroplast Genome Sequence of the Western Poison Oak, Toxicodendron diversilobum (Anacardiaceae), from California

   https://doi.org/10.1128/mra.01279-22  

   Huitron Vazquez, Laura I.; Aviles, Perla E.; Bailon, Samantha A.; Cabanillas, Abner G.; Fernandez, Andrea; Galarza, Juan I.; Guerrero, Brianna; Hernandez, Araceli B.; Hernandez, Daniel; Jarrett, Khegan; et al (March 2023, Microbiology Resource Announcements)

   Pritchard, Leighton (Ed.)

   ABSTRACT Here, we present the complete chloroplast genome sequence of Toxicodendron diversilobum , western poison oak, from Pacific Grove, California. The genome is 159,543 bp in length, contains 133 genes, and has a high level of gene synteny to other species of Toxicodendron . 

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3. A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

   https://doi.org/10.1111/nph.20463  

   Larson, Drew_A; Staton, Margaret_E; Kapoor, Beant; Islam‐Faridi, Nurul; Zhebentyayeva, Tetyana; Fan, Shenghua; Stork, Jozsef; Thomas, Austin; Ahmed, Alaa_S; Stanton, Elizabeth_C; et al (February 2025, New Phytologist)

   Summary White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important.We report the first haplotype‐resolved chromosome‐scale genome assembly ofQ. albaand conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data.Despite strongly conserved chromosome synteny and genome size acrossQuercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found thatQ. albahas high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus.The white oak genome represents a major new resource for studying genome diversity and evolution inQuercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution inQuercus. 

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4. The reference genome assembly of the bright cobblestone lichen, Acarospora socialis

   https://doi.org/10.1093/jhered/esad052  

   Adams, Julia N.; Escalona, Merly; Marimuthu, Mohan P. A.; Fairbairn, Colin W.; Beraut, Eric; Seligmann, William; Nguyen, Oanh; Chumchim, Noravit; Stajich, Jason E.; Olsen, ed., Kenneth (September 2023, Journal of Heredity)

   Abstract Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California. 

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5. Insights into longhorn beetle (Cerambycidae) evolution from comparative analyses of the red-headed ash borer ( Neoclytus acuminatus acuminatus ) genome

   https://doi.org/10.1093/jhered/esaf016  

   Sylvester, Terrence; Adams, Richard; Mitchell, Robert F; Ray, Ann M; Shen, Rongrong; Shin, Na Ra; Daundasekara, Kasuni C; McKenna, Duane D (March 2025, Journal of Heredity)

   Neoclytus acuminatus acuminatus, the red-headed ash borer, is a wood-boring longhorn beetle (Cerambycidae: Cerambycinae) native to North America and introduced in Eurasia and South America. Its larvae develop in dying or recently dead hardwood trees, including ecologically and economically significant species of ash, hickory, and oak. We sequenced, assembled, and annotated the genome of a female N. acuminatus and compared it to the publicly available genomes of other cerambycid species. The 508 Mb N. acuminatus genome assembly spanned 20 contigs (19 nuclear + 1 mitochondrial), with an N50 of 52.59 Mb and largest contig of 61.20 Mb. A moderately high fraction of the genome (62.63%) comprised repetitive sequences, with nearly all (99.4%) expected single-copy orthologous genes (BUSCOs) present and fully assembled. We identified 2 contigs as fragments of the N. acuminatus sex chromosome. Genome annotation identified 12,899 genes, including 109 putative horizontally transferred loci. Synteny analysis identified well-conserved blocks of collinearity between the N. acuminatus genome and other Cerambycidae. The genome contains a similar number of genes encoding putative plant cell wall degrading enzymes as other Cerambycidae. The N. acuminatus genome provides new insights into genome evolution in the family Cerambycidae, known for its rich diversity of xylophagous species, and provides a new viewpoint from which to study the evolution and genomic basis of traits such as wood-feeding and olfaction in beetles and other insects. 

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