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1. Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae)

   https://doi.org/10.1093/g3journal/jkad224  

   Dial, Dustin T; Weglarz, Kathryn M; Brunet, Bryan_M T; Havill, Nathan P; von_Dohlen, Carol D; Burke, Gaelen R (September 2023, G3: Genes, Genomes, Genetics)

   McIntyre, L (Ed.)

   Abstract The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha. 

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2. A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides

   https://doi.org/10.1093/jhered/esad054  

   Schiebelhut, Lauren M; DeBiasse, Melissa B; Gabriel, Lars; Hoff, Katharina J; Dawson, Michael N (September 2023, Journal of Heredity)

   Meyer, Rachel (Ed.)

   Abstract Wildlife diseases, such as the sea star wasting (SSW) epizootic that outbroke in the mid-2010s, appear to be associated with acute and/or chronic abiotic environmental change; dissociating the effects of different drivers can be difficult. The sunflower sea star, Pycnopodia helianthoides, was the species most severely impacted during the SSW outbreak, which overlapped with periods of anomalous atmospheric and oceanographic conditions, and there is not yet a consensus on the cause(s). Genomic data may reveal underlying molecular signatures that implicate a subset of factors and, thus, clarify past events while also setting the scene for effective restoration efforts. To advance this goal, we used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to generate a highly contiguous genome assembly that was then annotated using RNA-seq-informed gene prediction. The genome assembly is 484 Mb long, with contig N50 of 1.9 Mb, scaffold N50 of 21.8 Mb, BUSCO completeness score of 96.1%, and 22 major scaffolds consistent with prior evidence that sea star genomes comprise 22 autosomes. These statistics generally fall between those of other recently assembled chromosome-scale assemblies for two species in the distantly related asteroid genus Pisaster. These novel genomic resources for P. helianthoides will underwrite population genomic, comparative genomic, and phylogenomic analyses—as well as their integration across scales—of SSW and environmental stressors. 

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3. The reference genome of a Sierra Nevada endemic, the cut-leaved monkeyflower, Mimulus laciniatus (syn. Erythranthe lacinata )

   https://doi.org/10.1093/jhered/esaf059  

   Martínez-Gómez, Jesús; Escalona, Merly; Colicchio, Jack M; Hamm, Lauren N; Marimuthu, Mohan_P A; Nguyen, Oanh; Chumchim, Noravit; Seligmann, William; Meyer, Rachel S; Sexton, Jason P; et al (August 2025, Journal of Heredity)

   Abstract Mimulus laciniatus (syn. Erythranthe lacinata) is an annual plant endemic to the Sierra Nevada region of California. Mimulus laciniatus is notable for its specialized ecological niche, thriving in granite outcrops of alpine environments characterized by shallow soils that dry out rapidly as the snowpack is exhausted during season-ending droughts. Due to its narrow habitat range and sensitivity to environmental change, this species serves as an important model for studying adaptation and survival in marginal habitats. As part of the California Conservation Genomics Project, here we report the sequencing and assembly of a high-quality nuclear genome and chloroplast genome of M. laciniatus. The primary assembly is 309.96 Mb and consists of 104 scaffolds with a scaffold N50 of 20.99 Mb, a largest contig size of 24.29 Mb and a contig N50 of 11.09 Mb, The alternate haplotype assembly consists of 194 scaffolds spanning 213.84 Mb. BUSCO completeness of the primary assembly is 98.6%. This high quality genome adds a valuable resource to the expanding collection of sequenced genomes of the monkeyflowers (Mimulus sensu lato), which have become a model clade for studying ecological adaptation, speciation, and evolutionary genetics. 

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4. Reference genome for the American rubyspot damselfly, Hetaerina americana

   https://doi.org/10.1093/jhered/esad031  

   Grether, Gregory F; Beninde, Joscha; Beraut, Eric; Chumchim, Noravit; Escalona, Merly; MacDonald, Zachary G; Miller, Courtney; Sahasrabudhe, Ruta; Shedlock, Andrew M; Toffelmier, Erin; et al (May 2023, Journal of Heredity)

   Sethuraman, Arun (Ed.)

   Abstract Damselflies and dragonflies (Order: Odonata) play important roles in both aquatic and terrestrial food webs and can serve as sentinels of ecosystem health and predictors of population trends in other taxa. The habitat requirements and limited dispersal of lotic damselflies make them especially sensitive to habitat loss and fragmentation. As such, landscape genomic studies of these taxa can help focus conservation efforts on watersheds with high levels of genetic diversity, local adaptation, and even cryptic endemism. Here, as part of the California Conservation Genomics Project (CCGP), we report the first reference genome for the American rubyspot damselfly, Hetaerina americana, a species associated with springs, streams and rivers throughout California. Following the CCGP assembly pipeline, we produced two de novo genome assemblies. The primary assembly includes 1,630,044,487 base pairs, with a contig N50 of 5.4 Mb, a scaffold N50 of 86.2 Mb, and a BUSCO completeness score of 97.6%. This is the seventh Odonata genome to be made publicly available and the first for the subfamily Hetaerininae. This reference genome fills an important phylogenetic gap in our understanding of Odonata genome evolution, and provides a genomic resource for a host of interesting ecological, evolutionary, and conservation questions for which the rubyspot damselfly genus Hetaerina is an important model system. 

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5. A haplotype-resolved chromosomal reference genome for the porcini mushroom Boletus edulis

   https://doi.org/10.1093/g3journal/jkaf069  

   Brejon_Lamartinière, Etienne; Tremble, Keaton; Dentinger, Bryn_T M; Dasmahapatra, Kanchon K; Hoffman, Joseph I (April 2025, G3: Genes, Genomes, Genetics)

   Sachs, M (Ed.)

   Abstract Haplotype-resolved chromosomal reference genomes are increasingly available for many fungi, offering insights into the evolution of pathogenic and symbiotic lifestyles. However, these resources remain scarce for ectomycorrhizal fungi, which play crucial roles in forest ecosystems. Here, we used a combination of chromatin conformation capture and PacBio sequencing to construct a haplotype-resolved chromosomal genome assembly for Boletus edulis, a prized edible fungus and emerging model for ectomycorrhizal fungal research. Our new reference assembly, “BolEdBiel_h2,” derives from a B. edulis sporocarp sampled in Bielefeld, Germany. The genome assembly spans 41.8 Mb, with a scaffold N50 of 4.1 Mb, and includes 11 chromosome-level scaffolds, achieving near telomere-to-telomere coverage across multiple chromosomes. We annotated a total of 15,406 genes, with a Benchmarking Universal Single-Copy Orthologs score of 96.2%. Key genomic features such as mating loci, carbohydrate-active enzymes, and effector proteins, were identified. As a first application of this new genomic resource, we mapped whole-genome resequencing data from 53 genets to investigate the population structure and genetic diversity of the European lineage of B. edulis. We identified 2 distinct genetic clusters and found that high-latitude populations from Iceland and Fennoscandia exhibited greater nucleotide diversity than populations from the United Kingdom and Central Europe. Additionally, we discovered a 0.4-Mb inversion on chromosome 3 and identified several regions of locally elevated nucleotide diversity, which may represent candidates for ecological adaptation. This genomic resource will facilitate a deeper understanding of this ecologically and commercially important wild fungus. 

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