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1. 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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2. Chromosome-level genome assembly of the blue crab, Callinectes sapidus

   https://doi.org/doi.org/10.1093/g3journal/jkab212  

   Bachvaroff, T.R. (June 2021, Genes genomes genomics)

   null (Ed.)

   The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200× coverage Illumina paired-end reads, a 60× 8 kb mate-paired library, and 50× PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The 50 largest scaffolds span 810 Mb are 1.5–37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10 kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but 9 scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species. 

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3. A chromosome-level genome assembly for the eastern fence lizard (Sceloporus undulatus), a reptile model for physiological and evolutionary ecology.

   https://doi.org/10.1093/gigascience/giab066  

   Westfall, A. K.; Telemeco, R. S.; Grizante, M. B.; Waits, D. S.; Clark, A. D.; Simpson D. Y.; Klabacka, R. L.; Sullivan, A. P.; Perry, G. H.; Sears, M. W.; et al (October 2021, GigaScience)

   Background High-quality genomic resources facilitate investigations into behavioral ecology, morphological and physiological adaptations, and the evolution of genomic architecture. Lizards in the genus Sceloporus have a long history as important ecological, evolutionary, and physiological models, making them a valuable target for the development of genomic resources. Findings We present a high-quality chromosome-level reference genome assembly, SceUnd1.0 (using 10X Genomics Chromium, HiC, and Pacific Biosciences data), and tissue/developmental stage transcriptomes for the eastern fence lizard, Sceloporus undulatus. We performed synteny analysis with other snake and lizard assemblies to identify broad patterns of chromosome evolution including the fusion of micro- and macrochromosomes. We also used this new assembly to provide improved reference-based genome assemblies for 34 additional Sceloporus species. Finally, we used RNAseq and whole-genome resequencing data to compare 3 assemblies, each representing an increased level of cost and effort: Supernova Assembly with data from 10X Genomics Chromium, HiRise Assembly that added data from HiC, and PBJelly Assembly that added data from Pacific Biosciences sequencing. We found that the Supernova Assembly contained the full genome and was a suitable reference for RNAseq and single-nucleotide polymorphism calling, but the chromosome-level scaffolds provided by the addition of HiC data allowed synteny and whole-genome association mapping analyses. The subsequent addition of PacBio data doubled the contig N50 but provided negligible gains in scaffold length. Conclusions These new genomic resources provide valuable tools for advanced molecular analysis of an organism that has become a model in physiology and evolutionary ecology. 

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4. Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

   https://doi.org/10.1093/jhered/esad037  

   Bishop, Anusha P; Westeen, Erin P; Yuan, Michael L; Escalona, Merly; Beraut, Eric; Fairbairn, Colin; Marimuthu, Mohan_P A; Nguyen, Oanh; Chumchim, Noravit; Toffelmier, Erin; et al (June 2023, Journal of Heredity)

   Shapiro, Beth (Ed.)

   Abstract Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards. 

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5. Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

   https://doi.org/10.1093/gigascience/giac025  

   Robledo-Ruiz, Diana A; Gan, Han Ming; Kaur, Parwinder; Dudchenko, Olga; Weisz, David; Khan, Ruqayya; Lieberman Aiden, Erez; Osipova, Ekaterina; Hiller, Michael; Morales, Hernán E; et al (January 2022, GigaScience)

   Abstract Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population is the subject of genetic rescue. To understand, monitor, and modulate the effects of genetic rescue on the helmeted honeyeater genome, a chromosome-length genome and a high-density linkage map are required. Results We used a combination of Illumina, Oxford Nanopore, and Hi-C sequencing technologies to assemble a chromosome-length genome of the helmeted honeyeater, comprising 906 scaffolds, with length of 1.1 Gb and scaffold N50 of 63.8 Mb. Annotation comprised 57,181 gene models. Using a pedigree of 257 birds and 53,111 single-nucleotide polymorphisms, we obtained high-density linkage and recombination maps for 25 autosomes and Z chromosome. The total sex-averaged linkage map was 1,347 cM long, with the male map being 6.7% longer than the female map. Recombination maps revealed sexually dimorphic recombination rates (overall higher in males), with average recombination rate of 1.8 cM/Mb. Comparative analyses revealed high synteny of the helmeted honeyeater genome with that of 3 passerine species (e.g., 32 Hi-C scaffolds mapped to 30 zebra finch autosomes and Z chromosome). The genome assembly and linkage map suggest that the helmeted honeyeater exhibits a fission of chromosome 1A into 2 chromosomes relative to zebra finch. PSMC analysis showed a ∼15-fold decline in effective population size to ∼60,000 from mid- to late Pleistocene. Conclusions The annotated chromosome-length genome and high-density linkage map provide rich resources for evolutionary studies and will be fundamental in guiding conservation efforts for the helmeted honeyeater. 

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