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1. Whole genome assembly and annotation of the endangered Caribbean coral Acropora cervicornis

   https://doi.org/10.1093/g3journal/jkad232  

   Selwyn, Jason D; Vollmer, Steven V (October 2023, G3: Genes, Genomes, Genetics)

   Vogel, K (Ed.)

   Abstract Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade. 

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2. Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus , an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

   https://doi.org/10.1093/gigascience/giac070  

   Wang, Haolong; Su, Baofeng; Butts, Ian A. E.; Dunham, Rex A.; Wang, Xu (July 2022, GigaScience)

   Abstract BackgroundThe blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. ResultsThe blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. ConclusionsWe reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish. 

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3. 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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4. Exploring chromosome evolution in 250 million year old groups of dragonflies and damselflies (Insecta:Odonata)

   https://doi.org/10.1111/mec.17147  

   Tolman, Ethan R; Beatty, Christopher D; Bush, Jonas; Kohli, Manpreet K; Frandsen, Paul B; Gosnell, J Stephen; Ware, Jessica L (November 2023, Molecular Ecology)

   Abstract Using recently published chromosome‐length genome assemblies of two damselfly species,Ischnura elegansandPlatycnemis pennipes, and two dragonfly species,Pantala flavescensandTanypteryx hageni, we demonstrate that the autosomes of Odonata have undergone few fission, fusion, or inversion events, despite 250 million years of separation. In the four genomes discussed here, our results show that all autosomes have a clear ortholog in the ancestral karyotype. Despite this clear chromosomal orthology, we demonstrate that different factors, including concentration of repeat dynamics, GC content, relative position on the chromosome, and the relative proportion of coding sequence all influence the density of syntenic blocks across chromosomes. However, these factors do not interact to influence synteny the same way in any two pairs of species, nor is any one factor retained in all four species. Furthermore, it was previously unknown whether the micro‐chromosomes in Odonata are descended from one ancestral chromosome. Despite structural rearrangements, our evidence suggests that the micro‐chromosomes in the sampled Odonata do indeed descend from an ancestral chromosome, and that the micro‐chromosome inP. flavescenswas lost through fusion with autosomes. 

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5. Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis

   https://doi.org/10.1111/nph.18521  

   Tremble, Keaton; Hoffman, J. I.; Dentinger, Bryn T. (January 2023, New Phytologist)

   Summary In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome‐wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis , a globally distributed species complex with broad ecological amplitude. By whole‐genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome‐wide differentiation and to identify the adaptive processes shaping global population structure. We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62–2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene–Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation. Our study uncovers striking patterns of genome‐wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation. 

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