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1. De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)

   https://doi.org/10.1186/s12864-022-09000-x  

   Linscott, T. Mason ; González-González, Andrea ; Hirano, Takahiro ; Parent, Christine E. ( December 2022 , BMC Genomics)

   Abstract Background Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO 3 ), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species. Results Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2–3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome . Conclusions Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO 3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs. 

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2. The C-Fern (Ceratopteris richardii) genome: insights into plant genome evolution with the first partial homosporous fern genome assembly

   https://doi.org/10.1038/s41598-019-53968-8  

   Marchant, D. Blaine ; Sessa, Emily B. ; Wolf, Paul G. ; Heo, Kweon ; Barbazuk, W. Brad ; Soltis, Pamela S. ; Soltis, Douglas E. ( December 2019 , Scientific Reports)

   Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern speciesCeratopteris richardiito address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies ofCeratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history ofCeratopterisbased on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes.

    

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3. Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

   https://doi.org/10.1093/gbe/evy157  

   Perry, Blair W ; Card, Daren C ; McGlothlin, Joel W ; Pasquesi, Giulia I ; Adams, Richard H ; Schield, Drew R ; Hales, Nicole R ; Corbin, Andrew B ; Demuth, Jeffery P ; Hoffmann, Federico G ; et al ( July 2018 , Genome Biology and Evolution)
4. Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model

   https://doi.org/10.3390/ijms22010347  

   Decker, Brandon ; Liput, Michal ; Abdellatif, Hussam ; Yergeau, Donald ; Bae, Yongho ; Jornet, Josep M. ; Stachowiak, Ewa K. ; Stachowiak, Michal K. ( January 2021 , International Journal of Molecular Sciences)

   null (Ed.)

   During the development of mouse embryonic stem cells (ESC) to neuronal committed cells (NCC), coordinated changes in the expression of 2851 genes take place, mediated by the nuclear form of FGFR1. In this paper, widespread differences are demonstrated in the ESC and NCC inter- and intra-chromosomal interactions, chromatin looping, the formation of CTCF- and nFGFR1-linked Topologically Associating Domains (TADs) on a genome-wide scale and in exemplary HoxA-D loci. The analysis centered on HoxA cluster shows that blocking FGFR1 disrupts the loop formation. FGFR1 binding and genome locales are predictive of the genome interactions; likewise, chromatin interactions along with nFGFR1 binding are predictive of the genome function and correlate with genome regulatory attributes and gene expression. This study advances a topologically integrated genome archipelago model that undergoes structural transformations through the formation of nFGFR1-associated TADs. The makeover of the TAD islands serves to recruit distinct ontogenic programs during the development of the ESC to NCC. 

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5. A pan‐genome and chromosome‐length reference genome of narrow‐leafed lupin ( Lupinus angustifolius ) reveals genomic diversity and insights into key industry and biological traits

   https://doi.org/10.1111/tpj.15885  

   Garg, Gagan ; Kamphuis, Lars G. ; Bayer, Philipp E. ; Kaur, Parwinder ; Dudchenko, Olga ; Taylor, Candy M. ; Frick, Karen M. ; Foley, Rhonda C. ; Gao, Ling‐Ling ; Aiden, Erez Lieberman ; et al ( September 2022 , The Plant Journal)