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1. Rapid macrosatellite evolution promotes X-Linked hybrid male sterility in a feline interspecies cross

   https://doi.org/10.1093/molbev/msab274  

   Bredemeyer, Kevin R ; Seabury, Christopher M ; Stickney, Mark J ; McCarrey, John R ; vonHoldt, Bridgett M ; Murphy, William J ( September 2021 , Molecular Biology and Evolution)

   Gojobori, Jun (Ed.)

   Abstract The sterility or inviability of hybrid offspring produced from an interspecific mating results from incompatibilities between parental genotypes that are thought to result from divergence of loci involved in epistatic interactions. However, attributes contributing to the rapid evolution of these regions also complicates their assembly, thus discovery of candidate hybrid sterility loci is difficult and has been restricted to a small number of model systems. Here we reported rapid interspecific divergence at the DXZ4 macrosatellite locus in an interspecific cross between two closely related mammalian species: the domestic cat (Felis silvestris catus) and the Jungle cat (Felis chaus). DXZ4 is an interesting candidate due to its structural complexity, copy number variability, and described role in the critical yet complex biological process of X-chromosome inactivation. However, the full structure of DXZ4 was absent or incomplete in nearly every available mammalian genome assembly given its repetitive complexity. We compared highly continuous genomes for three cat species, each containing a complete DXZ4 locus, and discovered that the felid DXZ4 locus differs substantially from the human ortholog, and that it varies in copy number between cat species. Additionally, we reported expression, methylation, and structural conformation profiles of DXZ4 and the X chromosome during stages of spermatogenesis that have been previously associated with hybrid male sterility. Collectively, these findings suggest a new role for DXZ4 in male meiosis and a proposed mechanism of feline interspecific incompatibility through rapid satellite divergence. 

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2. The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids

   https://doi.org/10.1073/pnas.2310763120  

   Yuan, Jiaqing ; Kitchener, Andrew C. ; Lackey, Laurie Bingaman ; Sun, Ting ; Jiangzuo, Qigao ; Tuohetahong, Yilamujiang ; Zhao, Le ; Yang, Peng ; Wang, Guiqiang ; Huang, Chen ; et al ( January 2024 , Proceedings of the National Academy of Sciences)

   Habitat degradation and loss of genetic diversity are common threats faced by almost all of today’s wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat,Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.

    

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3. Structural and functional characterization of three Type B and C chloramphenicol acetyltransferases from Vibrio species

   https://doi.org/10.1002/pro.3793  

   Alcala, Ashley ; Ramirez, Guadalupe ; Solis, Allan ; Kim, Youngchang ; Tan, Kemin ; Luna, Oscar ; Nguyen, Karen ; Vazquez, Daniel ; Ward, Michael ; Zhou, Min ; et al ( December 2019 , Protein Science)

   Chloramphenicol acetyltransferases (CATs) were among the first antibiotic resistance enzymes identified and have long been studied as model enzymes for examining plasmid‐mediated antibiotic resistance. These enzymes acetylate the antibiotic chloramphenicol, which renders it incapable of inhibiting bacterial protein synthesis. CATs can be classified into different types: Type A CATs are known to be important for antibiotic resistance to chloramphenicol and fusidic acid. Type B CATs are often called xenobiotic acetyltransferases and adopt a similar structural fold to streptogramin acetyltransferases, which are known to be critical for streptogramin antibiotic resistance. Type C CATs have recently been identified and can also acetylate chloramphenicol, but their roles in antibiotic resistance are largely unknown. Here, we structurally and kinetically characterized threeVibrioCAT proteins from a nonpathogenic species (Aliivibrio fisheri) and two important human pathogens (Vibrio choleraeandVibrio vulnificus). We found all three proteins, including one in a superintegron (V. cholerae), acetylated chloramphenicol, but did not acetylate aminoglycosides or dalfopristin. We also determined the 3D crystal structures of these CATs alone and in complex with crystal violet and taurocholate. These compounds are known inhibitors of Type A CATs, but have not been explored in Type B and Type C CATs. Based on sequence, structure, and kinetic analysis, we concluded that theV. choleraeandV. vulnificusCATs belong to the Type B class and theA. fisheriCAT belongs to the Type C class. Ultimately, our results provide a framework for studying the evolution of antibiotic resistance gene acquisition and chloramphenicol acetylation inVibrioand other species.

    

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4. The macroecology and evolution of avian competence for Borrelia burgdorferi

   https://doi.org/10.1111/geb.13256  

   Becker, Daniel J. ; Han, Barbara A. ; Kamath, ed., Pauline ( January 2021 , Global Ecology and Biogeography)

   Prediction of novel reservoirs of zoonotic pathogens would be improved by the identification of interspecific drivers of host competence (i.e., the ability to transmit pathogens to new hosts or vectors). Tick‐borne pathogens can provide a useful model system, because larvae become infected only when feeding on a competent host during their first blood meal. For tick‐borne diseases, competence has been studied best forBorrelia burgdorferisensu lato (Bbsl), which causes Lyme borreliosis. Major reservoirs include several small mammal species, but birds might play an under‐recognized role in human risk given their ability to disperse infected ticks across large spatial scales. Here, we provide a global synthesis of the ecological and evolutionary factors that determine the ability of bird species to infect larval ticks withBbsl.

   Global.

   1983–2019.

   Birds.

   We compiled a dataset ofBbsl competence across 183 bird species and applied meta‐analysis, phylogenetic factorization and boosted regression trees to describe spatial and temporal patterns in competence, characterize its phylogenetic distribution across birds, reconstruct its evolution and evaluate the trait profiles associated with competent avian species.

   Half of the sampled bird species show evidence of competence forBbsl. Competence displays moderate phylogenetic signal, has evolved multiple times across bird species and is pronounced in the genusTurdus. Trait‐based analyses distinguished competent birds with 80% accuracy and showed that such species have low baseline corticosterone, exist on both ends of the pace‐of‐life continuum, breed and winter at high latitudes and have broad migratory movements into their breeding range. We used these trait profiles to predict various likely but unsampled competent species, including novel concentrations of avian reservoirs within the Neotropics.

   Our results can generate new hypotheses for how birds contribute to the dynamics of tick‐borne pathogens and help to prioritize surveillance of likely but unsampled competent birds. Our findings also emphasize that birds display under‐recognized variation in their contributions to enzootic cycles ofBbsl and the broader need to consider competence in ecological and predictive studies of multi‐host pathogens.

    

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5. Gene Editing in Dimorphic Fungi Using CRISPR/Cas9

   https://doi.org/10.1002/cpmc.132  

   Kujoth, Gregory C. ; Sullivan, Thomas D. ; Klein, Bruce S. ( December 2020 , Current Protocols in Microbiology)

   Dimorphic fungi in the generaBlastomyces,Histoplasma,Coccidioides, andParacoccidioidesare important human pathogens that affect human health in many countries throughout the world. Understanding the biology of these fungi is important for the development of effective treatments and vaccines. Gene editing is a critically important tool for research into these organisms. In recent years, gene targeting approaches employing RNA‐guided DNA nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated nuclease 9 (Cas9), have exploded in popularity. Here, we provide a detailed description of the steps involved in applying CRISPR/Cas9 technology to dimorphic fungi, withBlastomyces dermatitidisin particular as our model fungal pathogen. We discuss the design and construction of single guide RNA and Cas9‐expressing targeting vectors (including multiplexed vectors) as well as introduction of these plasmids intoBlastomycesusingAgrobacterium‐mediated transformation. Finally, we cover the outcomes that may be expected in terms of gene‐editing efficiency and types of gene alterations produced. © 2020 Wiley Periodicals LLC.

   Basic Protocol 1: Construction of CRISPR/Cas9 targeting vectors

   Support Protocol 1: Choosing protospacers in the target gene

   Basic Protocol 2:Agrobacterium‐mediated transformation ofBlastomyces

   Support Protocol 2: Preparation of electrocompetentAgrobacterium

   Support Protocol 3: Preparation and recovery ofBlastomycesfrozen stocks

    

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