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1. A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus

   https://doi.org/10.1093/jhered/esab002  

   Heaton, Michael P ; Smith, Timothy P ; Bickhart, Derek M ; Vander Ley, Brian L ; Kuehn, Larry A ; Oppenheimer, Jonas ; Shafer, Wade R ; Schuetze, Fred T ; Stroud, Brad ; McClure, Jennifer C ; et al ( January 2021 , Journal of Heredity)

   Koepfli, Klaus-Peter (Ed.)

   Abstract Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison–cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date. 

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2. Reintroducing bison results in long-running and resilient increases in grassland diversity

   https://doi.org/10.1073/pnas.2210433119  

   Ratajczak, Zak ; Collins, Scott L. ; Blair, John M. ; Koerner, Sally E. ; Louthan, Allison M. ; Smith, Melinda D. ; Taylor, Jeffrey H. ; Nippert, Jesse B. ( September 2022 , Proceedings of the National Academy of Sciences)

   The widespread extirpation of megafauna may have destabilized ecosystems and altered biodiversity globally. Most megafauna extinctions occurred before the modern record, leaving it unclear how their loss impacts current biodiversity. We report the long-term effects of reintroducing plains bison ( Bison bison ) in a tallgrass prairie versus two land uses that commonly occur in many North American grasslands: 1) no grazing and 2) intensive growing-season grazing by domesticated cattle ( Bos taurus ). Compared to ungrazed areas, reintroducing bison increased native plant species richness by 103% at local scales (10 m 2 ) and 86% at the catchment scale. Gains in richness continued for 29 y and were resilient to the most extreme drought in four decades. These gains are now among the largest recorded increases in species richness due to grazing in grasslands globally. Grazing by domestic cattle also increased native plant species richness, but by less than half as much as bison. This study indicates that some ecosystems maintain a latent potential for increased native plant species richness following the reintroduction of native herbivores, which was unmatched by domesticated grazers. Native-grazer gains in richness were resilient to an extreme drought, a pressure likely to become more common under future global environmental change. 

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3. A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus

   https://doi.org/10.1111/tpj.16433  

   Mansfeld, Ben N. ; Yocca, Alan ; Ou, Shujun ; Harkess, Alex ; Burchard, Erik ; Gutierrez, Benjamin ; van Nocker, Steve ; Gottschalk, Christopher ( August 2023 , The Plant Journal)

   The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus×domestica). With a range extending from Alaska to Northern California,M. fuscais extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization ofM. fuscahave been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation forM. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome ofM. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wildMalusspecies. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.

    

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4. The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies

   https://doi.org/10.1093/jhered/esae013  

   Bredemeyer, Kevin R. ; vonHoldt, Bridgett M. ; Foley, Nicole M. ; Childers, Isabella R. ; Brzeski, Kristin E. ; Murphy, William J. ; Shapiro, ed., Beth ( February 2024 , Journal of Heredity)

   Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics.

    

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5. Methane efflux from an American bison herd

   https://doi.org/10.5194/bg-18-961-2021  

   Stoy, Paul C. ; Cook, Adam A. ; Dore, John E. ; Kljun, Natascha ; Kleindl, William ; Brookshire, E. N. ; Gerken, Tobias ( January 2021 , Biogeosciences)

   null (Ed.)

   Abstract. American bison (Bison bison L.) have recovered from the brink ofextinction over the past century. Bison reintroduction creates multipleenvironmental benefits, but impacts on greenhouse gas emissions are poorlyunderstood. Bison are thought to have produced some 2 Tg yr−1 of theestimated 9–15 Tg yr−1 of pre-industrial enteric methane emissions,but few measurements have been made due to their mobile grazing habits andsafety issues associated with measuring non-domesticated animals. Here, wemeasure methane and carbon dioxide fluxes from a bison herd on an enclosedpasture during daytime periods in winter using eddy covariance. Methaneemissions from the study area were negligible in the absence of bison(mean ± standard deviation = −0.0009 ± 0.008 µmol m−2 s−1) and were significantly greater than zero,0.048 ± 0.082 µmol m−2 s−1, with a positively skeweddistribution, when bison were present. We coupled bison location estimatesfrom automated camera images with two independent flux footprint models tocalculate a mean per-animal methane efflux of 58.5 µmol s−1 per bison, similar to eddy covariance measurements ofmethane efflux from a cattle feedlot during winter. When we sum theobservations over time with conservative uncertainty estimates we arrive at81 g CH4 per bison d−1 with 95 % confidence intervalsbetween 54 and 109 g CH4 per bison d−1. Uncertainty wasdominated by bison location estimates (46 % of the total uncertainty),then the flux footprint model (33 %) and the eddy covariance measurements(21 %), suggesting that making higher-resolution animal location estimatesis a logical starting point for decreasing total uncertainty. Annualmeasurements are ultimately necessary to determine the full greenhouse gasburden of bison grazing systems. Our observations highlight the need tocompare greenhouse gas emissions from different ruminant grazing systems anddemonstrate the potential for using eddy covariance to measure methaneefflux from non-domesticated animals. 

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