TY  - JOUR
AB  - The COVID-19 pandemic has catalyzed unprecedented scientific data and reagent sharing and collaboration, which enabled understanding the virology of the SARS-CoV-2 virus and vaccine development at record speed. The pandemic, however, has also raised awareness of the danger posed by the family of coronaviruses, of which 7 are known to infect humans and dozens have been identified in reservoir species, such as bats, rodents, or livestock. To facilitate understanding the commonalities and specifics of coronavirus infections and aspects of viral biology that determine their level of lethality to the human host, we have generated a collection of freely available clones encoding nearly all human coronavirus proteins known to date. We hope that this flexible, Gateway-compatible vector collection will encourage further research into the interactions of coronaviruses with their human host, to increase preparedness for future zoonotic viral outbreaks.
AU  - Weller, B.
AU  - Lin, C.-W.
AU  - Pogoutse, O.*
AU  - Sauer, M.
AU  - Marin De La Rosa, N.A.
AU  - Strobel, A.
AU  - Young, V.
AU  - Knapp, J.J.*
AU  - Rayhan, A.*
AU  - Falter, C.
AU  - Kim, D.K.*
AU  - Roth, F.P.*
AU  - Falter-Braun, P.
C1  - 67856
C2  - 54334
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
TI  - A resource of human coronavirus protein-coding sequences in a flexible, multipurpose Gateway Entry clone collection.
JO  - Genes Genomes Genetics G3
VL  - 13
IS  - 7
PB  - Oxford Univ Press Inc
PY  - 2023
SN  - 2160-1836
ER  - 

TY  - JOUR
AB  - Combining samples for genetic association is standard practice in human genetic analysis of complex traits, but is rarely undertaken in rodent genetics. Here, using 23 phenotypes and genotypes from two independent laboratories, we obtained a sample size of 3,076 commercially available outbred mice and identified 70 loci, more than double the number of loci identified in the component studies. Fine-mapping in the combined sample reduced the number of likely causal variants, with a median reduction in set size of 51%, and indicated novel gene associations, including Pnpo, Ttll6 and GM11545 with bone mineral density, and Psmb9 with weight. However replication at a nominal threshold of 0.05 between the two component studies was low, with less than a third of loci identified in one study replicated in the second. In addition to overestimates in the effect size in the discovery sample (Winner's Curse), we also found that heterogeneity between studies explained the poor replication, but the contribution of these two factors varied among traits. Leveraging these observations we integrated information about replication rates, study-specific heterogeneity, and Winner's Curse corrected estimates of power to assign variants to one of four confidence levels. Our approach addresses concerns about reproducibility, and demonstrates how to obtain robust results from mapping complex traits in any genome-wide association study.
AU  - Zou, J.*
AU  - Gopalakrishnan, S.*
AU  - Parker, C.C.*
AU  - Nicod, J.*
AU  - Mott, R.*
AU  - Cai, N.
AU  - Lionikas, A.*
AU  - Davies, R.W.*
AU  - Palmer, A.A.*
AU  - Flint, J.*
C1  - 63640
C2  - 51648
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
TI  - Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility.
JO  - Genes Genomes Genetics G3
VL  - 12
IS  - 1
PB  - Oxford Univ Press Inc
PY  - 2022
SN  - 2160-1836
ER  - 

TY  - JOUR
AB  - Barley (Hordeum vulgare) was domesticated from its wild ancestral form ca. 10,000 years ago in the Fertile Crescent and is widely cultivated throughout the world, except for in tropical areas. The genome size of both cultivated barley and its conspecific wild ancestor is approximately 5 Gb. High-quality chromosome-level assemblies of 19 cultivated and one wild barley genotype were recently established by pan-genome analysis. Here, we release another equivalent short-read assembly of the wild barley accession "OUH602." A series of genetic and genomic resources were developed for this genotype in prior studies. Our assembly contains more than 4.4 Gb of sequence, with a scaffold N50 value of over 10 Mb. The haplotype shows high collinearity with the most recently updated barley reference genome, "Morex" V3, with some inversions. Gene projections based on "Morex" gene models revealed 46,807 protein-coding sequences and 43,375 protein-coding genes. Alignments to publicly available sequences of bacterial artificial chromosome (BAC) clones of "OUH602" confirm the high accuracy of the assembly. Since more loci of interest have been identified in "OUH602," the release of this assembly, with detailed genomic information, should accelerate gene identification and the utilization of this key wild barley accession.
AU  - Sato, K.*
AU  - Mascher, M.*
AU  - Himmelbach, A.*
AU  - Haberer, G.
AU  - Spannagl, M.
AU  - Stein, N.*
C1  - 63106
C2  - 51310
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
TI  - Chromosome-scale assembly of wild barley accession "OUH602".
JO  - Genes Genomes Genetics G3
VL  - 11
IS  - 10
PB  - Oxford Univ Press Inc
PY  - 2021
SN  - 2160-1836
ER  - 

TY  - JOUR
AB  - Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2,245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.
AU  - Wang, L.*
AU  - Zhu, T.*
AU  - Rodriguez, J.C.*
AU  - Deal, K.R.*
AU  - Dubcovsky, J.*
AU  - McGuire, P.E.*
AU  - Lux, T.
AU  - Spannagl, M.
AU  - Mayer, K.F.X.
AU  - Baldrich, P.*
AU  - Meyers, B.C.*
AU  - Huo, N.*
AU  - Gu, Y.Q.*
AU  - Zhou, H.*
AU  - Devos, K.M.*
AU  - Bennetzen, J.L.*
AU  - Unver, T.*
AU  - Budak, H.*
AU  - Gulick, P.J.*
AU  - Galiba, G.*
AU  - Kalapos, B.*
AU  - Nelson, D.R.*
AU  - Li, P.*
AU  - You, F.M.*
AU  - Luo, M.C.*
AU  - Dvorak, J.*
C1  - 63060
C2  - 51256
CY  - Journals Dept, 2001 Evans Rd, Cary, Nc 27513 Usa
TI  - Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation.
JO  - Genes Genomes Genetics G3
VL  - 11
IS  - 12
PB  - Oxford Univ Press Inc
PY  - 2021
SN  - 2160-1836
ER  - 

TY  - JOUR
AB  - Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced biotic and abiotic stress resistance in tomato breeding. S. chilense also serves as a model to study adaptation of plants to drought and the evolution of seed banks. The absence of a well-annotated reference genome in this compulsory outcrossing, very diverse species limits in-depth studies on the genes involved.We generated similar to 134 Gb of DNA and 157 Gb of RNA sequence data for S chilense, which yielded a draft genome with an estimated length of 914 Mb, encoding 25,885 high-confidence predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% of these gene models are supported by RNA-seq data derived from leaf tissue samples. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% of BUSCO genes. To further verify the genome annotation completeness and accuracy, we manually inspected the NLR resistance gene family and assessed its assembly quality. We find subfamilies of NLRs unique to S. chilense. Synteny analysis suggests significant degree of the gene order conservation between the S. chilense, S. lycopersicum and S. pennellii genomes.We generated the first genome and transcriptome sequence assemblies for the wild tomato species Solanum chilense and demonstrated their value in comparative genomics analyses. These data are an important resource for studies on adaptation to biotic and abiotic stress in Solanaceae, on evolution of self-incompatibility and for tomato breeding.
AU  - Stam, R.*
AU  - Nosenko, T.
AU  - Hörger, A.C.*
AU  - Stephan, W.*
AU  - Seidel, M.
AU  - Kuhn, J.M.M.*
AU  - Haberer, G.
AU  - Tellier, A.*
C1  - 57631
C2  - 47871
CY  - 9650 Rockville Ave, Bethesda, Md 20814 Usa
SP  - 3933-3941
TI  - The de novo reference genome and transcriptome assemblies of the wild Ttmato species solanum chilense highlights birth and death of NLR genes between tomato species.
JO  - Genes Genomes Genetics G3
VL  - 9
IS  - 12
PB  - Genetics Society America
PY  - 2019
SN  - 2160-1836
ER  - 

TY  - JOUR
AB  - The vertebrate Scube (Signal peptide, CUB and EGF-like domain-containing protein) family consists of three independent members Scube1-3, which encode secreted cell surface-associated membrane glycoproteins. Limited information about the general function of this gene family is available, and their roles during adulthood. Here, we present the first Scube3 mutant mouse line (Scube3N294K/N294K) that clearly shows phenotypic alterations by carrying a missense mutation in exon 8, and thus contributes to understand SCUBE3 functions. We performed a detailed phenotypic characterization in the German Mouse Clinic (GMC). Scube3N294K/N294K mutants showed morphological abnormalities of the skeleton, alterations of parameters relevant for bone metabolism, changes in renal function and hearing impairments. These findings correlate with characteristics of the rare metabolic bone disorder Paget disease of bone (PDB), associated with the chromosomal region of human SCUBE3. In addition, alterations in energy metabolism, behavior and neurological functions were detected in Scube3N294K/N294K mice. The Scube3N294K/N294K mutant mouse line may serve as a new model for further studying the effect of impaired SCUBE3 gene function.
AU  - Fuchs, H.
AU  - Sabrautzki, S.
AU  - Przemeck, G.K.H.
AU  - Leuchtenberger, S.
AU  - Lorenz-Depiereux, B.
AU  - Becker, L.
AU  - Rathkolb, B.
AU  - Horsch, M.
AU  - Garrett, L.
AU  - Östereicher, M.A.
AU  - Hans, W.
AU  - Abe, K.*
AU  - Sagawa, N.*
AU  - Rozman, J.
AU  - Vargas Panesso, I.L.
AU  - Sandholzer, M.
AU  - Lisse, T.S.
AU  - Adler, T.
AU  - Aguilar-Pimentel, J.A.
AU  - Calzada-Wack, J.
AU  - Ehrhard, N.
AU  - Elvert, R.
AU  - Gau, C.
AU  - Hölter, S.M.
AU  - Micklich, K.
AU  - Moreth, K.
AU  - Prehn, C.
AU  - Puk, O.
AU  - Rácz, I.*
AU  - Stoeger, C.
AU  - Vernaleken, A.
AU  - Michel, D.
AU  - Diener, S.
AU  - Wieland, T.
AU  - Adamski, J.
AU  - Bekeredjian, R.*
AU  - Lengger, C.
AU  - Maier, H.
AU  - Neff, F.
AU  - Ollert, M.*
AU  - Stöger, T.
AU  - Yildirim, A.Ö.
AU  - Strom, T.M.
AU  - Zimmer, A.*
AU  - Wolf, E.*
AU  - Wurst, W.
AU  - Klopstock, T.*
AU  - Beckers, J.
AU  - Gailus-Durner, V.
AU  - Hrabě de Angelis, M.
C1  - 49816
C2  - 41847
CY  - Bethesda
SP  - 4035-4046
TI  - The first Scube3 mutant mouse line with pleiotropic phenotypic alterations.
JO  - Genes Genomes Genetics G3
VL  - 6
IS  - 12
PB  - Genetics Society America
PY  - 2016
SN  - 2160-1836
ER  - 

TY  - JOUR
AB  - The date palm (Phoenix dactylifera L.) is one of the oldest cultivated trees and is intimately tied to the history of human civilization. There are hundreds of commercial cultivars with distinct fruit shapes, colors and sizes growing mainly in arid lands from the west of North Africa to India. The origin of date palm domestication is still uncertain and few studies have attempted to document genetic diversity across multiple regions. We conducted genotyping-by-sequencing on 70 female cultivar samples from across the date palm-growing regions, including four Phoenix species as outgroup. Here, for the first time we generate genome-wide genotyping data for 13,000 - 65,000 SNPs in a diverse set of date palm fruit and leaf samples. Our analysis provides the first genome-wide evidence confirming recent findings that the date palm cultivars segregate into two main regions of shared genetic background from North Africa and the Arabian Gulf. We identify genomic regions with high densities of geographically segregating SNPs and also observe higher levels of allele fixation on the recently described X-chromosome than on the autosomes. Our results fit a model with two centers of earliest cultivation including date palms autochthonous to North Africa. These results adjust our understanding of human agriculture history and will provide the foundation for more directed functional studies and a better understanding of genetic diversity in date palm.
AU  - Mathew, L.S.*
AU  - Seidel, M.
AU  - George, B.*
AU  - Mathew, S.*
AU  - Spannagl, M.
AU  - Haberer, G.
AU  - Torres, M.F.*
AU  - Al-Dous, E.K.*
AU  - Al-Azwani, E.K.*
AU  - Diboun, I.*
AU  - Krueger, R.R.*
AU  - Mayer, K.F.X.
AU  - Mohamoud, Y.A.*
AU  - Suhre, K.
AU  - Malek, J.A.*
C1  - 44810
C2  - 37064
CY  - Bethesda
SP  - 1429-1438
TI  - A genome-wide survey of date palm cultivars supports two major subpopulations in Phoenix dactylifera.
JO  - Genes Genomes Genetics G3
VL  - 5
IS  - 7
PB  - Genetics Society America
PY  - 2015
SN  - 2160-1836
ER  - 

TY  - JOUR
AB  - Fusarium head blight is a prevalent disease of bread wheat (Triticum aestivum L. ), which leads to considerable losses in yield and quality. Quantitative resistance to the causative fungus Fusarium graminearum is yet poorly understood. We integrated transcriptomics and metabolomics data to dissect the molecular response to the fungus and its main virulence factor, the toxin deoxynivalenol in near-isogenic lines segregating for two resistance quantitative trait loci, Fhb1 and Qfhs.ifa-5A. The data sets portrait rearrangements in the primary metabolism and the translational machinery to counter the fungus and the effects of the toxin and highlight distinct changes in the metabolism of glutamate in lines carrying Qfhs.ifa-5A. These observations are possibly due to the activity of two amino acid permeases located in the QTL confidence interval, which may contribute to increased pathogen endurance. Mapping to the highly resolved region of Fhb1 reduced the list of candidates to few genes that are specifically expressed in presence of the QTL and in response to the pathogen, which include a receptor-like protein kinase, a protein kinase, and an E3 ubiquitin-protein ligase. On a genome-scale level the individual subgenomes of hexaploid wheat contribute differentially to defense: Especially the D subgenome exhibited a pronounced response to the pathogen and contributed significantly to the overall defense response.
AU  - Nussbaumer, T.
AU  - Warth, B.*
AU  - Sharma, S.
AU  - Ametz, C.*
AU  - Bueschl, C.*
AU  - Parich, A.*
AU  - Pfeifer, M.
AU  - Siegwart, G.*
AU  - Steiner, B.*
AU  - Lemmens, M.*
AU  - Schuhmacher, R.*
AU  - Buerstmayr, H.*
AU  - Mayer, K.F.X.
AU  - Kugler, K.G.
AU  - Schweiger, W.*
C1  - 47409
C2  - 39299
SP  - 2579-2592
TI  - Joint tanscriptomic and metabolomic analyses reveal changes in the primary metabolism and imbalances in the subgenome orchestration in the bread wheat molecular response to Fusarium graminearum.
JO  - Genes Genomes Genetics G3
VL  - 5
IS  - 12
PY  - 2015
SN  - 2160-1836
ER  -