Article
Agriculture, Dairy & Animal Science
Maulana M. Naji, Yuri T. Utsunomiya, Johann Solkner, Benjamin D. Rosen, Gabor Meszaros
Summary: This study compared the alignment of sequence data from different breeds of cattle to two different reference genomes, revealing that aligning to UOA_Brahman_1 detected more SNVs, especially in cross-subspecies alignments. Unexpectedly low SNV counts in certain regions suggest the presence of taurine DNA in the UOA_Brahman_1 reference genome. Analysis of taurine-introgressed loci using principal component and admixture analyses confirmed the presence of these loci.
GENETICS SELECTION EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
H. Trebes, Y. Wang, E. Reynolds, K. Tiplady, C. Harland, T. Lopdell, T. Johnson, S. Davis, B. Harris, R. Spelman, C. Couldrey
Summary: Chromosome X is often excluded from bovine genetic studies due to complications caused by its sex-specific nature. This study demonstrates the importance of including X chromosome in dairy genetic studies and identifies missense mutations in MOSPD1 and CCDC160 genes associated with milk production traits.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Genetics & Heredity
Minou Bina
Summary: Using a whole-genome assembly of Bos taurus, the author applied a bioinformatics strategy to identify candidate imprinting control regions (ICRs) throughout the genome. The study focused on the role of genomic imprinting in mammalian embryogenesis. By analyzing peaks in plots and examining genes near candidate ICRs, potential imprinted genes were identified. The ENCODE data from mouse studies provided valuable insights into the regulatory mechanisms for cattle.
Article
Multidisciplinary Sciences
Mackenzie A. Marrella, Fernando H. Biase
Summary: Infertility or subfertility is a significant challenge in cattle production, especially in heifers. Well-nourished heifers can still be infertile due to physiological and genetic causes, making them an ideal model for studying infertility. Through genomic and proteomic analysis, we identified two SNPs and two genes associated with heifer fertility. Additionally, we found differences in protein abundance between fertile and sub-fertile heifers. This study highlights the complex nature of female fertility and the importance of molecular differences in heifers' fertility status.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Jun Ma, Tianliu Zhang, Wenxiang Wang, Yan Chen, Wentao Cai, Bo Zhu, Lingyang Xu, Huijiang Gao, Lupei Zhang, Junya Li, Xue Gao
Summary: Through transcriptome analysis of gayal, yak, and cattle, it was found that there are differences in gene expression among them in the plateau environment. Gayal and yak have highly similar adaptability to high-altitude environments, involving multiple physiological functions. Additionally, gayal and yak have many unique expression regulatory genes in adapting to high-altitude environments. These findings provide valuable insights into the complex transcriptome expression pattern and regulatory mechanisms of high-altitude domestication in gayal and yak.
FRONTIERS IN GENETICS
(2022)
Article
Biology
Mehrnush Forutan, Elizabeth Ross, Amanda J. Chamberlain, Loan Nguyen, Brett Mason, Stephen Moore, Josie B. Garner, Ruidong Xiang, Ben J. Hayes
Summary: By profiling genome-wide transcriptional start sites (TSSs) in two subspecies of cattle, researchers identified evolutionary and developmental differences in TSSs, with some SNPs located in differentially used TSS clusters showing significant shifts in allele frequency. Additionally, higher relative TSS expression of heat shock protein genes was observed in Bos indicus compared to Bos taurus, which may contribute to the tropical adaptation of Bos indicus. This study provides insights into cattle adaptation and highlights the rapid evolution of TSS between recently diverged subspecies.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jisung Jang, Jaehoon Jung, Young Ho Lee, Sanghyun Lee, Myunggi Baik, Heebal Kim
Summary: This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. A pangenome graph of 14 B. taurus genome assemblies was constructed. The assembly showed high-quality with a genome completeness of 95.8%, contig N50 over 55 Mb, and scaffold N50 over 89 Mb. 27,314 protein-coding genes were identified, including 2,012 unknown proteins, and the pangenome graph revealed non-reference regions and Hanwoo-specific regions.
Article
Biochemistry & Molecular Biology
Evgenia Solodneva, Gulnara Svishcheva, Rodion Smolnikov, Sergey Bazhenov, Evgenii Konorov, Vera Mukhina, Yurii Stolpovsky
Summary: Every week, 1-2 breeds of farm animals, including local cattle, disappear in the world. As the keepers of rare allelic variants, native breeds potentially expand the range of genetic solutions to possible problems of the future, which means that the study of the genetic structure of these breeds is an urgent task. Providing nomadic herders with valuable resources necessary for life, domestic yaks have also become an important object of study.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Spyros Tastsoglou, Giorgos Skoufos, Marios Miliotis, Dimitra Karagkouni, Ioannis Koutsoukos, Anna Karavangeli, Filippos S. Kardaras, Artemis G. Hatzigeorgiou
Summary: DIANA-miRPath is an online miRNA analysis platform that allows exploration of combined miRNA effects through predicted or experimentally supported miRNA interactions. Its latest version introduces a customizable target-based miRNA functional analysis engine, enriched with interaction, annotation, and parameterization options. The platform integrates various datasets and enables enrichment analysis on GO terms, pathways, and expression data for a wide range of states. Additionally, it provides a module for utilizing CRISPR knock-out screen datasets to identify miRNAs with potentially crucial roles.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Phillip Wyss, Carol Song, Minou Bina
Summary: This study presents a bioinformatics strategy to locate candidate ICRs systematically throughout the Bos taurus genome. By analyzing the positions of ZFP57 binding sites and CpG-rich sequences, density plots were created to identify known and potential ICRs in cattle DNA. The robustness of this approach was validated, and additional peaks in the density plots could correspond to candidate ICRs for imprinted gene expression.
Article
Agriculture, Dairy & Animal Science
Blazej Westfalewicz, Mariola Slowinska, Sylwia Judycka, Andrzej Ciereszko, Mariola A. Dietrich
Summary: This study compared sperm quality and proteomic profiles of cryopreserved semen from young and adult Holstein Friesian bulls. Proteomic analysis revealed differences in protein composition, with adult bull sperm containing proteins related to fertilization ability, while young bull sperm contained proteins related to cytoskeleton development. The results suggest that age influences the proteome of sperm, impacting sperm quality and fertilizing ability.
Article
Microbiology
Gentry L. Lewis, Robert J. Fenton, Etsuko N. Moriyama, John Dustin Loy, Rodney A. Moxley
Summary: In this study, researchers found that MDR Salmonella isolates in cattle are frequently associated with ISVsa3 and carried on IncC plasmids. Among the 111 bovine Salmonella isolates analyzed, 33 exhibited MDR phenotype. The analysis of 41 isolates using whole-genome sequencing and PCR confirmed that the presence of ISVsa3 is strongly associated with MDR genotype.
Article
Biochemical Research Methods
Anne Listrat, Celine Boby, Jeremy Tournayre, Celine Jousse
Summary: In this study, the researchers provide the first definition of the matrisome of a livestock species, Bos taurus. This finding is significant as it can be used as a model to study cell behavior, mechanotransduction, and identify novel biomarkers for diseases and cancers involving ECM. Additionally, the dataset can be valuable for studying product quality and lactation in the livestock industry.
JOURNAL OF PROTEOMICS
(2023)
Article
Microbiology
Suzanne Paley, Ingrid M. Keseler, Markus Krummenacker, Peter D. Karp
Summary: The researchers developed a method to automatically propagate curated gene and protein knowledge from one database to related strains, significantly increasing the value and utility of the target databases. The target databases received updates for a large number of proteins, with additional protein complexes, reaction assignments, and GO annotations.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Agronomy
Qianqian Zhang, Anna Amanda Schonherz, Mogens Sando Lund, Bernt Guldbrandtsen
Summary: This study demonstrates the combined effects of positive selection and adaptive introgression on the modern bovine genome through in-depth assessment of sequence variation on a whole-genome scale. The observed hotspots of runs of homozygosity (ROH) haplotypes were confirmed to be results of positive selection and were associated with productive traits in modern Bos taurus cattle breeds. The study also identifies the introgression events of haplotypes from Bos indicus to Bos taurus, contributing to the formation of the current bovine genome.
Article
Biology
Benjamin D. Rosen, Derek M. Bickhart, Robert D. Schnabel, Sergey Koren, Christine G. Elsik, Elizabeth Tseng, Troy N. Rowan, Wai Y. Low, Aleksey Zimin, Christine Couldrey, Richard Hall, Wenli Li, Arang Rhie, Jay Ghurye, Stephanie D. McKay, Francoise Thibaud-Nissen, Jinna Hoffman, Brenda M. Murdoch, Warren M. Snelling, Tara G. McDaneld, John A. Hammond, John C. Schwartz, Wilson Nandolo, Darren E. Hagen, Christian Dreischer, Sebastian J. Schultheiss, Steven G. Schroeder, Adam M. Phillippy, John B. Cole, Curtis P. Van Tassell, George Liu, Timothy P. L. Smith, Juan F. Medrano
Article
Multidisciplinary Sciences
Bridget K. Behe, Patricia T. Huddleston, Kevin L. Childs, Jiaoping Chen, Iago S. Muraro
Article
Entomology
Lelania Bilodeau, Christine Elsik
Article
Biochemistry & Molecular Biology
Bertrand Fouks, Philipp Brand, Hung N. Nguyen, Jacob Herman, Francisco Camara, Daniel Ence, Darren E. Hagen, Katharina J. Hoff, Stefanie Nachweide, Lars Romoth, Kimberly K. O. Walden, Roderic Guigo, Mario Stanke, Giuseppe Narzisi, Mark Yandell, Hugh M. Robertson, Nikolaus Koeniger, Panuwan Chantawannakul, Michael C. Schatz, Kim C. Worley, Gene E. Robinson, Christine G. Elsik, Olav Rueppell
Summary: This study compared the genomes of three different subgenera of honey bees and revealed a complex gene regulation pattern and the role of positive selection in adaptive evolution among honey bee species.
Article
Biochemistry & Molecular Biology
Z. Zhao, C. G. Elsik, B. E. Hibbard, K. S. Shelby
Summary: The study investigated the alternative splicing patterns in western corn rootworm and found that a high percentage of genes are alternatively spliced. Additionally, it suggested that alternatively spliced isoforms of peritrophic matrix protein may be associated with eCry3.1Ab resistance in western corn rootworm.
INSECT MOLECULAR BIOLOGY
(2021)
Article
Genetics & Heredity
Andrew W. Thompson, M. Brent Hawkins, Elise Parey, Dustin J. Wcisel, Tatsuya Ota, Kazuhiko Kawasaki, Emily Funk, Mauricio Losilla, Olivia E. Fitch, Qiaowei Pan, Romain Feron, Alexandra Louis, Jerome Montfort, Marine Milhes, Brett L. Racicot, Kevin L. Childs, Quenton Fontenot, Allyse Ferrara, Solomon R. David, Amy R. McCune, Alex Dornburg, Jeffrey A. Yoder, Yann Guiguen, Hugues Roest Crollius, Camille Berthelot, Matthew P. Harris, Ingo Braasch
Summary: The analysis of a chromosome-level bowfin genome assembly sheds light on the evolution of neopterygian fishes. Through examining chromatin accessibility and gene expression profiling, insights into bowfin embryonic development have been provided. The resources obtained from this study connect developmental evolution among bony fishes, emphasizing the importance of bowfin in illustrating vertebrate biology and diversity in the genomic era.
Article
Entomology
Anna K. Childers, Scott M. Geib, Sheina B. Sim, Monica F. Poelchau, Brad S. Coates, Tyler J. Simmonds, Erin D. Scully, Timothy P. L. Smith, Christopher P. Childers, Renee L. Corpuz, Kevin Hackett, Brian Scheffler
Summary: High-quality genome assemblies are crucial for modern biological research, and advancements in sequencing methods have made it possible to sequence and assemble many insect genomes at scale. The Ag100Pest Initiative aims to assemble reference-quality genomes of important arthropod pest species to advance agricultural research. The project has already made progress in assembling genomes of multiple species and has expanded the original goal to include a total of 158 species in the pipeline.
Article
Biotechnology & Applied Microbiology
Daniel B. Weaver, Brandi L. Cantarel, Christine G. Elsik, Dawn L. Boncristiani, Jay D. Evans
Summary: Through studying resistant and susceptible honey bee lineages, significant differences were found in terms of viral loads and bee gene expression. It was also discovered that honey bee lineages with naturally low levels of mite-vectored viruses also had lower levels of non-mite vectored viruses. This research provides insights into the genetic responses to viral infection and mite parasitism in different honey bee lineages, identifying candidate proteins for mite tolerance and virus resistance.
Article
Biochemistry & Molecular Biology
Amy T. Walsh, Deborah A. Triant, Justin J. Le Tourneau, Md Shamimuzzaman, Christine G. Elsik
Summary: This article presents an update of the Hymenoptera Genome Database, with a significant increase in the number of species represented and enhancements to the Gene Ontology annotations and orthology datasets available. The database continues to provide genomic data mining capabilities and genome browsers for researchers in the field.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
J. R. Standish, E. Gongora-Castillo, M. J. Bowman, K. L. Childs, M. Tian, L. M. Quesada-Ocampo
Summary: In this study, a bioinformatics pipeline was developed to predict specific diagnostic markers for Peronospora belbahrii, the causative agent of basil downy mildew. These markers were validated and used to develop a highly sensitive qPCR assay for detecting P. belbahrii in leaf tissue and seed samples. The assay was able to detect low concentrations of P. belbahrii genomic DNA and a small number of sporangia. This research is valuable for diagnostics and identifying contaminated seed lots to mitigate the effects of basil downy mildew epidemics.
Article
Entomology
Heli Salmela, Gyan P. Harwood, Daniel Munch, Christine G. Elsik, Elias Herrero-Galan, Maria K. Vartiainen, Gro Amdam
Summary: This study demonstrates that a structural subunit of honey bee Vitellogenin (Vg) can translocate into cell nuclei and bind with DNA. Chromatin immunoprecipitation with sequencing (ChIP-seq) reveals binding sites of Vg at genes influencing immunity and behavior. These findings suggest a new fundamental regulatory role for Vg in the nucleus.
Article
Multidisciplinary Sciences
Rocio Melissa Rivera, Anna Katherine Goldkamp, Bhaumik Narendrabhai Patel, Darren Erich Hagen, Edgar Joel Soto-Moreno, Yahan Li, Chris Kim, Cliff Miller, Fred Williams, Elizabeth Jannaman, Yao Xiao, Paula Tribulo, Eliab Estrada-Cortes, Astrid Roshealy Brau-Rodriguez, Peter James Hansen, Zhoulin Wu, Christine Marie Spinka, Neal Martin, Christine G. Elsik
Summary: This study investigates the large/abnormal offspring syndrome (LOS/AOS) in cattle resulting from in vitro production of embryos. The researchers suggest that fetal ultrasonography and maternal blood markers may be useful in identifying LOS during pregnancy in cattle.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Jose Planta, Yu-Ya Liang, Haoyang Xin, Matthew T. Chansler, L. Alan Prather, Ning Jiang, Jiming Jiang, Kevin L. Childs
Summary: This study expands the sequenced genomes of monocots by including four related species from Cyperaceae and Juncaceae. High-quality genome sequences were obtained by combining Nanopore long reads, Illumina short reads, and Hi-C sequencing data. Repeat landscapes and transposable elements were analyzed, revealing differences in the distribution patterns between the two families. These genome sequences and annotations will facilitate comparative analysis within monocots.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
J. Mitchell McGrath, Andrew Funk, Paul Galewski, Shujun Ou, Belinda Townsend, Karen Davenport, Hajnalka Daligault, Shannon Johnson, Joyce Lee, Alex Hastie, Aude Darracq, Glenda Willems, Steve Barnes, Ivan Liachko, Shawn Sullivan, Sergey Koren, Adam Phillippy, Jie Wang, Tiffany Liu, Jane Pulman, Kevin Childs, Shengqiang Shu, Anastasia Yocum, Damian Fermin, Effie Mutasa-Gottgens, Piergiorgio Stevanato, Kazunori Taguchi, Rachel Naegele, Kevin M. Dorn
Summary: A contiguous assembly of the 'EL10' sugar beet genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly is highly congruent with the published sugar beet reference genome, with 96.2% of the genome contained in nine chromosome-sized pseudomolecules.
Article
Plant Sciences
Noah Fahlgren, Muskan Kapoor, Galabina Yordanova, Irene Papatheodorou, Jamie Waese, Benjamin Cole, Peter Harrison, Doreen Ware, Timothy Tickle, Benedict Paten, Tony Burdett, Christine G. Elsik, Christopher K. Tuggle, Nicholas J. Provart
Summary: Building a data infrastructure for the Plant Cell Atlas using existing infrastructure and platforms will allow biologists and data scientists to gain new insights into plant biology. The development of the Human Cell Atlas and the Single Cell Expression Atlas by the European Bioinformatics Institute has laid the foundation for constructing the data infrastructure for the Plant Cell Atlas. The utilization of appropriate ontologies is crucial for describing plant single cell experiments.