Article
Biochemical Research Methods
Michael Schneider, Asis Shrestha, Agim Ballvora, Jens Leon
Summary: The proposed strategy accurately identifies the allele frequency of populations at low cost. This is particularly important for evolutionary plant breeding of crops with large genomes, such as barley. Whole-genome low coverage re-sequencing at 0.03x coverage per genotype accurately estimates allele frequency when a loci-based haplotyping approach is applied. The implementation of annotated haplotypes capitalizes on the biological background and statistical robustness.
Article
Multidisciplinary Sciences
John A. Morris, Christina Caragine, Zharko Daniloski, Julia Domingo, Timothy Barry, Lu Lu, Kyrie Davis, Marcello Ziosi, Dafni A. Glinos, Stephanie Hao, Eleni P. Mimitou, Peter Smibert, Kathryn Roeder, Eugene Katsevich, Tuuli Lappalainen, Neville E. Sanjana
Summary: By using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we have identified 124 cis target genes of 91 noncoding blood trait GWAS loci. Through precise variant insertion via base editing, we have connected specific variants with gene expression changes. We have also discovered trans-effect networks of noncoding loci when cis target genes encode transcription factors or microRNAs.
Article
Biochemistry & Molecular Biology
Roberta Piredda, Guido W. Grimm, Ernst-Detlef Schulze, Thomas Denk, Marco Cosimo Simeone
Summary: Measuring biological diversity in oaks is a challenging task due to complex differentiation in morphology, ecology, biogeography, and genetics. This pilot study successfully used high-throughput sequencing data and reference datasets to assess genetic diversity in oaks for automated genotaxonomy applications.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Agriculture, Dairy & Animal Science
M. Kinukawa, M. Ito, Y. Uemoto, A. Ogino, S. Haruta, K. Kurogi, T. Watanabe, S. Sasaki, Y. Naniwa, K. Uchiyama, K. Togashi
Summary: There is considerable variation in the bull conception rate (BCR) of Japanese Black cattle, and some bulls with a low BCR have been identified. In this study, a genome-wide association study with whole-exome sequencing was conducted to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. The g.116408653G > A SNP in Bos taurus autosome 5 was found to have a significant effect on BCR.
Article
Biochemistry & Molecular Biology
Cornelis A. M. Wagemaker, Liesje Mommer, Eric J. W. Visser, Alexandra Weigelt, Thomas P. van Gurp, Maarten Postuma, Annemiek E. Smit-Tiekstra, Hans de Kroon
Summary: Plant interactions belowground are important and difficult to quantify accurately. The msGBS method presented in this study allows for high taxonomic resolution and parallel quantification of multiple species in root samples. Compared to qPCR, msGBS offers similar results with advantages in revealing hidden belowground interactions.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biology
Alix E. Matthews, Than J. Boves, Katie L. Percy, Wendy M. Schelsky, Asela J. Wijeratne
Summary: Microscopic symbionts, such as feather mites, pose challenges in high-throughput sequencing (HTS) studies due to their small size and minimal DNA yields. This study used a strategic Pool-Seq approach to overcome these challenges and assess genetic diversity in feather mites. The results showed that samples containing multiple mites had more sequencing reads mapping to the mite reference genome than samples with only a single mite. The genetic structure of mite infrapopulations was primarily determined by individual hosts, indicating evolutionary processes at the infrapopulation level. This work highlights the importance of both individual-level and infrapopulation-level sequencing in understanding host-symbiont coevolution.
Article
Genetics & Heredity
Elena N. Pushkova, George S. Krasnov, Valentina A. Lakunina, Roman O. Novakovskiy, Liubov Povkhova, Ekaterina M. Dvorianinova, Artemy D. Beniaminov, Maria S. Fedorova, Anastasiya Snezhkina, Anna Kudryavtseva, Alexey A. Dmitriev, Nataliya Melnikova
Summary: Transcriptome sequencing and genome sequencing were performed for the first time on leaves, catkin axes, and flowers from male and female trees of Populus x sibirica, revealing allele-specific expression in the sex-determining region (SDR) genes. The study identified differences in allelic variants of TCP, CLC, and MET1 genes in females and males of P. x sibirica, providing new insights into sex-associated differences in Populus species.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Thomas A. Delomas, Stuart C. Willis
Summary: New methods have been developed for estimating microhaplotype allele frequency from low-coverage whole genome sequencing and pooled sequencing data, which have been validated using datasets from three non-model organisms. These methods will allow the design of microhaplotype panels and the discovery and evaluation of candidate loci using low-coverage WGS and pool-seq data.
BMC BIOINFORMATICS
(2023)
Article
Biology
Jingjing Zhang, Toshihiko Matsuo, Ichiro Hamasaki, Kazuhiro Sato
Summary: This study used a QTL-sequencing pipeline and SNP index calculation method to investigate the genetic background of comitant strabismus. The results suggest that esotropia and exotropia have different genetic backgrounds.
Article
Biotechnology & Applied Microbiology
Jan Burian, Vincent K. Libis, Yozen A. Hernandez, Liliana Guerrero-Porras, Melinda A. Ternei, Sean F. Brady
Summary: The capture of metagenomic DNA in large clone libraries allows for the study of microbial diversity that cannot be accessed using culture-dependent methods. In this study, a CRISPR counter-selection interruption circuit (CCIC) using nuclease-deficient Cas9 was developed to retrieve target clones from complex libraries. Combining modern sequencing methods with CCIC cloning enables rapid access to the genetic diversity present in natural ecosystems. A CRISPRi method was used to retrieve sequences of interest from large metagenomic libraries.
NATURE BIOTECHNOLOGY
(2023)
Article
Biology
Bokang Ko, Jeremy M. Van Raamsdonk
Summary: Gene expression studies provide valuable insights into biological processes, such as aging. This study shows that pooling individual RNA samples before sequencing can yield similar results as sequencing them individually, reducing the cost of experiments. Analysis of gene expression changes across the genome is a powerful and unbiased tool for understanding molecular mechanisms.
Article
Multidisciplinary Sciences
Binsheng Gong, Rebecca Kusko, Wendell Jones, Weida Tong, Joshua Xu
Summary: This study developed four reference samples and sequenced them with eight oncopanels at independent test laboratories with ultra-deep sequencing depth. The resulting dataset provided valuable information for assessing the clinical applicability of oncopanels and optimizing bioinformatics pipelines and sequencing parameters.
Article
Biochemistry & Molecular Biology
Kara J. Andres, Suresh A. Sethi, David M. Lodge, Jose Andres
Summary: Advances in environmental DNA (eDNA) methodologies have shown the capability to detect intraspecific diversity in the nuclear genome, estimate allele frequencies, and assess genetic contributors in eDNA samples. Results from experimental and field trials indicate high correlation between eDNA-based allele frequencies and those from genotyped tissue samples, suggesting reliable amplification of nuclear markers from water samples. DNA mixture analyses successfully estimated the number of genetic contributors in eDNA samples and simulated mixtures, with the accuracy influenced by the filtering scheme of low-frequency alleles.
Article
Cell Biology
Alex Hildebrandt, Benedikt Kirchner, Agnes S. Meidert, Florian Brandes, Anja Lindemann, Gero Doose, Alexander Doege, Rolf Weidenhagen, Marlene Reithmair, Gustav Schelling, Michael W. Pfaffl
Summary: The study analyzed serum-derived miRNA profiles from patients and volunteers to identify potential biomarkers for atherosclerosis. The differential expression analysis found 27 differentially expressed miRNAs in patients compared to healthy volunteers, with specific miRNA fingerprints for different atherosclerotic manifestations. Overrepresentation analysis revealed relevant biological processes related to atherosclerosis, indicating the potential of these miRNAs as biomarker candidates.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Editorial Material
Cell Biology
Tenzin Phuntsok, Manisha Tambe, Selma Z. D'Silva, Jyoti Rajak, Meenakshi Singh
Summary: The novel HLA-B*13:02:01:18 allele differs from HLA-B*13:02:01:01 with an A->G nucleotide change at gDNA 2477.
Article
Biochemical Research Methods
Nicholas J. Dimonaco, Wayne Aubrey, Kim Kenobi, Amanda Clare, Christopher J. Creevey
Summary: This article presents an evaluation framework for assessing the performance of CDS prediction tools based on a comprehensive set of primary and secondary metrics. The research found that no individual tool ranked as the most accurate across all genomes or metrics analyzed, and even top-ranked tools produced conflicting gene collections.
Article
Multidisciplinary Sciences
Geoffrey N. Gobert, Donald P. McManus, Geoff McMullan, Christopher J. Creevey, Jack Carson, Malcolm K. Jones, Sujeevi S. K. Nawaratna, Kosala G. Weerakoon, Hong You
Summary: This study used FISH and microbial profiling techniques to demonstrate for the first time the presence of bacteria on the epithelial surfaces of adult schistosomes, which differ from the host blood and bile. These schistosome surface-associated bacteria are considered an important component of the host-parasite interaction.
Article
Multidisciplinary Sciences
Elizabeth H. Hart, Sarah R. Christofides, Teri E. Davies, Pauline Rees Stevens, Christopher J. Creevey, Carsten T. Mueller, Hilary J. Rogers, Alison H. Kingston-Smith
Summary: This study investigated how the plant response to climate change affects forage quality and subsequent rumen fermentation. The results indicate that breeding future forage varieties should target tolerance of acute stress rather than long term climate.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Jiangang Han, Sijia Ma, Benmeng Liang, Tianyou Bai, Yuhetian Zhao, Yuehui Ma, David E. MacHugh, Lina Ma, Lin Jiang
Summary: In this study, the researchers investigated the development of fat tail in fat-tail sheep through histological assays, transcriptome analysis, and functional assays. They discovered that fat deposition occurs in the tail at an early embryonic stage, and identified many differentially expressed genes and pathways involved in metabolism. The MTFP1 gene was found to play a crucial role in fat tail development and was highly correlated with other genes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biology
Emmeline W. Hill, Martin A. Stoffel, Beatrice A. McGivney, David E. MacHugh, Josephine M. Pemberton
Summary: This study used genomic data from horses to investigate the effects of inbreeding on race performance and identified a genetic haplotype associated with a reduced probability of racing and increased risk of musculoskeletal injury.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
James A. Ward, Gillian P. McHugo, Michael J. Dover, Thomas J. Hall, Said Ismael Ng'ang'a, Tad S. Sonstegard, Daniel G. Bradley, Laurent A. F. Frantz, Michael Salter-Townshend, David E. MacHugh
Summary: The phenotypic diversity of African cattle is a result of adaptation to environmental conditions and human selection, with evidence for coevolution between mitochondrially targeted nuclear genes.
Article
Agriculture, Dairy & Animal Science
Donagh P. Berry, Emily K. Herman, Tara R. Carthy, Rebecca Jennings, Nahid Bandi-Kenari, Rebecca E. O'Connor, John F. Mee, Jim O'Donovan, Daragh Mathews, Paul Stothard
Summary: Swyer syndrome refers to individuals who have the typical male chromosome but exhibit female characteristics. The absence of a functional SRY gene on the Y chromosome is associated with some cases of Swyer syndrome, although individuals with a fully functional SRY gene have also been found. This study analyzed the whole genome sequence of eight cattle with suspected Swyer syndrome and confirmed that all of them had the 60,XY sex reversal Swyer syndrome.
Article
Biochemistry & Molecular Biology
Charley G. P. McCarthy, Peter O. Mulhair, Karen Siu-Ting, Christopher J. Creevey, Mary J. O'Connell
Summary: There is conflicting evidence regarding whether sponges or comb jellies are at the root of the animal phylogeny, and dataset size, construction, and model fit all influence animal root inference.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Lorenzo A. Santorelli, Toby Wilkinson, Ronke Abdulmalik, Yuma Rai, Christopher J. Creevey, Sharon Huws, Jorge Gutierrez-Merino
Summary: This study investigates the bacterial communities in different beehives and finds that each hive has its own distinct microbiome, which is influenced by plants, beekeeping methods, and the bacterial communities in the surrounding environment. Therefore, the microbiome of beehives can be used as a valuable biosensor to inform the health of honeybees and their surrounding environment.
ENVIRONMENTAL MICROBIOME
(2023)
Article
Agriculture, Dairy & Animal Science
Amy R. Holtby, Thomas J. Hall, Beatrice A. McGivney, Haige Han, Keith J. Murphy, David E. MacHugh, Lisa M. Katz, Emmeline W. Hill
Summary: Using genomics analyses, we identified SNPs associated with behaviour in yearling Thoroughbred horses, which help horses adapt to training and reduce stress. These SNPs are near genes involved in social behaviour, autism spectrum disorder, suicide, stress-induced anxiety and depression, Alzheimer's disease, neurodevelopmental disorders, neuroinflammatory disease, fear-induced behaviours, and alcohol and cocaine addiction. These findings contribute to improving racehorse welfare by developing genetic markers.
Article
Agriculture, Dairy & Animal Science
Emmeline W. W. Hill, Beatrice A. A. McGivney, David E. E. MacHugh
Summary: The proportion of the genome containing runs of homozygosity affects production traits in livestock populations. In European and Australasian Thoroughbreds, inbreeding quantified using ROH is associated with the probability of ever racing. In North American Thoroughbred horses, F-ROH was not associated with the probability of ever racing but was significantly associated with the number of race starts.
Article
Agriculture, Dairy & Animal Science
M. Frizzarin, I. C. Gormley, D. P. Berry, S. McParland
Summary: The study aims to estimate the change in body condition score (BCS) using mid-infrared spectra of milk. The results show that estimating ABCS with spectral data reduces the RMSEV, especially for cows losing BCS quickly. This approach can be used to generate routine estimates of ABCS for farm decisions.
JOURNAL OF DAIRY SCIENCE
(2023)
Meeting Abstract
Infectious Diseases
Lucy Dillon, Nicholas J. Dimonaco, Christopher J. Creevey
JAC-ANTIMICROBIAL RESISTANCE
(2023)
Review
Agriculture, Dairy & Animal Science
D. P. Berry, M. L. Spangler
Summary: Access to high-dimensional genomic information in livestock species is accelerating, which has significant implications for various applications and research.
Article
Agriculture, Dairy & Animal Science
A. Pakrashi, C. Ryan, C. Gueret, D. P. Berry, M. Corcoran, M. T. Keane, B. Mac Namee
Summary: Subclinical mastitis in cows has negative effects on their health, well-being, longevity, and performance, leading to reduced productivity and profit. Predictive models built using machine learning techniques can accurately detect subclinical mastitis up to 7 days before its occurrence, allowing dairy farmers to take interventions to mitigate its effect.
JOURNAL OF DAIRY SCIENCE
(2023)