Article
Biochemistry & Molecular Biology
Chaowei Zhang, Kerry Reid, Arthur F. Sands, Antoine Fraimout, Mikkel Heide Schierup, Juha Merila
Summary: Mutation rate is a critical parameter in population genetics, but accurate estimates for wild organisms are limited. This study estimated mutation rates in two marine populations of nine-spined stickleback using pedigrees, whole-genome resequencing, and a high-quality reference genome. The results showed high levels of parental mosaicism and increased estimated divergence times after recalibration with the mutation rate.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biotechnology & Applied Microbiology
Marije J. Steensma, Y. L. Lee, A. C. Bouwman, C. Pita Barros, M. F. L. Derks, M. C. A. M. Bink, B. Harlizius, A. E. Huisman, R. P. M. A. Crooijmans, M. A. M. Groenen, H. A. Mulder, C. M. Rochus
Summary: This study identified four de novo structural variants (dnSVs) in pig germline, all located in intronic regions of protein-coding genes. The study provides an estimation of the dnSV rate in the pig germline and highlights the complexity of dnSVs.
Article
Cardiac & Cardiovascular Systems
Hao Li, Yoonhee Nam, Ran Huo, Weilun Fu, Biaobin Jiang, Qiuxia Zhou, Dong Song, Yingxi Yang, Yuming Jiao, Jiancong Weng, Zihan Yan, Lin Di, Jie Li, Jie Wang, Hongyuan Xu, Shuo Wang, Jizong Zhao, Zilong Wen, Jiguang Wang, Yong Cao
Summary: By analyzing a dataset from 269 patients, we found abnormal expression of endothelial and mesenchymal markers in bAVM lesions at both bulk and single-cell level. Additionally, de novo germline mutations affecting genes such as EXPH5 and vessel-related genes like EPAS1 and ENG were identified, with knockdown of epas1 in zebrafish embryos showing AVM-like phenotype exclusively in the brain. Furthermore, somatic KRAS mutations were detected in 72% of cases and shown to be associated with bleeding as the first symptom, with experimental studies demonstrating that KRAS mutations independently regulated EndMT features.
CIRCULATION RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Eugenio Lopez-Cortegano, Rory J. Craig, Jobran Chebib, Toby Samuels, Andrew D. Morgan, Susanne A. Kraemer, Katharina B. Boendel, Rob W. Ness, Nick Colegrave, Peter D. Keightley
Summary: De novo mutations play a crucial role in evolution by providing genetic variation, but studying them is challenging and often limited to model species, leading to a restricted understanding of mutation rate evolution among closely related species. Through a mutation accumulation experiment and comparative analysis between Chlamydomonas incerta and Chlamydomonas reinhardtii, researchers found variability in the mutation rate and differing mutation spectra, indicating similarities in genomic factors influencing mutation rate but a greater divergence in mutation spectra between the two species.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Haoling Xie, Wen Li, Yuqiong Hu, Cheng Yang, Jiansen Lu, Yuqing Guo, Lu Wen, Fuchou Tang
Summary: This study achieved high continuity human genome assembly using single-cell genome long-read sequencing technology and explored the impact of different assemblers and sequencing strategies on genome assembly. It is of great significance for the practice of single-cell genome de novo assembly.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Maya Gombosh, Yuval Yogev, Noam Hadar, Regina Proskorovski-Ohayon, Sarit Aharoni, Libe Gradstein, Ohad S. Birk
Summary: Knudson's two hit hypothesis proposes that cancer is caused by a primary germline mutation followed by a somatic mutation in the second allele. This hypothesis suggests that the loss of heterozygosity due to a deletion mutation in the second hit is responsible for the manifestation of autosomal recessive diseases. We present a case of infantile high myopia caused by a paternally inherited missense mutation in RBP3 and a de-novo germline heterozygous deletion encompassing RBP3, supporting the concept of loss of heterozygosity in inherited heterozygous mutations.
Review
Genetics & Heredity
Mohiuddin Mohiuddin, R. Frank Kooy, Christopher E. Pearson
Summary: Mosaicism, the existence of genetically distinct populations of cells, is a significant cause of genetic diseases. Neurodevelopmental or neuropsychiatric disorders, such as autism, often arise from de novo mutations that are not present in either parent. The timing and mode of mutations can affect the burden and distribution of mutations.
FRONTIERS IN GENETICS
(2022)
Article
Biology
David Berger, Josefine Stangberg, Julian Baur, Richard J. Walters
Summary: Research suggests that rising global temperatures will intensify natural selection throughout the genome. While environmental stress per se did not increase mean selection on de novo mutation, elevated temperature increased the mean strength of selection on genome-wide polymorphism.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Masaki Nishioka, An-a Kazuno, Takumi Nakamura, Naomi Sakai, Takashi Hayama, Kumiko Fujii, Koji Matsuo, Atsuko Komori, Mizuho Ishiwata, Yoshinori Watanabe, Takashi Oka, Nana Matoba, Muneko Kataoka, Ahmed N. Alkanaq, Kohei Hamanaka, Takashi Tsuboi, Toru Sengoku, Kazuhiro Ogata, Nakao Iwata, Masashi Ikeda, Naomichi Matsumoto, Tadafumi Kato, Atsushi Takata
Summary: This study analyzed rare genetic mutations in trios with bipolar disorder, finding contributions of both germline and postzygotic mutations to the risk of the disorder. The analysis supports the hypothesis that postzygotic mutations of developmental disorder genes may play a role in bipolar disorder.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Amanda K. Broz, Gus Waneka, Zhiqiang Wu, Matheus Fernandes Gyorfy, Daniel B. Sloan
Summary: The study used high-fidelity Duplex Sequencing technique to analyze mitochondrial mutations in multiple angiosperms from the genus Silene, revealing extreme variations in rates of mitochondrial sequence evolution among different species. While Silene latifolia maintained low variant frequencies, Silene conica showed higher variant frequencies and a biased mutational spectrum. This suggests historical fluctuations in mutation rates drive the extreme variation in plant mitochondrial sequence evolution.
Article
Engineering, Environmental
Selina B. I. Schmidt, Alexandro Rodriguez-Rojas, Jens Rolff, Frank Schreiber
Summary: Antimicrobial resistance (AMR) is a global health problem and the environment plays a significant role in the evolution and transmission of AMR. This study shows that active substances used in material preservatives can increase mutation and conjugation rates in a species- and substance-dependent manner. The RpoS-mediated general stress and RecA-linked SOS response are also found to be associated with increased rates of mutation and conjugation.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Cell Biology
Tian Tian, Xuanye Cao, Yongyan Chen, Lei Jin, Zhiwen Li, Xiao Han, Ying Lin, Bogdan J. Wlodarczyk, Richard H. Finnell, Zhengwei Yuan, Linlin Wang, Aiguo Ren, Yunping Lei
Summary: This study identified functional variants of MED genes associated with the etiology of some NTDs. Cellular functional studies showed that MED12 gene mutation affected the regulation of MED12 on the canonical-WNT signaling pathway. A Med12 p.Arg1784Cys knock-in mouse model exhibited exencephaly and spina bifida, validating the human findings in mice using CRISPR/Cas9 technology.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Anne-Perrine Foray, Sophie Candon, Sara Hildebrand, Cindy Marquet, Fabrice Valette, Coralie Pecquet, Sebastien Lemoine, Francina Langa-Vives, Michael Dumas, Peipei Hu, Pere Santamaria, Sylvaine You, Stephen Lyon, Lindsay Scott, Chun Hui Bu, Tao Wang, Darui Xu, Eva Marie Y. Moresco, Claudio Scazzocchio, Jean-Francois Bach, Bruce Beutler, Lucienne Chatenoud
Summary: Insulin-dependent or type 1 diabetes (T1D) is a complex polygenic autoimmune disease with contributions from both common and rare genetic variants. Using NOD mice, researchers identified a recessive missense mutation in the Dusp70 gene that significantly increased disease incidence, highlighting the role of rare variants in altering disease phenotype. This study also revealed new insights into the genetic factors affecting T1D susceptibility and provided a potential target for therapeutic intervention.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Evolutionary Biology
Richard J. Wang, Yadira Pena-Garcia, Madeleine G. Bibby, Muthuswamy Raveendran, R. Alan Harris, Heiko T. Jansen, Charles T. Robbins, Jeffrey Rogers, Joanna L. Kelley, Matthew W. Hahn
Summary: This study examines the per-generation mutation rate in a brown bear pedigree and finds that both male bias and per-generation mutation rates are similar to that of non-hibernating species, contradicting previous theories. These findings provide new evidence for the determinants of mutation rates and mutation biases.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Wafaa B. Alsoussi, Sameer Kumar Malladi, Julian Q. Zhou, Zhuoming Liu, Baoling Ying, Wooseob Kim, Aaron J. Schmitz, Tingting Lei, Stephen C. Horvath, Alexandria J. Sturtz, Katherine M. McIntire, Birk Evavold, Fangjie Han, Suzanne M. Scheaffer, Isabella F. Fox, Senaa F. Mirza, Luis Parra-Rodriguez, Raffael Nachbagauer, Biliana Nestorova, Spyros Chalkias, Christopher W. Farnsworth, Michael K. Klebert, Iskra Pusic, Benjamin S. Strnad, William D. Middleton, Sharlene A. Teefey, Sean P. J. Whelan, Michael S. Diamond, Robert Paris, Jane A. O'Halloran, Rachel M. Presti, Jackson S. Turner, Ali H. Ellebedy
Summary: Boosting with COVID-19 vaccines induces robust immune responses and can generate new antibody responses targeting variant-specific epitopes. The B cells involved in the immune response can mature and produce antibodies that recognize the original virus as well as the variants.
Article
Biochemistry & Molecular Biology
Jesus Murga-Moreno, Marta Coronado-Zamora, Alejandra Bodelon, Antonio Barbadilla, Sonia Casillas
NUCLEIC ACIDS RESEARCH
(2019)
Article
Evolutionary Biology
Marta Coronado-Zamora, Irepan Salvador-Martinez, David Castellano, Antonio Barbadilla, Isaac Salazar-Ciudad
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Biochemistry & Molecular Biology
Jesus Murga-Moreno, Marta Coronado-Zamora, Sergi Hervas, sonia Casillas, Antonio Barbadilla
NUCLEIC ACIDS RESEARCH
(2019)
Article
Genetics & Heredity
Felix Dietlein, Donate Weghorn, Amaro Taylor-Weiner, Andre Richters, Brendan Reardon, David Liu, Eric S. Lander, Eliezer M. Van Allen, Shamil R. Sunyaev
Article
Biochemistry & Molecular Biology
Martin Kapun, Joaquin C. B. Nunez, Maria Bogaerts-Marquez, Jesus Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P. Garcia Guerreiro, Sonia Casillas, Dorcas J. Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S. Onder, Jessica K. Abbott, Stephen W. Schaeffer, Subhash Rajpurohit, Emily L. Behrman, Mads F. Schou, Thomas J. S. Merritt, Brian P. Lazzaro, Amanda Glaser-Schmitt, Eliza Argyridou, Fabian Staubach, Yun Wang, Eran Tauber, Svitlana Serga, Daniel K. Fabian, Kelly A. Dyer, Christopher W. Wheat, John Parsch, Sonja Grath, Marija Savic Veselinovic, Marina Stamenkovic-Radak, Mihailo Jelic, Antonio J. Buendia-Ruiz, Maria Josefa Gomez-Julian, Maria Luisa Espinosa-Jimenez, Francisco D. Gallardo-Jimenez, Aleksandra Patenkovic, Katarina Eric, Marija Tanaskovic, Anna Ullastres, Lain Guio, Miriam Merenciano, Sara Guirao-Rico, Vivien Horvath, Darren J. Obbard, Elena Pasyukova, Vladimir E. Alatortsev, Cristina P. Vieira, Jorge Vieira, Jorge Roberto Torres, Iryna Kozeretska, Oleksandr M. Maistrenko, Catherine Montchamp-Moreau, Dmitry Mukha, Heather E. Machado, Keric Lamb, Tania Paulo, Leeban Yusuf, Antonio Barbadilla, Dmitri Petrov, Paul Schmidt, Josefa Gonzalez, Thomas Flatt, Alan O. Bergland
Summary: Utilizing a newly developed bioinformatics pipeline, Drosophila melanogaster's Pool-Seq data is mapped to a hologenome to create the largest genomic data repository to date, called DEST, including 271 population samples from over 100 locations worldwide. This dataset can be used to study spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Aina Colomer-Vilaplana, Jesus Murga-Moreno, Aleix Canalda-Baltrons, Clara Inserte, Daniel Soto, Marta Coronado-Zamora, Antonio Barbadilla, Sonia Casillas
Summary: This study introduces PopHumanVar, an interactive online application designed to facilitate the exploration and thorough analysis of candidate genomic regions to identify variants potentially responsible for recent selective sweeps. It integrates functional and population genomics data, providing useful summary reports and gathering information from various databases to accurately estimate selection statistics and known causal variants. PopHumanVar successfully identifies causal variants in frequently reported candidate selection regions, such as EDAR, ACKR1 (DARC), and LCT/MCM6 in different populations.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Jesus Murga-Moreno, Marta Coronado-Zamora, Sonia Casillas, Antonio Barbadilla
Summary: The McDonald and Kreitman test is a widely used method to detect and quantify natural selection in DNA sequence data. However, it has limitations in underestimating positive selection due to the presence of slightly deleterious variants at low frequencies. This study presents a new approach called the imputed McDonald and Kreitman test (impMKT), which overcomes these limitations and increases the statistical evidence of positive selection at the gene level.
G3-GENES GENOMES GENETICS
(2022)
Correction
Genetics & Heredity
S. Casillas, A. Barbadilla