Article
Biochemistry & Molecular Biology
Haoxuan Liu, Jianzhi Zhang
Summary: This study challenges the theory that mutations are blind to their consequences by finding that the plant Arabidopsis thaliana has lower mutation rates in genomic regions where mutations are more likely to be deleterious. However, further analysis of mutational data from baker's yeast and humans does not support this finding. The study also suggests that the extra mutations detected in Arabidopsis may be sequencing errors.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Yongsan Yang, Fengcui Qian, Xuecang Li, Yanyu Li, Liwei Zhou, Qiuyu Wang, Xinyuan Zhou, Jian Zhang, Chao Song, Zhengmin Yu, Ting Cui, Chenchen Feng, Jiang Zhu, Desi Shang, Jiaqi Liu, Mengfei Sun, Yuexin Zhang, Huifang Tang, Chunquan Li
Summary: GREAP is a powerful platform for genomic region enrichment analysis, providing comprehensive annotation and enrichment analysis capabilities for genomic regions, along with a customizable genome browser.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Chandan Roy, Philomin Juliana, Muhammad R. Kabir, Krishna K. Roy, Navin C. Gahtyari, Felix Marza, Xinyao He, Gyanendra P. Singh, Aakash Chawade, Arun K. Joshi, Pawan K. Singh
Summary: The study evaluated genotypes from India and Bangladesh for wheat blast resistance and conducted a GWAS, identifying 40 significant markers associated with resistance, primarily located in the 2NS/2AS chromosome segment. The 2NS translocation is currently the main source of resistance against wheat blast in South Asia, but the identification of non-2NS/2AS genomic regions offers hope for broadening and diversifying resistance in the future.
Article
Biochemical Research Methods
Bernhard Haubold, Fabian Kloetzl, Lars Hellberg, Daniel Thompson, Markus Cavalar
Summary: The study introduces a program called Fur for finding unique genomic regions and compares it to genmap. The results show that genmap can provide more marker sequences but with lower accuracy. The study also designs PCR primers based on marker sequences, which demonstrate high sensitivity and specificity in experiments.
Article
Plant Sciences
Miguel Munoz Mazon, J. Sebastian Tello, Manuel J. Macia, Jonathan A. Myers, Peter M. Jorgensen, Victoria Cala, Alfredo F. Fuentes, Vania Torrez, Gabriel Arellano
Summary: Differences in species pools alone did not explain observed differences in beta diversity among biogeographic regions. In 3/4 regions, the environment explained more of the variation in beta diversity than spatial variables. Spatial variables explained more beta diversity in regions with higher diversity and productivity compared to regions with lower diversity and productivity.
JOURNAL OF VEGETATION SCIENCE
(2021)
Article
Biodiversity Conservation
Annika Vilmi, Corentin Gibert, Gilles Escarguel, Konsta Happonen, Jani Heino, Aurelien Jamoneau, Sophia I. Passy, Felix Picazo, Janne Soininen, Juliette Tison-Rosebery, Jianjun Wang
Summary: Patterns in community composition are scale-dependent and difficult to distinguish. The proposed dispersal-niche continuum index (DNCI) helps quantify the relative strength of dispersal and niche processes in community assembly. DNCI suggested that dispersal was the dominant process in observational datasets, but varied across organismal groups and study contexts.
Article
Engineering, Industrial
Timothy L. Urban
Summary: Selective assembly is an effective approach for producing high-precision assemblies using low-precision components or subassemblies. This research investigates component ordering policies that consider the stochastic nature of binning process and demand. It provides an approximation of completed assemblies using extreme-value theory, and presents an implicit-enumeration procedure to determine the order quantity to meet demand with a given service level. Computational results demonstrate the effectiveness of this method in controlling component inventories.
INTERNATIONAL JOURNAL OF PRODUCTION RESEARCH
(2022)
Article
Biochemical Research Methods
Quanzhong Liu, Honglin Fang, Xiao Wang, Miao Wang, Shuqin Li, Lachlan J. M. Coin, Fuyi Li, Jiangning Song
Summary: This study proposes a general deep learning framework called DeepGenGrep for systematically identifying multiple different genomic signals and regions (GSRs) from genomic DNA sequences. Benchmarking experiments show that DeepGenGrep outperforms other methods in several eukaryotic species, making it an effective tool for identifying potential GSRs in eukaryotic genomes.
Article
Genetics & Heredity
Nai-Yi Xu, Zhen-Yu Liu, Qi-Meng Yang, Pei-Pei Bian, Ming Li, Xin Zhao
Summary: This study conducted a genomic analysis of indigenous chickens inhabiting different tropical climates to identify selection signatures and genes related to hot adaptation. The results show that the hot adaptability of chickens in different tropical regions has evolved through different genetic pathways.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Lisi Hai, Xiao-Qian Li, Jing-Bo Zhang, Xiao-Guo Xiang, Rui-Qi Li, Florian Jabbour, Rosa del C. Ortiz, An-Ming Lu, Zhi-Duan Chen, Wei Wang
Summary: This study explores the evolution and formation of subtropical East Asian evergreen broadleaved forests through the analysis of dominant Fagaceae species. The research reveals that high precipitation in summer and low temperature in winter are the key climatic factors influencing the distribution of this biome. The study also highlights the time lag between species invasion and becoming dominant within the region.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Jeong-An Gim
Summary: This review discusses the recent advancements in personalized therapies and health management based on genomic information. It explores the development and clinical applications of a genomic information management system and the analysis of genomic information as big data. Furthermore, it examines the regulations and privacy protection surrounding the use of genetic information.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Edgar Escobar, Atena Oladzad, Kristin Simons, Phillip Miklas, Rian K. Lee, Stephan Schroder, Nonoy Bandillo, Michael Wunsch, Phillip E. McClean, Juan M. Osorno
Summary: Dry bean production is threatened by white mold, but breeding for improved genetic resistance is challenging. A study utilized a MAGIC population to identify resistant lines and associated genomic regions. Using different phenotypic distributions and SNPs, significant genomic intervals were identified. New resistant germplasm and genomic regions are now available for further investigation.
Article
Biodiversity Conservation
N. A. Aravind, Maanya Uma Shaanker, Poorna H. N. Bhat, Bipin Charles, Uma R. Shaanker, Manzoor A. Shah, G. Ravikanth
Summary: This study analyzes the niche shifts of 33 of the world's top invasive species and finds that 90% of them have largely stayed within similar habitats rather than moving to completely new ones. This indicates the potential inertia that species may face when leaving their fundamental niche and suggests that niche conservatism may play a role in dampening the rates of invasion.
BIODIVERSITY AND CONSERVATION
(2022)
Article
Agronomy
Alexandrina Bodrug-Schepers, Nancy Stralis-Pavese, Hermann Buerstmayr, Juliane C. Dohm, Heinz Himmelbauer
Summary: This study suggests utilizing natural variation between individuals of a population for genome assembly scaffolding, demonstrating the potential value of haplotype information from distantly related individuals in grouping and ordering contigs for generating pseudomolecules.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang
Summary: OpenAnnotate is the first web server developed to efficiently annotate openness of massive genomic regions across various biosample types, tissues, and biological systems. It provides user-friendly functionalities, ultra-efficient calculation, real-time browsing, and intuitive visualization.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
David M. Geiser, Abdullah M. S. Al-Hatmi, Takayuki Aoki, Tsutomu Arie, Virgilio Balmas, Irene Barnes, Gary C. Bergstrom, Madan K. Bhattacharyya, Cheryl L. Blomquist, Robert L. Bowden, Balazs Brankovics, Daren W. Brown, Lester W. Burgess, Kathryn Bushley, Mark Busman, Jose F. Cano-Lira, Joseph D. Carrillo, Hao-Xun Chang, Chi-Yu Chen, Wanquan Chen, Martin Chilvers, Sofia Chulze, Jeffrey J. Coleman, Christina A. Cuomo, Z. Wilhelm de Beer, G. Sybren de Hoog, Johanna Del Castillo-Munera, Emerson M. Del Ponte, Javier Dieguez-Uribeondo, Antonio Di Pietro, Veronique Edel-Hermann, Wade H. Elmer, Lynn Epstein, Akif Eskalen, Maria Carmela Esposto, Kathryne L. Everts, Sylvia P. Fernandez-Pavia, Gilvan Ferreira da Silva, Nora A. Foroud, Gerda Fourie, Rasmus J. N. Frandsen, Stanley Freeman, Michael Freitag, Omer Frenkel, Kevin K. Fuller, Tatiana Gagkaeva, Donald M. Gardiner, Anthony E. Glenn, Scott E. Gold, Thomas R. Gordon, Nancy F. Gregory, Marieka Gryzenhout, Josep Guarro, Beth K. Gugino, Santiago Gutierrez, Kim E. Hammond-Kosack, Linda J. Harris, Monika Homa, Cheng-Fang Hong, Laszlo Hornok, Jenn-Wen Huang, Macit Ilkit, Adriaana Jacobs, Karin Jacobs, Cong Jiang, Maria Del Mar Jimenez-Gasco, Seogchan Kang, Matthew T. Kasson, Kemal Kazan, John C. Kennell, Hye-Seon Kim, H. Corby Kistler, Gretchen A. Kuldau, Tomasz Kulik, Oliver Kurzai, Imane Laraba, Matthew H. Laurence, Theresa Lee, Yin-Won Lee, Yong-Hwan Lee, John F. Leslie, Edward C. Y. Liew, Lily W. Lofton, Antonio F. Logrieco, Manuel S. Lopez-Berges, Alicia G. Luque, Erik Lysoe, Li-Jun Ma, Robert E. Marra, Frank N. Martin, Sara R. May, Susan P. McCormick, Chyanna McGee, Jacques F. Meis, Quirico Migheli, N. M. I. Mohamed Nor, Michel Monod, Antonio Moretti, Diane Mostert, Giuseppina Mule, Francoise Munaut, Gary P. Munkvold, Paul Nicholson, Marcio Nucci, Kerry O'Donnell, Matias Pasquali, Ludwig H. Pfenning, Anna Prigitano, Robert H. Proctor, Stephane Ranque, Stephen A. Rehner, Martijn Rep, Gerardo Rodriguez-Alvarado, Lindy Joy Rose, Mitchell G. Roth, Carmen Ruiz-Roldan, Amgad A. Saleh, Baharuddin Salleh, Hyunkyu Sang, Maria Mercedes Scandiani, Jonathan Scauflaire, David G. Schmale, Dylan P. G. Short, Adnan Sisic, Jason A. Smith, Christopher W. Smyth, Hokyoung Son, Ellie Spahr, Jason E. Stajich, Emma Steenkamp, Christian Steinberg, Rajagopal Subramaniam, Haruhisa Suga, Brett A. Summerell, Antonella Susca, Cassandra L. Swett, Christopher Toomajian, Terry J. Torres-Cruz, Anna M. Tortorano, Martin Urban, Lisa J. Vaillancourt, Gary E. Vallad, Theo A. J. van der Lee, Dan Vanderpool, Anne D. van Diepeningen, Martha M. Vaughan, Eduard Venter, Marcele Vermeulen, Paul E. Verweij, Altus Viljoen, Cees Waalwijk, Emma C. Wallace, Grit Walther, Jie Wang, Todd J. Ward, Brian L. Wickes, Nathan P. Wiederhold, Michael J. Wingfield, Ana K. M. Wood, Jin-Rong Xu, Xiao-Bing Yang, Tapani Yli-Mattila, Sung-Hwan Yun, Latiffah Zakaria, Hao Zhang, Ning Zhang, Sean X. Zhang, Xue Zhang
Summary: The debate over the classification of the Fusarium genus in recent years has focused on whether the FSSC should be included in Fusarium, but molecular phylogenetic research has shown strong support for the monophyly of Fusarium including the FSSC, which is considered the best taxonomic option available.
Review
Plant Sciences
Emerson M. Del Ponte, Glaucia M. Moreira, Todd J. Ward, Kerry O'Donnell, Camila P. Nicolli, Franklin J. Machado, Maira R. Duffeck, Kaique S. Alves, Dauri J. Tessmann, Cees Waalwijk, Theo van der Lee, Hao Zhang, Sofia N. Chulze, Sebastian A. Stenglein, Dinorah Pan, Silvana Vero, Lisa J. Vaillancourt, David G. Schmale, Paul D. Esker, Antonio Moretti, Antonio F. Logrieco, H. Corby Kistler, Gary C. Bergstrom, Altus Viljoen, Lindy J. Rose, Gert J. van Coller, Theresa Lee
Summary: Fusarium graminearum, one of the top five destructive fungal pathogens affecting agroecosystems, was systematically reviewed in this study. Two main data tables were created, summarizing information on species and chemotypes of 16,274 strains sampled across six continents and 32 countries. The publicly available database and interactive interface allow for searches, summarization, and mapping of strain distribution. The findings provide valuable guidance for future surveys and investigations into factors related to species distribution, such as climate and land use. Authors are encouraged to contribute data at the strain level to the accessible database.
Article
Entomology
Jozef J. M. van der Steen, Marc J. A. Hendriks, Anne D. van Diepeningen, Marga P. E. van Gent-Pelzer, Theo A. J. van der Lee
Summary: A study was conducted to develop new quantitative detection tools for Nosema ceranae and Nosema apis, with a focus on the efficacy of gamma radiation in killing N. ceranae spores and the infection of N. ceranae in honey bees and bumble bees. The results indicated that N. ceranae found in honey bees cannot infect commercially reared bumble bees and that gamma radiation effectively kills N. ceranae.
JOURNAL OF APICULTURAL RESEARCH
(2022)
Article
Plant Sciences
Bart. T. L. H. van de Vossenberg, Charlotte Prodhomme, Jack H. Vossen, Theo A. J. van der Lee
Summary: This review provides an overview of the importance of potato wart disease and the research progress on the pathogen and its host. It covers taxonomy, epidemiology, pathology, and pathogen-host interaction.
MOLECULAR PLANT PATHOLOGY
(2022)
Article
Plant Sciences
Zhen Yan, Wanquan Chen, Theo van der Lee, Cees Waalwijk, Anne D. van Diepeningen, Jie Feng, Hao Zhang, Taiguo Liu
Summary: Exploiting wheat cultivars with stable resistance to Fusarium Head blight and toxin accumulation is an effective strategy to reduce yield losses and mycotoxin contamination. Investigation in China's major wheat growing regions revealed that growing region and cultivar significantly affect the occurrence of FHB and mycotoxin accumulation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Eef M. Jonkheer, Dirk-Jan M. van Workum, Siavash Sheikhizadeh Anari, Balazs Brankovics, Jorn R. de Haan, Lidija Berke, Theo A. J. van der Lee, Dick de Ridder, Sandra Smit
Summary: This article presents the latest update of PanTools, which enables the construction and comparative analysis of pangenomes, as well as the integration of functional annotations and phylogenetic analysis.
Article
Multidisciplinary Sciences
Wasin Poncheewin, Anne D. van Diepeningen, Theo A. J. van der Lee, Maria Suarez-Diez, Peter J. Schaap
Summary: This study used genome properties and machine learning to establish the relationship between Pseudomonas strains isolated from the rhizosphere and phyllosphere and their plant-associated lifestyle. It identified 28 discriminating features and demonstrated the potential of genome properties annotation as a computational tool for classifying plant-associated lifestyles.
SCIENTIFIC REPORTS
(2022)
Article
Agronomy
Inge M. Krijger, Max Strating, Marga van Gent-Pelzer, Theo A. J. van der Lee, Sara A. Burt, Fleur H. Schroeten, Robin de Vries, Marieke de Cock, Miriam Maas, Bastiaan G. Meerburg
Summary: Rodents in the Netherlands have developed resistance to anticoagulant rodenticides, particularly brodifacoum. A study found genetic mutations at codon 139 of the Vkorc1 gene in both Norway rats and house mice. These results provide a baseline for integrated pest management strategies in the Netherlands.
PEST MANAGEMENT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Ping Zhang, Hao Xin, Theo van der Lee
Summary: This study integrates transcriptome and metabolome sequencing data to investigate the impact of Armillaria solidipes on Bacillus velezensis BY6. The growth of BY6 is inhibited by A. solidipes, causing damage to the cell wall and membrane. Gene and metabolite network analysis reveals the involvement of several pathways in the inhibition of BY6's biocontrol ability. This knowledge contributes to a better understanding of the mechanism and potential targets for overcoming drug resistance.
BIOLOGICAL CONTROL
(2023)
Article
Plant Sciences
Lishu Yi, Meixin Yang, Cees Waalwijk, Jin Xu, Jingsheng Xu, Orsolya Molnar, Wanquan Chen, Jie Feng, Hao Zhang
Summary: Carbendazim resistance was detected in Fusarium graminearum species complex isolates collected from wheat-producing regions in China from 2018 to 2020. The majority of resistant isolates were found in Jiangsu and Anhui Provinces, with F167Y being the predominant point mutation. F. asiaticum isolates were more likely to be resistant. The study also detected carbendazim resistance in Hebei, Shaanxi, Sichuan, and Hunan Provinces for the first time, and found a stable resistance population in Jiangsu, Anhui, and Zhejiang Provinces. The frequency of carbendazim resistance showed similar trends to Fusarium Head Blight epidemic.
Article
Forestry
Ping Zhang, Mingru Kong, Guangqiang Xie, Theo van der Lee, Lihai Wang, Yanqiu Xing
Summary: The article introduces a method for monitoring root infection using X-ray computed tomography, and verifies and measures parameters in the interaction between poplar and Armillaria solidipes.
Article
Plant Sciences
Xiaoqing Huang, Xina Wang, Lianzhu Zhou, Fanfang Kong, Yongqiang Liu, Zhongyue Wang, Hao Zhang
Summary: This study developed a rapid detection method for resistance to QoI fungicide azoxystrobin in Plasmopara viticola and identified resistant isolates in China for the first time. The method showed high specificity and sensitivity and could quantify the resistance allele even at low concentrations. This provides important references for resistance management and fungicide selection, benefiting grape production in Chinese vineyards.