Article
Plant Sciences
Sheng-Kai Tang, Pei-Hsuan Lee, Wei-Ting Liou, Chen-Hsiang Lin, Yao-Moan Huang, Li-Yaung Kuo
Summary: Spores and pollen of plants are used as flow cytometric materials to infer genome sizes efficiently, making them potential plant genome size standards. In this study, we investigated the conditions and genome sizes of three fern spore collections and examined the quality and quantity of spore nucleus extractions stored at different ages. Our study is the first to develop and apply dried and refrigerated spores for genome size standards, which are ready to use and feature long-term storage.
Article
Genetics & Heredity
Kuo Sun, De-Long Guan, Hua-Teng Huang, Sheng-Quan Xu
Summary: This study measured the genome size of Gryllotalpa orientalis and identified nuclear repetitive elements. The estimated haploid genome size was 3.14 Gb by flow cytometry and ranged from 3.17 Gb to 3.77 Gb based on two k-mer methods. Class I-LINE retrotransposon elements were the most common families among the annotated repetitive elements.
Review
Biochemical Research Methods
Kai Pang, Sihan Dong, Yuxi Zhu, Xi Zhu, Quanyu Zhou, Bobo Gu, Wei Jin, Rui Zhang, Yuting Fu, Bingchen Yu, Da Sun, Duanmu Zheng, Xunbin Wei
Summary: Flow cytometry is a versatile tool for detecting and measuring characteristics of cells or particles. Recent advancements in techniques such as in vivo photoacoustic FC, coherent Raman FC, and microfluidic FC have expanded the applications of FC in basic research and clinical practice.
JOURNAL OF BIOPHOTONICS
(2023)
Article
Ecology
Zhao Chen, Yongzhuo Guan, Mengli Han, Yuxia Guo, Jingxue Zhang, Zhipeng Guo, Genlou Sun, Xuebing Yan
Summary: Genome size variation and hybridization in plants are influenced by altitude. This study found a strong correlation between altitude and genome size in Elymus species, and larger genome size variations occurred in mid-altitude populations compared to other altitudes.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Deli Zhan, Cheng Si, Zhaowei Bie, Lihui Wang, Xuemei Sun, Shipeng Yang, Qiwen Zhong
Summary: This study aims to explore the genome size of Jerusalem artichoke and its interaction with the plant's agronomy. It estimated the genome size of Jerusalem artichoke using flow cytometry and K-mers analysis and found significant correlations between genome size and several agronomic traits.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Genetics & Heredity
Hao Yuan, Yuan Huang, Ying Mao, Nan Zhang, Yimeng Nie, Xue Zhang, Yafu Zhou, Shaoli Mao
Summary: Genomic size variation in Ensifera was studied by determining the genome size of 32 species using flow cytometry and constructing phylogenetic trees. The phylogenetic signal of genome size variation in Ensifera was found to be strong in both males and females. The evolutionary pattern of genome size in Ensifera showed complex evolution with different trends in different clades.
FRONTIERS IN GENETICS
(2021)
Article
Agronomy
Manqing Li, Miaoli Wang, Jingxue Zhang, Guilan Feng, Maryam Noor, Zhipeng Guo, Yuxia Guo, Yongzhuo Guan, Xuebing Yan
Summary: Understanding the cytological pattern of genome size and ploidy level of bermudagrass is essential for studying its evolution pattern and breeding. This study measured the genome size and ploidy level of bermudagrass along a longitudinal gradient and explored their relationship with climate factors. The tetraploid ploidy level was the most common, and aneuploidy was frequently observed in different regions.
Article
Physiology
Iris Louise Eleonora van de Pol, Adam Hermaniuk, Wilhelmus Cornelis Egbertus Petrus Verberk
Summary: Research shows that cell size affects gene expression, growth, and swimming performance of ectotherms at different temperatures, with these effects being temperature and ploidy-dependent. Triploids with larger cells outperformed diploids in cooler conditions, while diploids performed better in warmer conditions.
FRONTIERS IN PHYSIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Junpeng Shi, Zhixi Tian, Jinsheng Lai, Xuehui Huang
Summary: Plant genomes are highly diverse and most genomic sequences are not shared among individuals. Variable DNA sequences and conserved core sequences form a more sophisticated pan-genome, representing all non-redundant DNA in a species. Advances in genome sequencing technologies have accelerated plant pan-genomics research. This review focuses on driving forces of structural variations, methodological innovations, and major successes in constructing plant pan-genomes. Efforts are also summarized towards decoding dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources are expected to become new references for genetic studies and plant breeding.
Article
Plant Sciences
Shuang-feng Dai, Xun-ge Zhu, Ge-rang Hutang, Jia-yue Li, Jia-qi Tian, Xian-hui Jiang, Dan Zhang, Li-zhi Gao
Summary: This study investigated genome size variation in the genus Oryza using flow cytometry and k-mer analysis. The results showed that genome sizes varied greatly in Oryza, with similar sizes observed within the same genome types. Additionally, the amplification history of retrotransposons was found to be closely related to genome size variation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Fahimeh Fallah, Farrokh Ghahremaninejad
Summary: Genome size is a useful tool for defining taxa at different taxonomic levels, and flow cytometry has been used to measure the nuclear DNA content of twelve accessions of Hedera. The study revealed a significant difference in nuclear DNA content between H. crebrescens and H. hibernica, indicating that the newly described taxon is diploid rather than tetraploid as previously believed.
Article
Ecology
GaoMing Wei, Xuan Li, YanMing Fang
Summary: The study on four closely related oak species in Zijinshan, China, explored the variability of genome size within and among the species, as well as hybridization events, showing adaptation to the environment. The evolution of genome size in hybrid species was identified as expansion, with hybridization between sections possibly influenced by habitat disturbance. This research enhances understanding of Quercus evolution and aids in establishing guidelines for oak tree ecological protection.
ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Rithesh B. Natarajan, Pooja Pathania, Hardeep Singh, Anuradha Agrawal, Rajkumar Subramani
Summary: Genome size variation is an important attribute in evolutionary and species characterization. This study provides reliable information on the genome size and ploidy level of wild Musa species, which could be used in taxonomic and crop improvement programs.
Article
Plant Sciences
Fahad Al-Qurainy, Abdel-Rhman Z. Gaafar, Salim Khan, Mohammad Nadeem, Aref M. Alshameri, Mohamed Tarroum, Saleh Alansi, Naser B. Almarri, Norah S. Alfarraj
Summary: Genome size analysis of endemic species Reseda pentagyna and locally rare species Reseda lutea in Saudi Arabia was conducted using both flow cytometry and biocomputational methods, revealing discrepancies in genome size estimates likely due to the presence of long repetitive regions with high repeat content in both genomes. The study also identified potentially tetraploid or higher ploidy levels in Reseda lutea based on GenomeScope analysis. These findings provide fundamental cytogenetic information for future taxonomic studies and whole-genome sequencing of these species.
Article
Agronomy
Dariusz Sochacki, Malgorzata Podwyszynska, Aleksandra Machlanska, Barbara Dyki
Summary: The study concludes that the morphological traits and nuclear DNA content of narcissus can be used to determine the possible ploidy level. The information on the origin and parental forms of narcissus can also be helpful in determining the ploidy level. However, further confirmation of the ploidy level requires verification of chromosome number and preferably karyotyping.
Article
Plant Sciences
Lijuan Meng, Monica Hofte, Marie-Christine Van Labeke
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2019)
Article
Microbiology
Feyisara Eyiwumi Oni, Niels Geudens, Olumide Owolabi Omoboye, Lien Berber, Hoang Gia Khuong Hua, Amayana Adiobo, Davy Sinnaeve, Jose C. Martins, Monica Hofte
ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Feyisara Eyiwumi Oni, Oluwatoyin Faith Olorunleke, Monica Hofte
BIOLOGICAL CONTROL
(2019)
Article
Biochemistry & Molecular Biology
Lukasz Pawel Tarkowski, Bram Van de Poel, Monica Hoefte, Wim Van den Ende
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Biochemistry & Molecular Biology
Niels Geudens, Benjamin Kovacs, Davy Sinnaeve, Feyisara Eyiwumi Oni, Monica Hoefte, Jose C. Martins
Article
Agronomy
Jolien Claerbout, An Decombel, Anneleen Volckaert, Sofie Venneman, Isabel Vandevelde, Peter Bleyaert, Jenny Neukermans, Nicole Viaene, Monica Hofte
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2019)
Article
Plant Sciences
Olumide Owolabi Omoboye, Feyisara Eyiwumi Oni, Humaira Batool, Henok Zimene Yimer, Rene De Mot, Monica Hofte
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Agronomy
L. Tyvaert, E. Everaert, L. Lippens, W. J. M. Cuijpers, S. C. Franca, M. Hoefte
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Olumide Owolabi Omoboye, Niels Geudens, Matthieu Duban, Mickael Chevalier, Christophe Flahaut, Jose C. Martins, Valerie Leclere, Feyisara Eyiwumi Oni, Monica Hofte
Article
Plant Sciences
Ruben E. M. Verbeek, Evelien Van Buyten, Zahangir Alam, David De Vleesschauwer, Jonas Van Bockhaven, Takayuki Asano, Shoshi Kikuchi, Ashley Haeck, Kristof Demeestere, Godelieve Gheysen, Monica Hoefte, Tina Kyndt
FRONTIERS IN PLANT SCIENCE
(2019)
Article
Plant Sciences
Nirodha Weeraratne, Benjamin J. Stodart, Vittorio Venturi, Monica Hofte, Gia Khuong Hoang Hua, Marc Ongena, Sandra Savocchia, Christopher C. Steel, Gavin J. Ash
Article
Food Science & Technology
Kaat Jose Peeters, Ashley Haeck, Lies Harinck, Oluwatoyin Oluwakemi Afolabi, Kristof Demeestere, Kris Audenaert, Monica Hofte
Article
Plant Sciences
Lisa Heyman, Antonios Chrysargyris, Kristof Demeestere, Nikolaos Tzortzakis, Monica Hofte
Summary: This research investigates how grapevine responds to the concurrent challenge of drought stress and Plasmopara viticola, and how one stress affects the other. The study shows that drought can increase the susceptibility of grapevine leaves to pathogen infection, but both drought-tolerant and drought-sensitive cultivars exhibit resistance against the pathogen when inoculated in planta. Abscisic acid seems to play a prominent role in this resistance process. The findings suggest that irrigation practices to mitigate climate change effects may have a significant impact on plant pathogens.
Article
Microbiology
Lea Girard, Cedric Lood, Monica Hofte, Peter Vandamme, Hassan Rokni-Zadeh, Vera van Noort, Rob Lavigne, Rene De Mot
Summary: This study identified 43 new Pseudomonas species through whole genome sequencing and updated the evolutionary and taxonomic relationships within the genus. The importance of correct taxonomic assignment and phylogenetic classification was highlighted for integrative studies on genetic diversity, lifestyle, and metabolic potential of Pseudomonas spp.
Review
Biochemistry & Molecular Biology
Feyisara Eyiwumi Oni, Qassim Esmaeel, Joseph Tobias Onyeka, Rasheed Adeleke, Cedric Jacquard, Christophe Clement, Harald Gross, Essaid Ait Barka, Monica Hofte
Summary: Pseudomonas lipopeptides (Ps-LPs) play important roles in bacterial physiology, host-microbe interactions, and plant disease control. LP-producing pseudomonads and their molecules show specificity and follow a phylogenetic distribution. Understanding the taxonomy-molecule relationship can help classify and determine the agricultural relevance of unknown LPs. It is necessary to systematically elucidate the roles of different Ps-LP groups in plant-pathogen interactions and plant innate immunity.