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
Genetics & Heredity
Zuzana Chumova, Terezie Mandakova, Pavel Travnicek
Summary: Polyploidy plays a crucial role in plant evolution, with some species having limited understanding of their evolutionary history. This study used various techniques to investigate the origins of sweet vernal grass and alpine sweet vernal grass, revealing different polyploidization patterns and extensive variation among European populations.
Article
Biochemical Research Methods
Yuting Dai, Aining Xu, Jianfeng Li, Liang Wu, Shanhe Yu, Jun Chen, Weili Zhao, Xiao-Jian Sun, Jinyan Huang
Summary: CytoTree is a versatile tool for analyzing multidimensional flow and mass cytometry data, providing various computational functionalities and supporting the construction of tree-shaped trajectories. Its practical utility is demonstrated through several examples of mass cytometry and time-course flow cytometry data.
BMC BIOINFORMATICS
(2021)
Article
Ecology
Oluwafemi D. Olusoji, Jurg W. Spaak, Mark Holmes, Thomas Neyens, Marc Aerts, Frederik De Laender
Summary: Flow cytometry is commonly used in ecology to measure traits and population size of bacteria and phytoplankton, although distinguishing between different populations can be challenging. Gates are employed in the identification process of particles measured in flow cytometry, with the accuracy of gating functions being crucial for accurate analysis and interpretation of data.
ECOLOGICAL MODELLING
(2021)
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.
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
Biochemical Research Methods
Zhe Cui, Ya Cui, Tianyi Zang, Yadong Wang
Summary: This report introduces interacCircos, an R package that integrates JavaScript-based libraries to create interactive Circos plots simply and flexibly for presenting large-scale genomic data.
Article
Plant Sciences
Josef Greimler, Eva M. Temsch, Zhiqing Xue, Hanna Weiss-Schneeweiss, Polina Volkova, Markus Peintinger, Pawel Wasowicz, Hui Shang, Ivan Schanzer, Jorge O. Chiapella
Summary: This study investigated the variation in genome size and ploidy of Deschampsia cespitosa and related species in Eurasia. Significant regional differences were found between diploid and tetraploid grasses, with tetraploid plants showing habitat preferences related to their reproductive mode.
PLANT SYSTEMATICS AND EVOLUTION
(2022)
Article
Plant Sciences
Ali Bagheri, Azadeh Akhavan Roofigar, Zahra Nemati, Frank R. Blattner
Summary: This study examined the chromosome number and genome size of Astragalus section Hymenostegis. The results showed a strong correlation between genome size and chromosome numbers, and indicated that polyploidization contributes to the increased species number in Astragalus. However, it is not the main driver of speciation in section Hymenostegis.
Article
Agronomy
Vijayakumari Narukulla, Yogesh Lahane, Krutika Fiske, Shashi Pandey, Vasileios Ziogas
Summary: In this study, stable tetraploids were developed in citrus rootstock cultivars including Rough lemon, Rangpur lime, and Alemow through in vitro colchicine treatments. The treatment with 0.1% colchicine for 24 hours resulted in the highest tetraploid induction percentage (18.3%) in all the rootstock cultivars.
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
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)
Article
Plant Sciences
Dmitry D. Sokoloff, Mikhail Skaptsov, Nikolay A. Vislobokov, Sergey Smirnov, Alexander Shmakov, Margarita Remizowa
Summary: Investigating the morphological differences between cytotypes in the Acorus plants reveals a complex pattern of triploids and diploids across Asia. European triploids with the same genome size as Siberian triploids are abundant in the Ob river valley, while a population of aneuploid triploids with 33 chromosomes is found elsewhere in Siberia. The study confirms that diploids and triploids differ in leaf characteristics and fruit development, with diploids showing variability in seed development on a spadix and triploids producing uniform parthenocarpic fruits.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2021)
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
Genetics & Heredity
Luis Diaz-Garcia, Lorraine Rodriguez-Bonilla, Jessica Rohde, Tyler Smith, Juan Zalapa
Article
Biochemistry & Molecular Biology
Dane Cronin, Paul Kron, Brian C. Husband
Review
Biochemical Research Methods
Joao Loureiro, Paul Kron, Eva M. Temsch, Petr Koutecky, Sara Lopes, Mariana Castro, Silvia Castro
Summary: This article discusses the critical steps for obtaining accurate estimates of nuclear DNA content in plants, including releasing an adequate amount of nuclei while maintaining their integrity, protecting DNA from degradation, staining, and best practices.
Article
Biochemical Research Methods
Paul Kron, Joao Loureiro, Silvia Castro, Martin Certner
Summary: Pollen grains play a crucial role in plant reproduction and can be studied using flow cytometry. Despite the unique challenges posed by the complexity of pollen compared to single cells, research on the identification and isolation of pollen and its subunits, as well as the types of research applications, is essential for understanding key issues in plant reproduction.
Article
Plant Sciences
Victoria J. Nowell, Song Wang, Tyler W. Smith
Summary: Peripheral populations are important for genetic diversity and conservation, but they are also at greater risk of extinction. The study on Trichophorum planifolium showed that the species has low within-population diversity and high levels of inbreeding. The remaining Canadian population has low diversity but does not suffer from inbreeding depression. Populations within the core range also show similar isolation or higher genetic divergence compared to the peripheral population.
Article
Biodiversity Conservation
Sharla L. Foster, Heather M. Kharouba, Tyler W. Smith
Summary: Invasive species pose an increasing threat to global biodiversity, and accurate predictions of their spread are crucial for effective management. However, modelling the geographic distribution of invasive species using correlative species distribution models (SDMs) is challenging due to the assumption that species are in equilibrium with their environment. This assumption is likely to be violated for actively invading species.
Article
Plant Sciences
Michael J. J. McTavish, Tyler Smith, Subbaiah Mechanda, Sandy M. M. Smith, Robert S. S. Bourchier
Summary: Effective management of the introduced invasive grass common reed [Phragmites australis (Cav.) Trin. ex Steud.] requires the ability to differentiate between the introduced and native subspecies found in North America. Morphological identification is a low-cost and practical approach for distinguishing between the subspecies, in addition to genetic tools. A study conducted in southern Ontario, Canada, identified 22 morphological traits that differ between the subspecies, with four traits providing complete separation. A checklist of these traits has been compiled for simple and reliable identification of native and introduced P. australis.
INVASIVE PLANT SCIENCE AND MANAGEMENT
(2023)
Article
Plant Sciences
Elaina Greaves, Paul Kron, Brian C. Husband
Summary: This study found that hybridization between introduced apple and native crabapple can have impacts on the reproductive and population dynamics of the native species, not only through the production of viable hybrids, but also through increased asexual seed production.
AMERICAN JOURNAL OF BOTANY
(2023)
Review
Biochemical Research Methods
Petr Koutecky, Tyler Smith, Joao Loureiro, Paul Kron
Summary: This article discusses the importance of standardization and best practices for data acquisition and analysis in plant flow cytometry. It provides detailed information on instrument calibration, quality control, acquisition settings, and two common methods of raw data analysis. Best practice recommendations are summarized.
Article
Plant Sciences
Victoria J. Nowell, Song Wang, Tyler W. Smith
Summary: The genetic diversity of Trichophorum planifolium is remarkably low, but this is not unusual for the species and does not support the claim of elevated inbreeding depression in the remaining Canadian population. However, the geographically isolated and unique soil environment of this population may contribute to its long-term persistence.
Review
Biodiversity Conservation
Zoe Migicovsky, Beatrice Amyotte, Jens Ulrich, Tyler W. Smith, Nancy J. Turner, Joana Pico, Claudia Ciotir, Mehdi Sharifi, Gennifer Meldrum, Ben Stormes, Tara Moreau
Summary: This article examines the importance of plant biodiversity for food security and agriculture, using berries as a case study. It discusses the conservation, use, and public engagement of crop wild relatives and emphasizes the significance of these plants to Indigenous Peoples. The aim is to lay the foundation for future collaborative efforts and showcase berries as a useful example for the conservation of food plant biodiversity and public engagement.
PLANTS PEOPLE PLANET
(2022)
Article
Plant Sciences
Sara L. Martin, Tyler W. Smith, Tracey James, Fatma Shalabi, Paul Kron, Connie A. Sauder
