Article
Biochemistry & Molecular Biology
Yennifer Mata-Sucre, William Matzenauer, Natalia Castro, Bruno Huettel, Andrea Pedrosa-Harand, Andre Marques, Gustavo Souza
Summary: This study reassesses the systematics of the genus Juncus using genomic data and demonstrates the potential of comparative genomic analyses for understanding plant systematics and evolution. The results reveal the importance of repeat sequences in clarifying plant systematics and suggest an ancient hybridization event in the divergence of Juncus. The study also confirms the monocentricity of Juncus and identifies specific repeatome trends correlated with ancient origin.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Plant Sciences
Veit Herklotz, Ales Kovarik, Volker Wissemann, Jana Lunerova, Radka Vozarova, Sebastian Buschmann, Klaus Olbricht, Marco Groth, Christiane M. Ritz
Summary: Plant genomes contain non-coding repetitive DNA, with phylogenetic signals obtained from repeatome data. The study showed that repeatome data can support subfamilial classification within Rosaceae, distinguishing major evolutionary lineages in Fragaria and showing weak phylogenetic signals but geographic patterns in Rosa. Success of the method varies between taxonomic groups.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Tatiana E. Samatadze, Olga Yu. Yurkevich, Firdaus M. Khazieva, Irina V. Basalaeva, Olga M. Savchenko, Svyatoslav A. Zoshchuk, Alexander I. Morozov, Alexandra V. Amosova, Olga V. Muravenko
Summary: The taxonomically challenging genus Calendula L. (Asteraceae) includes medicinal species with high morphological and karyological variability. This study focused on the repeatome analysis and chromosome visualization of Calendula officinalis L. The results showed that C. officinalis had a distinct karyotype compared to other species, indicating its separate position in the Calendula phylogeny. However, common repeats were found in the genomes of all studied species, suggesting a common origin. Additionally, it was found that C. stellata contributed its genome to allotetraploid C. tripterocarpa, and C. arvensis is an allohexaploid hybrid between C. stellata and C. tripterocarpa. Further studies on the karyotype of different Calendula species are needed to understand chromosomal reorganization during speciation.
Article
Plant Sciences
Pavel Yu. Kroupin, Ekaterina D. Badaeva, Victoria M. Sokolova, Nadezhda N. Chikida, Maria Kh. Belousova, Sergei A. Surzhikov, Ekaterina A. Nikitina, Alina A. Kocheshkova, Daniil S. Ulyanov, Aleksey S. Ermolaev, Thi Mai Luong Khuat, Olga V. Razumova, Anna I. Yurkina, Gennady I. Karlov, Mikhail G. Divashuk
Summary: This study sequenced the genomes of Aegilops crassa and related species and analyzed their repetitive sequences, leading to the identification of several satellite repeats. Comparative analysis and fluorescence in situ hybridization (FISH) were used to assess the copy number and affinity of satellite repeats in different species and subgenomes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Dong Han, Hongmin Zhen, Xiaoyan Liu, Justyna Zulewska, Zhennai Yang
Summary: This study used both rRNA and gDNA sequencing on mouse cecal contents and found differences in microbial composition and functional predictions between the two methods. rRNA-derived sequencing improved identification capability of specific microorganisms and was more suitable for functional predictions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Plant Sciences
Hugo Merle, Alfonso Garmendia, Maria Ferriol
Summary: Hybridization and polyploidy play significant roles in plant evolution, and studies on Seridia in the Centaurea genus are limited. Through analysis of morphological characteristics and genomic data, we identified different taxa, detected introgressions, and discussed their evolutionary history. We found three genetically differentiated clusters and proposed a new species in the Centaurea genus.
Review
Plant Sciences
Vera Hemleben, Donald Grierson, Nikolai Borisjuk, Roman A. Volkov, Ales Kovarik
Summary: The history of rDNA research began almost 90 years ago with observations on the formation and function of nucleoli in maize, leading to the identification of ribosomes as the sites of protein synthesis in eukaryotic cells. Studies in the mid- to late 1960s on nuclear-encoded rRNA transcripts laid the groundwork for research on nucleolar dominance, epigenetic silencing, and rDNA loci interactions. Initial research on rDNA in plants at the dawn of molecular biology in the 60s and 80s provided a foundation for understanding the synthesis, processing, and organization of rRNA genes, as well as the impact of hybridization and allopolyploidy on rDNA expression and homogenization.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
Yan Wei, Yumeng Li, Yayu Wang, Xinyue Luo, Feirong Du, Weifang Liu, Li Xie, Jianwei Chen, Ziwei Ren, Shiqi Hou, Sunhaoyu Wang, Shaojie Fu, Yan Dang, Pengsong Li, Xin Liu
Summary: This study explored the microbial diversity in industrial effluents and verified the feasibility of tracking these effluents in sewer networks based on sequencing data. The results showed that microbial compositions varied greatly among samples from different locations in the sewer system. Furthermore, the study identified microbial markers that differentiate effluents from different factories, which can be used to track the sources of the effluents.
ENVIRONMENTAL RESEARCH
(2022)
Article
Veterinary Sciences
Haigang Wu, Xian Wu, Li Huang, Chongmei Ruan, Jinni Liu, Xiaoqing Chen, Jicheng Liu, Houqing Luo
Summary: This study found that andrographolide administration increased the proportions and abundance of beneficial bacteria, while amoxicillin treatment increased the proportion of pathogenic bacteria. The results suggest potential alternatives to antibiotics for reducing bacterial resistance and restoring intestinal flora balance.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Plant Sciences
Simone Cardoni, Roberta Piredda, Thomas Denk, Guido W. Grimm, Aristotelis C. Papageorgiou, Ernst-Detlef Schulze, Anna Scoppola, Parvin Salehi Shanjani, Yoshihisa Suyama, Nobuhiro Tomaru, James R. P. Worth, Marco Cosimo Simeone
Summary: The process of plant speciation is more complex than standard models suggest, involving factors such as isolation, lineage mixing, and intra-genomic competition. Modern species are genetic mosaics, representing a striking case of ongoing reticulate evolution over the past 55 million years.
Article
Microbiology
Hiu-Yin Lao, Timothy Ting-Leung Ng, Ryan Yik-Lam Wong, Celia Sze-Ting Wong, Lam-Kwong Lee, Denise Sze-Hang Wong, Chloe Toi-Mei Chan, Stephanie Hoi-Ching Jim, Jake Siu-Lun Leung, Hazel Wing-Hei Lo, Ivan Tak-Fai Wong, Miranda Chong-Yee Yau, Jimmy Yiu-Wing Lam, Alan Ka-Lun Wu, Gilman Kit-Hang Siu
Summary: In this study, two 16S rRNA gene sequencing tests based on the Illumina and Nanopore sequencing technologies were compared to identify clinical isolates that cannot be identified by MALDI-TOF MS. The results showed that the Nanopore workflow had a higher taxonomic resolution at the species level.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Alexander A. Gnutikov, Nikolai N. Nosov, Igor G. Loskutov, Elena V. Blinova, Viktoria S. Shneyer, Nina S. Probatova, Alexander V. Rodionov
Summary: Next-generation sequencing was used to analyze the genetic variation among seven diploid A-genome Avena species. The study identified multiple haplotypes and ribotypes, some of which were species-specific while others were shared between multiple species. Interestingly, a diploid C-genome species, A. clauda, was found to have two different families of ribotypes, indicating a potential hybridization between As-genome and C-genome oats.
Article
Environmental Sciences
Li Song, Zhenzhi Pan, Yi Dai, Lin Chen, Li Zhang, Qilin Liao, Xiezhi Yu, Hongyan Guo, Guisheng Zhou
Summary: This study investigated the effects of various degrees of long-term cadmium pollution on soil microorganisms at different soil depths. The results showed that cadmium contamination reduced the richness and diversity of soil microbes, significantly impacting the microbial communities in the polluted underlying soil layer, while leading to an increase in species richness in the mildly and severely polluted surface soils. This research provides insights into how long-term heavy metal contamination affects soil bacterial communities.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Biochemical Research Methods
Ze-Gang Wei, Xu Chen, Xiao-Dan Zhang, Hao Zhang, Xing-Guo Fan, Hong-Yan Gao, Fei Liu, Yu Qian
Summary: Recent advances in sequencing technology have led to a large amount of sequencing data, and clustering analysis is a powerful tool to study this data. However, comparison studies of clustering methods have limitations, and this study aims to provide a comprehensive benchmark for sequence clustering methods, helping biological analyzers choose appropriate algorithms and motivating algorithm designers to develop more efficient approaches.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Agriculture, Dairy & Animal Science
Han Aricha, Huasai Simujide, Chunjie Wang, Jian Zhang, Wenting Lv, Xirnud Jimisi, Bo Liu, Hao Chen, Chen Zhang, Lina He, Yinxue Cui, Ruijuan Gao, Chen Aorigele
Summary: The study found that the composition of the gut microbiota in Mongolian cattle from the grasslands was similar, while those from the desert areas showed distinct differences. The gut microbiota of Mongolian cattle is influenced by geographical factors, with cattle from the grasslands displaying closer clustering and distinct differences from those in the desert regions.
Article
Plant Sciences
Simona Barankova, Joan Pere Pascual-Diaz, Nusrat Sultana, Maria Pilar Alonso-Lifante, Manica Balant, Karina Barros, Ugo D'Ambrosio, Hana Malinska, Vratislav Peska, Ivan Perez Lorenzo, Ales Kovarik, Boris Vyskot, Bohuslav Janousek, Sonia Garcia
Article
Plant Sciences
Vratislav Peska, Martin Matl, Terezie Mandakova, Daniel Vitales, Petr Fajkus, Jiri Fajkus, Sonia Garcia
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Biodiversity Conservation
Joan Pere Pascual-Diaz, Sedat Serce, Ivana Hradecka, Martin Vanek, Bahar Sogutmaz Ozdemir, Nusrat Sultana, Mehtap Vural, Daniel Vitales, Sonia Garcia
Article
Multidisciplinary Sciences
Vratislav Peska, Petr Fajkus, Michal Bubenik, Vaclav Brazda, Natalia Bohalova, Vojtech Dvoracek, Jiri Fajkus, Sonia Garcia
Summary: Telomerase RNA (TR) plays a crucial role in telomere DNA synthesis and assembly, but its sequence diversity poses challenges in characterizing it. Long telomere units and corresponding TRs were found in certain fungal species. The presence of variable lengths in the annealing sequence of the template region suggests that species with the same telomere sequence may have different TR templates.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Jana Sochorova, Francisco Galvez, Roman Matyasek, Sonia Garcia, Ales Kovarik
Summary: The study reveals a high variability in 5S and 45S rDNA loci numbers in animals, with rare occurrences of karyotypes with extremely high loci numbers, generally converging to two 5S sites and two 45S rDNA sites per diploid genome. The position of 45S rDNA on sex chromosomes is relatively common, especially in arthropods, and is predominantly located in microchromosomes in birds and reptiles. Additionally, as the number of 45S rDNA loci increases, the proportion of active NORs progressively decreases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Natalia Borowska-Zuchowska, Ewa Robaszkiewicz, Serhii Mykhailyk, Joanna Wartini, Artur Pinski, Ales Kovarik, Robert Hasterok
Summary: Nucleolar dominance (ND) is an epigenetic phenomenon that describes the selective inactivation of 35S rDNA loci from one progenitor in hybrids or allopolyploids. This study found that the stability of ND in different genotypes of Brachypodium hybridum may vary, with genotype-specific loss possibly occurring after fertilization during development. This suggests that B. hybridum is an attractive model for studying ND in grasses.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Nusrat Sultana, Gerhard Menzel, Kathrin M. Seibt, Sonia Garcia, Beatrice Weber, Sedat Serce, Tony Heitkam
Summary: In this study, the LTR retrotransposon landscape in the Vaccinium macrocarpon genome was characterized. The results showed a diverse range of retrotransposon lineages and their associated structural features. This research has important implications for further analysis and breeding of Vaccinium genomes.
JOURNAL OF BERRY RESEARCH
(2022)
Article
Plant Sciences
Joan Pere Pascual-Diaz, Sonia Garcia, Daniel Vitales
Summary: Plastid genomes in Asteraceae are generally highly conserved, with specific rearrangements being phylogenetically informative. This study provided a comprehensive plastome-based phylogeny of Asteraceae, revealing structural information, genetic diversity, and repeat composition. Despite the presence of a double inversion in most species, there are exceptions in basal tribes lacking a specific pseudogene. The phylogenomic analysis based on protein-coding genes, transfer RNA genes, and ribosomal RNA genes showed consistency with the family's general consensus, while also highlighting some incongruences between nuclear and plastid DNA data at the tribe level.
Article
Plant Sciences
Natalia Borowska-Zuchowska, Magdalena Senderowicz, Dana Trunova, Bozena Kolano
Summary: Cytogenetics is a branch of genetics focused on cellular components, especially chromosomes, and their relationship to heredity, genome structure, function, and evolution. Modern cytogenetic approaches allow for the visualization of different sequences in the plant genome and contribute to understanding its evolutionary history.
Editorial Material
Plant Sciences
Roman A. Volkov, Nikolai Borisjuk, Sonia Garcia, Ales Kovarik, Julio Saez-Vasquez
FRONTIERS IN PLANT SCIENCE
(2022)
Editorial Material
Biochemistry & Molecular Biology
Robert Hasterok, Natalia Borowska-Zuchowska, Ewa Robaszkiewicz
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Manica Balant, Roi Rodriguez Gonzalez, Sonia Garcia, Teresa Garnatje, Jaume Pellicer, Joan Valles, Daniel Vitales, Oriane Hidalgo
Summary: Cannabis sativa, a versatile plant used in traditional medicine and for various purposes, exhibits a wide range of morphological and genetic diversity. This study used flow cytometry to explore the diversity of genome size and sex determination in Cannabis individuals. The results showed that there were significant differences in genome size between male and female individuals, although flow cytometry was not able to directly discriminate these differences.
Editorial Material
Biochemistry & Molecular Biology
Sonia Garcia, Bohuslav Janousek, Joan Pere Pascual-Diaz, Susanne S. S. Renner
Review
Ecology
Wencai Wang, Xianzhi Zhang, Sonia Garcia, Andrew R. Leitch, Ales Kovarik
Summary: The classical model of concerted evolution states that rDNA units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected. However, advanced sequencing techniques have revealed that rDNA homogenization in many organisms is not complete. This work summarizes the variation in rDNAs across different taxa and discusses the factors contributing to this incomplete concerted evolution.
Article
Plant Sciences
Michal Zavodnik, Petr Fajkus, Michal Franek, David Kopecky, Sonia Garcia, Steven Dodsworth, Andres Orejuela, Agata Kilar, Jiri Ptacek, Martin Matl, Anna Hyskova, Jiri Fajkus, Vratislav Peska
Summary: Telomerase, telomeric DNA, and associated proteins form a complex and conserved mechanism that maintains genome integrity by protecting chromosome ends. Evolutionary changes in telomere maintenance have given rise to species with unusual telomeric DNA sequences and telomerase components. Telomerase RNA (TR) plays a central role in telomere maintenance, and mutations in TR can disrupt telomere DNA synthesis and recognition by telomere proteins. Through bioinformatic and experimental analyses, this study investigates the evolutionary changes in TR that underlie telomere transitions in plants, and identifies telomere transitions corresponding to TR paralogs with diverse template regions.