Article
Plant Sciences
Djivan Prentout, Natasa Stajner, Andreja Cerenak, Theo Tricou, Celine Brochier-Armanet, Jernej Jakse, Jos Kafer, Gabriel A. B. Marais
Summary: A shared sex chromosome system was discovered in Cannabis and Humulus, with recombination suppression beginning 21-25 million years ago, leading to a degenerated Y chromosome.
Article
Agronomy
Joshua S. Havill, Briana J. Richardson, Charlie L. Rohwer, David H. Gent, John A. Henning, Gary J. Muehlbauer
Summary: Two QTL associated with powdery mildew resistance and sex determination were identified in hop using genetic mapping approaches. The high-density genetic map, QTL, and associated KASP markers will facilitate selection for sex and R1-mediated resistance in hop breeding programs.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Plant Sciences
Olga V. Razumova, Mikhail G. Divashuk, Oleg S. Alexandrov, Gennady I. Karlov
Summary: Dioecious plants with sex chromosome systems are rare and provide attractive models for studying sex chromosome evolution. This study on three related dioecious species of the Cannabaceae family reveals the accumulation of repetitive DNA sequences in the Y chromosomes and high genomic differentiation. The results suggest a long period of independent and advanced sex chromosome evolution, offering a valuable basis for future genomic studies of sex and highlighting the potential of the Cannabaceae family as a model for studying sex chromosome evolution.
Article
Biochemistry & Molecular Biology
Alexander Kostmann, Barbora Augstenova, Daniel Frynta, Lukas Kratochvil, Michail Rovatsos
Summary: Lizards of the Scincoidea clade, including cordylids, gerrhosaurids, skinks, and xantusiids, exhibit almost worldwide distribution and significant ecological and morphological diversity. Despite limited variability in cytogenetic traits, different species show conservation in diploid chromosome numbers but significant variation in chromosome morphology and the presence of interstitial telomeric sequences. Sex chromosomes, identified as XX/XY, are only found in Tiliqua scincoides within this clade, indicating a generally poor stage of differentiation in sex chromosomes among these lizards.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Yu Liu, Yan-Hui Bi, Zhi-Gang Zhou
Summary: This study reported the precise karyotype of Saccharina japonica, which provides important basis for genomic physical mapping and genetic breeding of this marine alga.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Genetics & Heredity
Shaun J. Clare, Ryan M. King, Anna L. Tawril, Joshua S. Havill, Gary J. Muehlbauer, Sarah B. Carey, Alex Harkess, Nahla Bassil, Kayla R. Altendorf
Summary: This study identified a diagnostic marker for hop sex determination, which can accurately and rapidly determine the gender of plants. The marker is highly scalable, accurate, and has the potential to improve hop breeding efficiency.
G3-GENES GENOMES GENETICS
(2023)
Review
Biology
Matthias Stoeck, Dmitrij Dedukh, Radka Reifova, Dunja K. Lamatsch, Zuzana Starostova, Karel Janko
Summary: The roles of sex chromosomes in vertebrate hybridization and speciation are dependent on the level of divergence, affecting the degree of reproductive isolation. Undifferentiated sex chromosomes are more susceptible to introgression and may give rise to new sex chromosome systems.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Multidisciplinary Sciences
Lauren S. Godwin, Joanna M. Bridger, Helen A. Foster
Summary: The DNA halo method uses high salt concentrations and nonionic detergents to generate DNA loops that remain anchored to structures within nuclei, providing increased resolution and facilitating physical mapping. This technique allows for studying genomic interactions with all the structures that the genome is anchored by, revealing gene loci, whole chromosomes, alpha satellite, telomeres, and even RNA. HALO-FISH provides insight into nuclear organization and function in normal cells and in disease progression such as with cancer.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Dandan Wu, Namei Yang, Qian Xiang, Mingkun Zhu, Zhongyan Fang, Wen Zheng, Jiale Lu, Lina Sha, Xing Fan, Yiran Cheng, Yi Wang, Houyang Kang, Haiqin Zhang, Yonghong Zhou
Summary: This study investigated the chromosomes of the Pseudoroegneria libanotica and identified its characteristics and intraspecific polymorphism. The findings provide important information for the study of the evolution of the P. libanotica genome. The study also suggested the heterozygosity and adaptation as factors influencing the polymorphism in P. libanotica.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agronomy
Sandra Afonso, Margarida Arrobas, M. Angelo Rodrigues
Summary: This study aimed to improve the productivity and homogeneity of hop fields in northeast Portugal by using plant biostimulants as foliar sprays. The results showed that plant vigour of the plot and the year significantly influenced crop performance and tissue nutrient concentration, while foliar treatments had a lesser effect on the elemental composition of plant tissue. The use of seaweed extracts as biostimulants was effective in mitigating the stress affecting the plants, particularly under conditions of severe stress.
Article
Genetics & Heredity
Diogo C. Cabral-de-Mello, Magda Zrzava, Svatava Kubickova, Pedro Rendon, Frantisek Marec
Summary: This study introduces seven new satellite DNAs in Lepidoptera and describes their characteristics, showing high variability within and between species, with some degree of conservation. Three of the satellite DNAs are abundant on the W chromosomes of Ostrinia nubilalis and Cydalima perspectalis, contributing to their differentiation from the Z chromosomes.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Jenny M. Vo-Phamhi, Kevin A. Yamauchi, Rafael Gomez-Sjoberg
Summary: This paper introduces an open-source toolkit and framework that incorporates crowdsourced and expert annotations as a source of ground truth for in situ transcriptomics image analysis. Through exploring and demonstrating the use of crowdsourced annotations for validating spot-calling algorithms and tuning parameters, it confirms that consensus crowdsourced annotations can substitute expert-generated ground truth. Advancements in in situ methods deepen our understanding of spatial organization in biological processes within tissues.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Jill Jasmine Dalimot, Ilka Mc Cormick Smith, Jasmin Gerkrath, Sylvia Hartmann, Oliver A. Cornely, Soo Chan Lee, Joseph Heitman, Volker Rickerts
Summary: This study focused on improving the accuracy of mucormycosis diagnosis from tissue samples using fluorescence in situ hybridization (FISH) targeting specific regions of fungal ribosomal RNA (rRNA) of Mucorales. While the probe combination showed success in targeting Mucorales and enhancing diagnosis, autofluorescence and variations in physiological states of fungi and antifungal therapy may impact the FISH signal obtained. Further studies are needed to determine the value of FISH in diagnosing mucormycosis from different clinical samples.
Review
Biochemistry & Molecular Biology
Yu-Sheng Wang, Jia Guo
Summary: The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial for understanding health and disease, and recent advances in multiplexed FISH methods have enabled comprehensive RNA profiling in individual cells.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Anne-Sophie Paguet, Ali Siah, Gabriel Lefevre, Sophie Moureu, Thierry Cadalen, Jennifer Samaillie, Franck Michels, Barbara Deracinois, Christophe Flahaut, Harmony Alves Dos Santos, Audrey Etienne-Debaecker, Caroline Rambaud, Sylvie Chollet, Roland Molinie, Jean-Xavier Fontaine, Christophe Waterlot, Marie-Laure Fauconnier, Sevser Sahpaz, Celine Riviere
Summary: This study investigates the genetic and chemical diversity of fifty wild hops collected from different locations in Northern France. The results show that wild hops exhibit high levels of genetic and chemical diversity, making them an important resource for the species.
Article
Plant Sciences
Olga V. Razumova, Mikhail G. Divashuk, Oleg S. Alexandrov, Gennady I. Karlov
Summary: Dioecious plants with sex chromosome systems are rare and provide attractive models for studying sex chromosome evolution. This study on three related dioecious species of the Cannabaceae family reveals the accumulation of repetitive DNA sequences in the Y chromosomes and high genomic differentiation. The results suggest a long period of independent and advanced sex chromosome evolution, offering a valuable basis for future genomic studies of sex and highlighting the potential of the Cannabaceae family as a model for studying sex chromosome evolution.
Article
Plant Sciences
Mikhail G. Divashuk, Ekaterina A. Nikitina, Victoria M. Sokolova, Anna I. Yurkina, Alina A. Kocheshkova, Olga V. Razumova, Gennady I. Karlov, Pavel Yu. Kroupin
Summary: qPCR is used as an auxiliary step in the preparation and selection of markers for FISH analysis in this article. Several cases were reviewed to compare closely related species and examine the transfer of tandem repeat sequences (TRs) between wheat and related species. The results showed high correlation between qPCR and FISH analysis, confirming the value of qPCR for cytogenetic studies.
Review
Biochemistry & Molecular Biology
Pavel Yu. Kroupin, Daniil S. S. Ulyanov, Gennady I. I. Karlov, Mikhail G. G. Divashuk
Summary: Fluorescence in situ hybridization is a useful tool for studying the genetic diversity of wheat and characterizing alien introgression into the wheat genome. This review highlights the progress made in developing methods for creating new chromosomal markers using DNA probes based on satellite repeats. The use of new-generation sequencing and bioinformatical tools has led to the discovery of numerous genome- and chromosome-specific markers. The review also discusses the specific localization of these markers in different wheat wild relatives and their applicability for detecting alien introgression.
Article
Agronomy
Pavel Yu. Kroupin, Ludmila A. Bespalova, Aleksandra Yu. Kroupina, Aleksey S. Yanovsky, Varvara A. Korobkova, Daniil S. Ulyanov, Gennady I. Karlov, Mikhail G. Divashuk
Summary: This study explored the influence of different allelic states of Glu-A1 and Glu-B1 genes on the quality of spring durum wheat. The analysis of 69 cultivars and promising lines revealed that Glu-B1al, Glu-B1d, and Glu-B1z* alleles positively impact gluten index, while Glu-B1e allele has a negative effect. Glu-B1al also increases protein, gluten, and SDS content, while Glu-B1d decreases these traits.
Article
Agronomy
Alla B. Mirgorodskaya, Rushana A. Kushnazarova, Lucia Ya. Zakharova, Alana A. Ulyanova, Dmitry Y. Litvinov, Andrey O. Blinkov, Mikhail G. Divashuk, Irina A. Kochanova, Liliya M. Nesterova
Summary: In this study, a new herbicidal formulation was developed using a gemini surfactant (16-6-16) as an adjuvant with clopyralid. The formation of a supramolecular surfactant-herbicide complex (SMC) in the formulation improved its wetting properties, increased the concentration of clopyralid on the leaf surface, and enhanced its penetrating ability. The efficacy of the clopyralid-16-6-16 SMC formulation was demonstrated to be superior to two commercial formulations of clopyralid.
Review
Agronomy
Olga V. Razumova, Oleg S. Alexandrov, Karina D. Bone, Gennady I. Karlov, Mikhail G. Divashuk
Summary: Unlike animals, dioecy is rare in flowering plants. Most angiosperm species have bisexual flowers, while about a quarter have dioecious flowers. The formation of dioecious plants' flowers is determined by genetic mechanisms, ranging from a single gene to the function of heteromorphic sex chromosomes. Recent advancements in sequencing techniques and molecular biology have increased interest in studying sex determination mechanisms in plants. This review summarizes current knowledge on sex chromosomes and sex determination mechanisms in dioecious plants, with a focus on agriculturally important species.
Article
Food Science & Technology
Aleksandra Yu. Kroupina, Aleksey S. Yanovsky, Varvara A. Korobkova, Ludmila A. Bespalova, Andrey V. Arkhipov, Galina I. Bukreeva, Anastasiya D. Voropaeva, Pavel Yu. Kroupin, Dmitry Y. Litvinov, Aleksandra A. Mudrova, Daniil S. Ulyanov, Gennady I. Karlov, Mikhail G. Divashuk
Summary: This study analyzed the allelic state of high-molecular-weight glutenin genes Glu-A1 and Glu-B1 in 76 accessions of winter durum wheat and assessed grain and pasta quality traits in a two-year field experiment. The results showed that the Glu-A1a allele had a positive effect on the gluten index, while Glu-A1c had a negative effect. The Glu-B1al and Glu-B1f alleles had a positive effect on protein and gluten quality and quantity, and the Glu-A1c + Glu-B1al genotypes were closest to the high-quality category in protein-associated quality traits.
Article
Plant Sciences
Varvara A. Korobkova, Ludmila A. Bespalova, Aleksey S. Yanovsky, Anastasiya G. Chernook, Pavel Yu. Kroupin, Andrey V. Arkhipov, Anna I. Yurkina, Lubov A. Nazarova, Aleksandra A. Mudrova, Anastasiya D. Voropaeva, Olga Yu. Puzyrnaya, Elena V. Agaeva, Gennady I. Karlov, Mikhail G. Divashuk
Summary: Wheat-rye translocations 1RS.1BL and 1RS.1AL are widely used in bread wheat breeding worldwide due to their advantages in disease resistance, pest resistance and performance under drought-stress conditions. However, these translocations are only found in experimental lines of durum wheat genotypes, despite their potential benefits.
Article
Biochemistry & Molecular Biology
Pavel Merkulov, Sofya Gvaramiya, Maxim Dudnikov, Roman Komakhin, Murad Omarov, Alina Kocheshkova, Zakhar Konstantinov, Alexander Soloviev, Gennady Karlov, Mikhail Divashuk, Ilya Kirov
Summary: Transposable element insertions (TEIs) are important for genomic innovation in plants, but identifying and tracking these insertions in complex genomes has been challenging. In this study, researchers combined Cas9-targeted Nanopore sequencing (CANS) with a novel pipeline called NanoCasTE to successfully trace both genetically inherited and somatic TEIs in plants. The study revealed the role of DNA methylation in shaping insertion preference and identified preferential targeting of genes downregulated during heat stress by the ONSEN transposon family. Hypomethylation of novel somatic insertions for two ONSENs was also detected. The study demonstrates the effectiveness of CANS and NanoCasTE in detecting TEIs and exploring mobilome organization in plants under stress and in different genetic backgrounds.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Correction
Plant Sciences
Pavel Yu. Kroupin, Ekaterina D. D. Badaeva, Victoria M. M. Sokolova, Nadezhda N. N. Chikida, Maria Kh. Belousova, Sergei A. A. Surzhikov, Ekaterina A. A. Nikitina, Alina A. A. Kocheshkova, Daniil S. S. Ulyanov, Aleksey S. S. Ermolaev, Thi Mai Luong Khuat, Olga V. V. Razumova, Anna I. I. Yurkina, Gennady I. I. Karlov, Mikhail G. G. Divashuk
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Agronomy
Sergey A. Bursakov, Pavel Yu. Kroupin, Gennady I. Karlov, Mikhail G. Divashuk
Summary: Optimizing all constituent conditions for high and even maximum yields is a recent trend in agriculture. Legumes, with their unique characteristics and symbiotic nodule bacteria, play a special role in storing protein and other important components for human and animal nutrition, as well as industry and agriculture. Molybdenum supply improves seed quality and promotes efficient use of molybdenum-containing enzymes in the plant and nodules, thereby enhancing nitrogen supply and avoiding competition with other trace elements.
