Article
Plant Sciences
Kun Zhang, Yiheng Wang, Xun Zhang, Zhiping Han, Xiaofei Shan
Summary: In this study, the complete mitochondrial genome of Hemerocallis citrina was sequenced using Illumina short-read and Oxford Nanopore long-read sequencing technologies. The mitogenome of H. citrina consists of three circular molecules and contains a total of 66 genes. Comparative analysis revealed conserved gene clusters and repeat-rich nature in the mitogenome. Codon usage analysis showed the preference for Leucine and Serine, and a tendency for codons to end with A or T. Additionally, RNA editing sites and selective pressure analysis were conducted. Phylogenetic analysis indicated the close relationship of H. citrina with Allium cepa and Asparagus officinalis. Overall, this study provides valuable information for the further research and breeding of H. citrina.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Sagar Yadav, Zarrine Raazi, Sheelavanta Matha Shivaraj, Deepika Somani, Ramya Prashant, Abhijeet Kulkarni, Rajeev Kumar, Suma Biradar, Shreenivas Desai, Narendra Kadoo
Summary: This study compared the genomes of 12 isolates of Bipolaris sorokiniana collected from wheat fields in India and found that the isolate D2 had the highest virulence and a larger genome with an expanded arsenal of pathogenicity genes, which may contribute to its higher virulence among the tested isolates.
Article
Biotechnology & Applied Microbiology
Bhramar Dutta, Urmi Halder, Annapurna Chitikineni, Rajeev K. Varshney, Rajib Bandopadhyay
Summary: This study presents the first whole genome analysis of Salinicoccus roseus strain RF1H, revealing its metabolic functionalities, biofilm formation, resistance mechanisms, and adaptation strategies to climate change. The strain's unique genome content contributes to its adaptability and provides important sources of compounds with potential beneficial applications in pharmaceuticals.
Article
Plant Sciences
Kristi E. Ledman, Veronica Roman-Reyna, Rebecca D. Curland, Nathaniel Heiden, Jonathan M. Jacobs, Ruth Dill-Macky
Summary: In this study, the complete genomes of Xanthomonas translucens pv. undulosa strains isolated from various hosts were sequenced and compared with publicly available genomes. The results showed little genomic variation among the strains, with high similarity. No unique features distinguishing strains isolated from wheat and non-wheat hosts were identified.
Article
Agronomy
Diego F. Garcia, Zhengyu Wang, Jiantao Guan, Lingjie Yin, Shuaifeng Geng, Aili Li, Long Mao
Summary: WheatGene is a database containing five wheat genomes and their expression information, accessible through a web browser for interactive search and comparison. It offers tools like BLAST, synteny viewer, and gene expression charts, while also linking genomics data with genetic maps and QTL for molecular breeding purposes.
Article
Genetics & Heredity
Ruilin Lai, Min Lin, Yongliang Yan, Shijie Jiang, Zhengfu Zhou, Jin Wang
Summary: The genus Geobacillus contains thermophilic gram-positive bacteria with wide distribution and high temperature tolerance, making them suitable for various biotechnology and industrial applications. In this study, the genome of Geobacillus stearothermophilus H6 was sequenced and analyzed, and the thermophilic enzyme in the strain was identified. The results could contribute to the development and application of industrial strains.
Article
Genetics & Heredity
Dongyun Jung, Soyoun Park, Janina Ruffini, Forest Dussault, Simon Dufour, Jennifer Ronholm
Summary: The study analyzed the genomes of MPEC and commensal E. coli isolates, finding distinct genetic markers in MPEC related to nutrient intake, metabolism, fitness, and virulence. Understanding these conserved MPEC genes may be crucial for unraveling the pathobiology of MPEC.
MICROBIAL GENOMICS
(2021)
Article
Agronomy
Xu Zhang, Wentao Wan, Mengli Li, Zhongyu Yu, Jia Liu, Katerina Holusova, Jan Vrana, Jaroslav Dolezel, Yufeng Wu, Haiyan Wang, Jin Xiao, Xiue Wang
Summary: The short arm of chromosome 6V (6VS) from Haynaldia villosa was sequenced and analyzed in this study, revealing genes related to resistance against powdery mildew and other diseases. High-confidence genes, supported by RNA sequencing data, were annotated, providing a foundation for future gene mining and utilization.
Article
Fisheries
Libao Wang, Hui Li, Wenjun Shi, Yi Qiao, Pan Wang, Zhijun Yu, Ran Zhao, Runhao Hu, Hui Shen, Jie Cheng, Ge Jiang, Xintong Huang, Xihe Wan
Summary: In this research, the whole genome of Enterocytozoon hepatopenaei (EHP), an obligate intracellular parasite of shrimp, was sequenced, and detailed functional annotation was conducted. Comparative genomic analysis revealed the evolutionary features of EHP, including gene family clustering, phylogenetic relationships, gene family expansion and contraction, and synteny. These findings deepen our understanding of the EHP genome.
AQUACULTURE INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Cameron M. Nugent, Tony Kess, Matthew K. Brachmann, Barbara L. Langille, Steven J. Duffy, Sarah J. Lehnert, Brendan F. Wringe, Paul Bentzen, Ian R. Bradbury
Summary: Despite the absence of physical barriers and the presence of pelagic stages in many marine taxa, environmental variation is widely recognized as a significant factor driving diversity in marine species. However, understanding the genomic and ecological processes that shape populations remains inadequate for most marine species, which often hinders management and conservation efforts.
Article
Biochemistry & Molecular Biology
Jefferson F. Paril, David J. Balding, Alexandre Fournier-Level
Summary: Mapping the genetic basis of complex traits in outbreeding species across a landscape is crucial for understanding species adaptation. Sampling more populations across the landscape using pool sequencing can lead to higher power in quantitative trait locus detection and prediction accuracy, compared to individual sequencing. It is recommended to sample populations from areas with high genetic diversity for more effective genetic mapping.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Genetics & Heredity
Honghong Dong, Ruixiang Gao, Yijie Dong, Qing Yao, Honghui Zhu
Summary: This study presented the high-quality genome assembly of Myxococcus xanthus R31, a strain with good biocontrol efficacy against tomato bacterial wilt. Comparative genomics analysis revealed the phylogenetic relationship between R31 and other M. xanthus strains, and identified strain-specific genes that may contribute to its predatory ability. These findings provide new insights into R31 and related species, and lay the foundation for further genetic studies on the predation mechanism of myxobacteria.
Review
Plant Sciences
Jagesh Kumar Tiwari, Suresh Reddy Yerasu, Nagendra Rai, Dhananjaya P. Singh, Achuit K. Singh, Suhas G. Karkute, Prabhakar M. Singh, Tusar K. Behera
Summary: Tomatoes are important vegetable crops, and genomics-assisted breeding shows great potential in this field. With the rapid development and cost reduction of sequencing technologies, as well as the use of high-throughput genotyping platforms and bioinformatics tools, the tomato genome has been decoded and extensively studied, providing valuable information for breeding programs. Genomics-assisted breeding has made progress in identifying genes and SNP markers associated with agronomic traits, and the genomic selection method is expected to improve breeding efficiency and genetic gain.
CRITICAL REVIEWS IN PLANT SCIENCES
(2022)
Article
Genetics & Heredity
Daren C. Card, Andrew G. Van Camp, Trenten Santonastaso, Michael I. Jensen-Seaman, Nicola M. Anthony, Scott V. Edwards
Summary: The study identified the core MHC genomic region in two squamate species and revealed similarities and differences in the genomic structure and composition of MHC regions between squamates and mammals. The investigation also highlighted unique features of the anole MHC, such as higher proportions of DNA transposons and larger MHC region size. Evolutionary analyses of MHC homologs in squamates and other amniotes demonstrated species-specific relationships and functional relevance of certain codons under diversifying selection.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Xuejin Cui, Kehong Liu, Sagheer Atta, Chunhua Zeng, Changyong Zhou, Xuefeng Wang
Summary: Two unique prophages, designated as P-PA19-1 and P-PA19-2, were identified in the CLas strain PA19 from Pakistan, with P-PA19-2 integrated into the PA19 chromosome, indicating the genomic diversity and evolution of CLas prophages.
Review
Biochemical Research Methods
Eva M. Temsch, Petr Koutecky, Tomas Urfus, Petr Smarda, Jaroslav Dolezel
Summary: The estimation of nuclear DNA content in plants using flow cytometry requires comparison to a reference standard of known DNA content, with internal standardization being mandatory for precise measurements. Various well-established standards are available to cover the range of plant genome sizes, but the selection and use of standards must be carefully reported. The introduction of a new standard species may be needed if none of the established standards fits, and the selected standard organism must meet a number of requirements to ensure high quality samples.
Article
Plant Sciences
Habib Rijzaani, Philipp E. Bayer, Mathieu Rouard, Jaroslav Dolezel, Jacqueline Batley, David Edwards
Summary: Banana from the Musaceae family has a complex genetic history, with different cultivated clones belonging to the Musa genus and Ensete species. The study presents the first cross-genus pangenome of banana, identifying genes that differentiate between species and potentially supporting breeding programs.
Article
Plant Sciences
Zuzana Tulpova, Ales Kovarik, Helena Toegelova, Pavla Navratilova, Veronika Kapustova, Eva Hribova, Jan Vrana, Jiri Macas, Jaroslav Dolezel, Hana Simkova
Summary: This study deciphered the genomic organization and tissue-specific expression of rDNA loci in hexaploid bread wheat, revealing the significant contribution of the 1B and 6B loci to rRNA transcription and the differential cytosine methylation level in the 5D locus. This provides insights into wheat evolution and transcriptional regulation.
Review
Agronomy
Petr Capal, Jaroslav Dolezel
Summary: Gregor Mendel established the foundations of genetics through his experiments with pea plant hybridization. Despite the challenges posed by the large size of the pea plant genome, recent advances in analysis techniques have made the pea plant an attractive candidate for studying gene cloning and molecular organization.
CZECH JOURNAL OF GENETICS AND PLANT BREEDING
(2022)
Article
Biochemistry & Molecular Biology
Jana Zwyrtkova, Nicolas Blavet, Alzbeta Dolezalova, Petr Capal, Mahmoud Said, Istvan Molnar, Jan Vrana, Jaroslav Dolezel, Eva Hribova
Summary: In this study, the complex genome of Crested wheatgrass was analyzed using flow sorting and DNA sequencing. Genes related to plant disease resistance and stress tolerance were identified, and a new DNA repeat element was discovered. Additionally, SSR markers were identified for future breeding purposes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Pavla Navratilova, Helena Toegelova, Zuzana Tulpova, Yi-Tzu Kuo, Nils Stein, Jaroslav Dolezel, Andreas Houben, Hana Simkova, Martin Mascher
Summary: The study analyzed sequence gaps in the barley genome and found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were missing in the genome assembly, primarily due to assembly breakdown in long stretches of satellite repeats. However, the missing sequences could not fully explain the difference between assembly size and flow cytometric genome size estimates. The prospects of closing these gaps using ultra-long sequence reads were discussed.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
H. Busra Cagirici, Hikmet Budak, Taner Z. Sen
Summary: G4Boost is a decision tree-based prediction tool that accurately predicts the folding state and thermodynamic stability of G-quadruplexes (G4s). It outperforms other machine-learning prediction tools in terms of accuracy and F1-score, and has important applications in gene regulation in both plants and humans.
BMC BIOINFORMATICS
(2022)
Review
Plant Sciences
Babar Hussain, Bala A. Akpinar, Michael Alaux, Ahmed M. Algharib, Deepmala Sehgal, Zulfiqar Ali, Gudbjorg I. Aradottir, Jacqueline Batley, Arnaud Bellec, Alison R. Bentley, Halise B. Cagirici, Luigi Cattivelli, Fred Choulet, James Cockram, Francesca Desiderio, Pierre Devaux, Munevver Dogramaci, Gabriel Dorado, Susanne Dreisigacker, David Edwards, Khaoula El-Hassouni, Kellye Eversole, Tzion Fahima, Melania Figueroa, Sergio Galvez, Kulvinder S. Gill, Liubov Govta, Alvina Gul, Goetz Hensel, Pilar Hernandez, Leonardo Abdiel Crespo-Herrera, Amir Ibrahim, Benjamin Kilian, Viktor Korzun, Tamar Krugman, Yinghui Li, Shuyu Liu, Amer F. Mahmoud, Alexey Morgounov, Tugdem Muslu, Faiza Naseer, Frank Ordon, Etienne Paux, Dragan Perovic, Gadi V. P. Reddy, Jochen Christoph Reif, Matthew Reynolds, Rajib Roychowdhury, Jackie Rudd, Taner Z. Sen, Sivakumar Sukumaran, Bahar Sogutmaz Ozdemir, Vijay Kumar Tiwari, Naimat Ullah, Turgay Unver, Selami Yazar, Rudi Appels, Hikmet Budak
Summary: Recent technological advances in next-generation sequencing have made DNA sequencing more accessible for species with large and complex genomes, including bread wheat. Despite its importance as a food crop, breeding in bread wheat has been limited by its large polyploid genome. However, after years of effort, draft and reference genome sequences of bread wheat have been released, providing valuable resources for breeding. These advances have also facilitated the use of genotyping arrays in wheat breeding, allowing for fast and reliable characterization of wheat lines. Additionally, gene-editing and genomic selection methods have shown promise in improving important traits in wheat breeding.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Bala Ani Akpinar, Tugdem Muslu, Gadi V. P. Reddy, Munevver Dogramaci, Hikmet Budak
Summary: This article examines long noncoding RNAs (lncRNAs), a type of noncoding RNA that is typically over 200 nucleotides in length but lacks coding potential. Through analyzing two different wheat varieties, potential lncRNAs were identified, and potential functional networks with microRNAs were observed. Additionally, lncRNAs with perfect or near-perfect matches to organellar genomes were discovered.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Natalia Conde e Silva, Martine Leguilloux, Arnaud Bellec, Nathalie Rodde, Juliette Aubert, Domenica Manicacci, Catherine Damerval, Helene Berges, Yves Deveaux
Summary: A self-regulatory loop similar to that regulating euAP3 in core eudicots controls AP3-3 gene expression in an early diverging eudicot, but distinct mechanisms regulate tissue specificities in Arabidopsis and Nigella. MADS-box transcription factors play important roles in floral organ identity by binding to specific motifs in the promoter of their target genes. In Nigella, the lack of expression of NdAP3-3 gene in the apetalous morph is due to a Miniature Inverted-repeat Transposable Element (MITE) insertion that affects mRNA splicing. Specific CArG features in the promoter of NdAP3-3 gene determine its petal-specific expression in Nigella.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Joanna Majka, Marek Glombik, Alzbeta Dolezalova, Jana Knerova, Marco Tulio Mendes Ferreira, Zbigniew Zwierzykowski, Martin Duchoslav, Bruno Studer, Jaroslav Dolezel, Jan Bartos, David Kopecky
Summary: We analyzed the chromosome composition of interspecific plant hybrids and found that the transmission of parental genomes varied in male and female meiosis. Festuca chromosomes were replaced by Lolium counterparts in female meiosis, while in male meiosis, Festuca chromosomes showed improper attachment and were gradually eliminated. The difference in behavior may be attributed to non-synonymous mutations and the exclusive expression of kinetochore proteins from the Lolium allele.
Article
Biochemistry & Molecular Biology
Ivona Kubalova, Amanda Souza Camara, Petr Capal, Tomas Beseda, Jean-Marie Rouillard, Gina Marie Krause, Katerina Holusova, Helena Toegelova, Axel Himmelbach, Nils Stein, Andreas Houben, Jaroslav Dolezel, Martin Mascher, Hana Simkova, Veit Schubert
Summary: Hi-C analysis, biopolymer modeling, and structured illumination microscopy were used to reveal the chromonema, a helically-wound chromatin thread forming barley mitotic chromatids. The helical turn size varies along the chromosome length and intermingles chromatin from adjacent turns. The observable dimensions of sister chromatid exchanges further support the helical chromonema model.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Arnaud Bellec, Mamadou Dia Sow, Caroline Pont, Peter Civan, Emile Mardoc, Wandrille Duchemin, David Armisen, Cecile Huneau, Johanne Thevenin, Vanessa Vernoud, Nathalie Depege-Fargeix, Laurent Maunas, Brigitte Escale, Bertrand Dubreucq, Peter Rogowsky, Helene Berges, Jerome Salse
Summary: This study compares the genomic data of ten grass species to uncover the structural and regulatory mechanisms of genome plasticity, revealing the possible attributes of long-term evolution and adaptation in plants. Polyploidy is closely tied to the evolutionary success of grasses over the past 100 million years, although it is challenging to attribute this success to specific genomic consequences of polyploidization, suggesting that polyploids utilize the potential of genome duplication in lineage-specific ways. Overall, this study demonstrates that post-polyploidization reprogramming is more complex than previously reported, calling for a critical and comprehensive comparison of independently polyploidized lineages.
Article
Multidisciplinary Sciences
Kaichi Huang, Mojtaba Jahani, Jerome Gouzy, Alexandra Legendre, Sebastien Carrere, Jose Miguel Lazaro-Guevara, Eric Gerardo Gonzalez Segovia, Marco Todesco, Baptiste Mayjonade, Nathalie Rodde, Stephane Cauet, Isabelle Dufau, S. Evan Staton, Nicolas Pouilly, Marie-Claude Boniface, Camille Tapy, Brigitte Mangin, Alexandra Duhnen, Veronique Gautier, Charles Poncet, Cecile Donnadieu, Tali Mandel, Sariel Hubner, John M. Burke, Sonia Vautrin, Arnaud Bellec, Gregory L. Owens, Nicolas Langlade, Stephane Munos, Loren H. Rieseberg
Summary: This study analyzed the impacts of wild introgressions in cultivated sunflower on the genomic and phenotypic level, as well as the consequences of linkage drag. It was found that introgressions had negative effects on yield and quality traits, and high-frequency introgressions had larger effects than low-frequency ones.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)