Article
Entomology
Miriam Silva Rafael, Leticia Cegatti Bridi, Igor Sharakhov, Osvaldo Marinotti, Maria Sharakhova, Vladimir Timoshevskiy, Giselle Moura Guimaraes-Marques, Valeria Silva Santos, Carlos Gustavo Nunes da Silva, Spartaco Astolfi-Filho, Wanderli Pedro Tadei
Summary: The study revealed substantial genome rearrangements in Anopheles darlingi mosquitoes, with physical mapping data aiding in improving genome assembly accuracy and understanding chromosomal evolution. Additionally, the relatively small genome size of An. darlingi and the use of techniques like fluorescence in situ hybridization contribute to the study of mosquito chromosomes.
Article
Genetics & Heredity
Thayne Woycinck Kowalski, Gabriela Barreto Caldas-Garcia, Julia do Amaral Gomes, Lucas Rosa Fraga, Lavinia Schuler-Faccini, Mariana Recamonde-Mendoza, Vanessa Rodrigues Paixao-Cortes, Fernanda Sales Luiz Vianna
Summary: This study compared sequence divergences between species affected or not affected by thalidomide and evaluated co-expression of regulated genes in a murine model. The analysis revealed differences in genes upstream of NOS3 in species with or without classic TE phenotype. The study suggests a deregulatory mechanism induced by Crbn in mice, even though they do not exhibit the classic TE phenotype.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Guignon Valentin, Toure Abdel, Droc Gaetan, Dufayard Jean-Francois, Conte Matthieu, Rouard Mathieu
Summary: Comparative genomics is the analysis of genomic relationships among different species, with GreenPhylDB providing a database for exploring gene families and homologous relationships among plant genomes. By harnessing multiple genome sequences by species, GreenPhylDBv5 introduces the concept of comparative pangenomics to predict homologous relationships and support community curation efforts.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Lijing Bu, Daibin Zhong, Lijun Lu, Eric S. Loker, Guiyun Yan, Si-Ming Zhang
Summary: This study compares the genomes of two homozygous lines of the freshwater snail to identify genomic differences related to resistance and susceptibility to the parasite Schistosoma mansoni. By constructing a genetic map and identifying quantitative trait loci associated with snail resistance/susceptibility and body pigmentation, the study provides insights into the genetic mechanisms of compatibility between the snail and the parasite. It offers valuable genomic resources for understanding vector snail biology and developing innovative control strategies.
COMMUNICATIONS BIOLOGY
(2022)
Article
Plant Sciences
Ravi Bika, Warren Copes, Fulya Baysal-Gurel
Summary: Calonectria pseudonaviculata and Pseudonectria foliicola cause significant economic loss in the horticultural industry. This study evaluated the efficacy of disinfecting chemicals in preventing pathogen transfer and reducing disease severity in boxwood cuttings. Effective treatments may help improve postharvest shelf life of boxwood cuttings.
Article
Plant Sciences
Francesco Pancaldi, Eibertus N. van Loo, Sylwia Senio, Mohamad Al Hassan, Kasper van der Cruijsen, Maria-Joao Paulo, Oene Dolstra, M. Eric Schranz, Luisa M. Trindade
Summary: This study found that there is significant intraspecific genetic variability in cell wall QTLs, including presence-absence gene variation, SNPs/INDELs, and changes in coded proteins. Additionally, cell wall genes were found to colocalize with QTLs in miscanthus and switchgrass, with relevant genes being retained in these regions. In conclusion, cell wall QTLs are valuable tools for screening germplasm and improving biomass quality, especially in understudied biomass crops.
Article
Horticulture
Mariya Kolchenko, Aidana Nurtaza, Alexandr Pozharskiy, Damira Dyussembekova, Anastasiya Kapytina, Gulnaz Nizamdinova, Marina Khusnitdinova, Aisha Taskuzhina, Almagul Kakimzhanova, Dilyara Gritsenko
Summary: Wild apples and their hybrids are valuable due to their genetic resistance to stress. This study focused on the fire blight resistance of Malus niedzwetzkyana, an endangered ornamental apple species. Different genotypes were tested, and while some showed symptoms of infection, the wild genotypes displayed resistance. The source of this resistance was not found to be associated with a specific genetic marker. Detailed genetic and phenotypic profiling of wild apple species is important for conservation efforts and apple breeding.
Article
Plant Sciences
Weiya Xue, Kathleen G. Haynes, Christopher R. Clarke, Xinshun Qu
Summary: This study investigates the genetic basis of early blight resistance in potato by using hybridization and field trials. Several quantitative trait loci (QTL) associated with early blight resistance were identified, providing new insights for marker-assisted selection in breeding for early blight resistance.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Agronomy
Sushan Ru, Shunping Ding, Jonathan E. Oliver, Ayodele Amodu
Summary: Stem blight of blueberry caused by fungal pathogens in the family Botryosphaeriaceae poses a significant challenge to global blueberry production. This review summarizes the latest information on the distribution and causal pathogens of this disease, the pathogenicity of fungal species, disease resistance of blueberry cultivars, and currently recommended management practices. The lack of effective management strategies or resistant cultivars makes disease control especially challenging, and developing reliable methods for screening resistant cultivars is a major bottleneck for future resistant-cultivar development.
Article
Agronomy
Farooq Ahmad, Sanja Baric
Summary: This study investigated the genetic characteristics of C. parasitica isolates from chestnut stands and a forest population in South Tyrol, Italy. The results showed a high genetic diversity, with 23 different vc types identified. EU-2, EU-1, and EU-13 were the most prevalent vc types, and both mating types were present in a close ratio of 1:1. The analysis of ITS sequences revealed three different haplotypes, indicating multiple introductions of C. parasitica to the region.
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2022)
Article
Plant Sciences
Caitlin E. E. Conn, Noah Howie, Marshall Lynch, Shanna Lee, Eden Young, Jared Westbrook, Jason Holliday, Qian Zhang, Martin L. L. Cipollini
Summary: We evaluated an alternative small stem assay (AltSSA) for blight resistance in backcross hybrid chestnut trees (Castanea dentata/mollissima). The AltSSA method involves cutting off 4- to 5-mm stems and inoculating the exposed stem tips with Cryphonectria parasitica inoculum. Results showed that AltSSAs performed well in distinguishing resistant and susceptible types of chestnut trees. The AltSSA method can detect blight resistance in seedlings early on and potentially reduce the number of susceptible trees that need to be out-planted and cared for.
Article
Microbiology
Shikha Pachauri, Rinat Zaid, Pramod D. Sherkhane, Jamela Easa, Ada Viterbo, Ilan Chet, Benjamin A. Horwitz, Prasun K. Mukherjee
Summary: Trichoderma virens is a beneficial fungus that enhances crop yields by helping plants fight pathogens and abiotic stresses. The P and Q strains of T. virens have distinct genetic and phenotypic differences, with the Q strain producing strong antimicrobial agents.
MICROBIOLOGY SPECTRUM
(2023)
Review
Plant Sciences
Xiaoyi Wang, Renbo Yu, Jingyang Li
Summary: Bananas are an important fruit crop threatened by the fungus Fusarium oxysporum f. sp. cubense (Foc) which causes Fusarium wilt. Functional genetic studies of the Musa genome and genome editing experiments can lead to the development of banana varieties with both Foc resistance and ideal plant architecture.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Sarah L. Emel, Shichen Wang, Richard P. Metz, Rachel B. Spigler
Summary: In SE Pennsylvania, USA, landscape heterogeneity shapes the genetic structure of S. angularis populations, primarily through isolation by resistance (IBR) rather than isolation by environment (IBE). Urbanization significantly restricts gene flow compared to natural habitats, while cropland poses a lower barrier. Surrounding human land use impacts genetic diversity and inbreeding in S. angularis populations.
Review
Plant Sciences
Ying Wu, William Sexton, Bing Yang, Shunyuan Xiao
Summary: Nonhost resistance (NHR) in plants refers to the immunity of most tested genotypes of a plant species against most tested variants of a pathogen species. NHR is a broad spectrum and durable defense mechanism that serves as a major barrier against potentially pathogenic microbes invading plants. Through genetic studies, researchers have made significant progress in understanding the molecular basis of NHR, which includes pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity. This review discusses the challenges in genetic studies of NHR and summarizes the approaches used to identify genes contributing to NHR, with a focus on dissecting multilayered NHR in model plants against filamentous pathogens.
MOLECULAR PLANT PATHOLOGY
(2023)
Article
Forestry
Margaret Staton, Charles Addo-Quaye, Nathaniel Cannon, Jiali Yu, Tetyana Zhebentyayeva, Matthew Huff, Nurul Islam-Faridi, Shenghua Fan, Laura L. Georgi, C. Dana Nelson, Emily Bellis, Sara Fitzsimmons, Nathan Henry, Daniela Drautz-Moses, Rooksana E. Noorai, Stephen Ficklin, Christopher Saski, Mihir Mandal, Tyler K. Wagner, Nicole Zembower, Catherine Bodenes, Jason Holliday, Jared Westbrook, Jesse Lasky, Frederick Hebard, Stephan C. Schuster, Albert G. Abbott, John E. Carlson
TREE GENETICS & GENOMES
(2020)
Article
Ecology
Marcin Nowicki, Logan C. Houston, Sarah L. Boggess, Anthony S. Aiello, Miriam Paya-Milans, Margaret E. Staton, Mitsuhiro Hayashida, Masahiro Yamanaka, Shigetoshi Eda, Robert N. Trigiano
ECOLOGY AND EVOLUTION
(2020)
Article
Forestry
Brian J. Stanton, Teodora Best, Nurul Islam-Faridi, Carlos Gantz, Kathy Haiby, Lianna J. Johnson, Rich Shuren, Alex Stanish, Margaret Staton, T. Casey Weathers, Di Wu, John E. Carlson
TREE GENETICS & GENOMES
(2020)
Article
Multidisciplinary Sciences
E. Anne Hatmaker, Phillip A. Wadl, Timothy A. Rinehart, Jennifer Carroll, Thomas S. Lane, Robert N. Trigiano, Margaret E. Staton, Edward E. Schilling
Article
Multidisciplinary Sciences
Nourolah Soltani, Margaret Staton, Kimberly D. Gwinn
Summary: This study aimed to elucidate the role of saponin in quinoa's resistance to Cucumber mosaic virus (CMV) by analyzing differential gene expression in CMV infection. Results showed upregulation of genes related to translation, lipid, nitrogen, amino acid metabolism, and terpenoid biosynthesis in CMV infections. The bitter variety 'Red Head' exhibited downregulation of a key saponin biosynthesis gene TSARL1 after four days of inoculation compared to the sweet and semi-sweet varieties.
Article
Plant Sciences
Trinity P. Hamm, Marcin Nowicki, Sarah L. Boggess, William E. Klingeman, Denita Hadziabdic, Matthew L. Huff, Margaret E. Staton, Robert N. Trigiano
Summary: The Viburnum genus, consisting of over 160 species, lacks molecular markers for investigating genetic diversity, prompting the development of 15 polymorphic gSSRs for a specific species within the genus. These markers, with varying allele numbers and heterozygosity levels, will be valuable for future studies on genetic variation and species distinction within the Viburnum genus and related genera.
Article
Biochemistry & Molecular Biology
Jiali Yu, Dennis Bennett, Christopher Dardick, Tetyana Zhebentyayeva, Albert G. Abbott, Zongrang Liu, Margaret E. Staton
Summary: Research on peach floral buds revealed that differentially expressed microRNAs and lncRNAs played a role in regulating genes involved in dormancy and flowering processes. Some lncRNAs were identified as potential targets of microRNAs, indicating a coordinated regulation between the two types of non-coding RNAs. This study highlights the complex interactions of non-coding RNAs in controlling transcriptional regulation during key developmental stages.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Biochemical Research Methods
Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simon, Kay Faaberg, Emily Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski, Sook Jung, Kelly Lager, Dorrie Main, Monica Poelchau, Risharde Ramnath, Peter Richter, Joe West, Stephen Ficklin
Summary: Online, open access biological knowledge databases are central repositories for research communities, facing challenges in growth, complexity and data integration. Shared infrastructure frameworks and Tripal platform address development burden, interoperability and sustainability.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Luis Fernando Samayoa, Bode A. Olukolu, Chin Jian Yang, Qiuyue Chen, Markus G. Stetter, Alessandra M. York, Jose de Jesus Sanchez-Gonzalez, Jeffrey C. Glaubitz, Peter J. Bradbury, Maria Cinta Romay, Qi Sun, Jinliang Yang, Jeffrey Ross-Ibarra, Edward S. Buckler, John F. Doebley, James B. Holland
Summary: Inbreeding depression is more pronounced in maize compared to teosinte, likely due to a greater segregating genetic load in the maize population. Despite strong inbreeding depression, additive effects still determine the majority of genetic value. Rare large-effect variants were found to be more important in teosinte, while polygenic load increased in maize following the domestication bottleneck.
Article
Plant Sciences
Jiali Yu, Amanda M. Hulse-Kemp, Ebrahiem Babiker, Margaret Staton
Summary: This study presents a chromosomal-scale genome of Vaccinium darrowii, utilizing PacBio sequencing and Hi-C scaffolding technologies to reveal its genome structure and gene expression features. The high-quality reference genome and accompanying annotation provide valuable resources for understanding the potential contribution of Vaccinium darrowii in commercial blueberry breeding.
HORTICULTURE RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Marcin Nowicki, Matthew L. Huff, Margaret E. Staton, Robert N. Trigiano
Summary: The complete chloroplast genome of Pyrus calleryana was assembled using whole-genome sequencing data. The genome had a quadripartite architecture with two inverted repeat regions and two single copy regions. Phylogenetic analysis based on the chloroplast genome placed P. calleryana among other Rosaceae plants.
JOURNAL OF APPLIED GENETICS
(2022)
Article
Microbiology
Grace M. Pietsch, Romina Gazis, William E. Klingeman, Matthew L. Huff, Margaret E. Staton, Miroslav Kolarik, Denita Hadziabdic
Summary: Symbiotic relationships between Geosmithia fungi and wood-boring and bark beetles typically do not cause disease in the plant host, but there are exceptions. To address the threat posed by these exceptions, researchers have developed a molecular diagnostic tool for detecting the pathogenicity of Geosmithia fungi.
Article
Genetics & Heredity
Yessica Rico, Gustavo P. Lorenzana, Carlos A. Benitez-Pineda, Bode A. Olukolu
Summary: This study conducted de novo genome assembly and annotation of three Bursera species, contributing to the generation of genomic resources for the under-researched genus and providing a foundation for studying gene flow, local adaptation, and hybridization dynamics.
Article
Horticulture
Xingbo Wu, Amanda M. Hulse-Kemp, Phillip A. Wadl, Zach Smith, Keithanne Mockaitis, Margaret E. Staton, Timothy A. Rinehart, Lisa W. Alexander
Summary: Hydrangea, an important ornamental crop cultivated for over 300 years, has been limited in genetic studies due to lack of genetic resources. However, a recent transcriptomic study and large-scale marker development have greatly expanded the genetic resources available for hydrangea, including high-density genetic linkage maps.
Article
Biodiversity Conservation
Ellen Crocker, Bradford Condon, Abdullah Almsaeed, Benjamin Jarret, C. Dana Nelson, Albert G. Abbott, Doreen Main, Margaret Staton
PLANTS PEOPLE PLANET
(2020)