Article
Cell Biology
Renate L. M. Jansen, Carlos Santana-Molina, Marco van den Noort, Damien P. Devos, Ida J. van der Klei
Summary: PEX genes encode proteins involved in peroxisome biogenesis and proliferation. A comparative genomics approach was used to clarify the evolutionary relationships between the 37 known PEX proteins in a representative set of eukaryotes, defining the core set of PEX proteins required for peroxisome formation. The molecular processes in peroxisome biogenesis in different organisms were analyzed, showing that peroxisomes are not static organelles in eukaryotic evolution.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(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
Biochemistry & Molecular Biology
Jiankai Wei, Penghui Liu, Fuyun Liu, An Jiang, Jinghan Qiao, Zhongqi Pu, Bingrou Wang, Jin Zhang, Dongning Jia, Yuli Li, Shi Wang, Bo Dong
Summary: Evolutionary developmental biology (evo-devo) is an interdisciplinary field that aims to understand the origin and evolution of developmental processes in different animals. EDomics is a comparative multi-omics database that provides comprehensive genomic, transcriptomic, and single-cell data for 40 representative species. It offers valuable resources and customized datasets for evo-devo research, allowing researchers to decipher the history of developmental evolution across the tree of life.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Plant Sciences
Yuanpeng Fang, Junmei Jiang, Xiaolong Hou, Jiyuan Guo, Xiangyang Li, Degang Zhao, Xin Xie
Summary: The evolution of gene families is crucial for understanding the evolutionary history and biodiversity of plants, as well as explaining their tolerance to environmental stresses. Studying the molecular evolution of plant gene families helps to gain insights into these important processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Yongjun Tan, Cindy Wang, Theresa Schneider, Huan Li, Robson Francisco de Souza, Xueming Tang, Kylie D. Swisher Grimm, Tzung-Fu Hsieh, Xu Wang, Xu Li, Dapeng Zhang
Summary: This study conducted an in-depth comparative genomic analysis of Liberibacter pathogens and their nonpathogenic ancestral species, identifying various types of prophage loci and novel toxins that are evolutionarily linked to the emergence of the pathogens. Genomic genes that were lost or gained in the ancestor of the pathogens were identified, with the lost genes related to the biosynthesis of cellular building blocks and the gained genes including previously unrecognized toxins.
MICROBIOLOGY SPECTRUM
(2021)
Article
Genetics & Heredity
Krystyna Cwiklinski, John Pius Dalton
Summary: By analyzing the publicly available sequencing datasets of Fasciola spp., this study reveals the complex profile and structure of proteases and anti-proteases families operating at various stages of the parasite's life cycle. The study also discovered distinct profiles of peptidases and their inhibitors expressed by the parasite stages in the intermediate snail host, providing insights into their movement, development, and nutrient extraction in different environmental niches. The comparative genomics analysis further sheds light on the evolution of these gene families and provides critical data for the analysis and interrogation of Fasciola spp. hybrids spreading throughout Asia and Africa.
Editorial Material
Multidisciplinary Sciences
Chris Amemiya
Summary: Genome sequencing and analysis of genomic interactions have revealed new insights into the evolution of the wing shapes in skates and rays, dating back over 200 million years.
Article
Ecology
Aurelie Labarre, David Lopez-Escard, Francisco Latorre, Guy Leonard, Francois Bucchini, Aleix Obiol, Corinne Cruaud, Michael E. Sieracki, Olivier Jaillon, Patrick Wincker, Klaas Vandepoele, Ramiro Logares, Ramon Massana
Summary: The study utilized single-cell genomics to analyze the genomes of 15 MAST species from marine surface plankton, revealing their potential for phagocytosis and ability to thrive in the photic ocean with the presence of rhodopsin genes. The complexity of phagocytosis machinery in microbial eukaryotes was highlighted, contrasting with the well-defined set of genes for photosynthesis, providing essential insights into the ecophysiology of uncultured species and the function of rhodopsins in stramenopiles.
Article
Biotechnology & Applied Microbiology
Jun Chen, Yu Zang, Shuo Liang, Song Xue, Shuai Shang, Meiling Zhu, Ying Wang, Xuexi Tang
Summary: This study sequenced and compared the mitochondrial genomes of Zostera japonica and Phyllospadix iwatensis, providing new evidence of genome size reduction, gene loss, and adaptive evolution in seagrasses. It found a large number of repeat sequences and extensive loss of ribosomal protein genes in seagrass species. Additionally, it identified positive selection genes associated with seagrass adaptation to the marine environment.
Article
Biotechnology & Applied Microbiology
Xuezhen Yang, Xiaoxue Liu, Yanchen Zhou, Fan Zhang, Lan Huang, Jun Wang, Jian Song, Lijuan Qiu
Summary: This study provides a comprehensive analysis of angiosperm ACP gene families and offers valuable insights for the future functional characterization of plant ACPs. The evolutionary history, gene structure conservation, duplication events, expression patterns, and cis-elements related to gene regulation were thoroughly investigated, shedding new light on the regulatory mechanisms of these key enzymes in the FAS system.
Editorial Material
Multidisciplinary Sciences
Martha I. Nelson, Elodie Ghedin
Summary: The evolutionary steps taken by the 1918 flu pandemic virus have been revealed through the analysis of lung samples stored in medical archives. Three genomes of the influenza A virus responsible for the global pandemic have been obtained, showing mutations that may have triggered the devastating second wave.
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Genetic material collected from permafrost reveals that northern Greenland was once a thriving forest.
Article
Plant Sciences
Radka Vozarova, Veit Herklotz, Ales Kovarik, Yuri O. Tynkevich, Roman A. Volkov, Christiane M. Ritz, Jana Lunerova
Summary: The study revealed that the rose genus has two distinct 5S rDNA families, namely 5S_A and 5S_B, found in species of two subgenera with different ratios in different sections. The 5S_B family is often co-localized with 35S rDNA, while the co-localization of the 5S_A family is less common. Allo-pentaploid dogroses exhibit a unique distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Stephan Majda, Daniela Beisser, Jens Boenigk
Summary: The study shows that heterotrophic taxa have a reduced genome size and higher GC content compared to phototrophic taxa, with a large pan genome but a small core genome indicating different specialization among lineages. Despite this, the pan genome of mixotrophs and heterotrophs together covers the complete functionality of phototrophic strains, suggesting a random reduction of genes.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xavier Farre, Ruben Molina, Fabio Barteri, Paul R. H. J. Timmers, Peter K. Joshi, Baldomero Oliva, Sandra Acosta, Borja Esteve-Altava, Arcadi Navarro, Gerard Muntane
Summary: The study identified amino acid changes and genes related to longevity in mammals, with pathways involved in regulating lifespan. It also found that certain genes explain a larger fraction of human lifespan heritability than expected, with longevity-associated proteins being significantly more stable. Overall, the research demonstrates the potential of comparative genomics in enhancing understanding of human genome-wide association studies.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
M. Estrella Santamaria, Alejandro Garcia, Ana Arnaiz, Irene Rosa-Diaz, Gara Romero-Hernandez, Isabel Diaz, Manuel Martinez
Summary: Plant molecular machinery is triggered to cope with various abiotic and biotic stresses, with specific mechanisms identified to optimize responses to individual threats. Transcriptomic analysis of different plant species and meta-analysis of responses reveal common mechanisms for herbivory and specific gene sets involved in particular interactions, highlighting the importance of jasmonate-induced pathways in plant stress responses.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Plant Sciences
Alfonso Munoz, M. Estrella Santamaria, Nuria Fernandez-Bautista, Silvina Mangano, Rene Toribio, Manuel Martinez, Marta Berrocal-Lobo, Isabel Diaz, M. Mar Castellano
Summary: The study investigates the involvement of HOP3 in the JA pathway in plants, showing increased susceptibility to pathogens and herbivores in the hop3-1 mutant. HOP3 may regulate COI1 activity and play a key role in the JA pathway.
Article
Multidisciplinary Sciences
Alejandro Garcia, M. Estrella Santamaria, Isabel Diaz, Manuel Martinez
Summary: The study reveals that transcriptomic meta-analysis is an effective approach to uncover physiological processes in plant responses to herbivores. Analysis of Arabidopsis-thaliana interactions with pests highlights key issues in plant responses, such as the specificity of perception and signaling pathways, and the variability in secondary metabolic pathways.
SCIENTIFIC REPORTS
(2021)
Review
Plant Sciences
Dairon Ojeda-Martinez, Isabel Diaz, M. Estrella Santamaria
Summary: Herbivore oviposition induces extensive genetic rearrangements and various cellular and hormonal responses in plants. This study analyzed the up-to-date techniques and databases to better understand the molecular behavior of plants in response to oviposition. The results revealed that oviposition triggers a large number of differentially expressed genes and shared processes, with hormonal cascades, defense mechanisms, and energy metabolism being the main altered processes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Ana Arnaiz, M. Estrella Santamaria, Irene Rosa-Diaz, Irene Garcia, Sameer Dixit, Saul Vallejos, Cecilia Gotor, Manuel Martinez, Vojislava Grbic, Isabel Diaz
Summary: Induction of a hydroxynitrile lyase-encoding gene in Arabidopsis helps regulate levels of toxic cyanide and cyanohydrins against Tetranychus urticae attack. The overexpression of this gene in Arabidopsis reduces leaf damage caused by spider mite feeding and restricts their ability to reproduce. Spider mites, in response, upregulate beta-cyanoalanine synthase gene to avoid respiratory damage caused by hydrogen cyanide. These findings provide important insights into the mutual defense mechanisms between Arabidopsis and spider mites.
Review
Plant Sciences
Gara Romero-Hernandez, Manuel Martinez
Summary: The success of plant response to environmental stressors depends on regulatory networks and phosphorylation plays a key role in activating or deactivating proteins. Protein kinases are responsible for phosphorylation and play an important role in signal transmission. This review focuses on the contribution of protein kinases to herbivore-triggered responses in plants.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Alejandro Garcia, Lucia Talavera-Mateo, M. Estrella Santamaria
Summary: Trichomes are hair-like appendages on plant epidermis that act as a protective barrier. We propose a new method based on machine learning for quantifying trichomes, which is fast, accessible, and adaptable to different plant species.
Article
Multidisciplinary Sciences
Estefania Contreras, Manuel Martinez
Summary: The economically important agricultural pest, Tetranychus urticae, feeds on various plant species. In an RNAseq experiment, four members of the Arabidopsis thaliana RIN4-like/NOI family were found to be significantly overexpressed after T. urticae infestation. The function of these members in herbivore defense remains unknown, but they likely have novel roles different from RIN4 in stress adaptation.
Article
Plant Sciences
Estefania Contreras, Jose J. J. Rodriguez-Herva, Isabel Diaz, Emilia Lopez-Solanilla, Manuel Martinez
Summary: Plant response to biotic stresses is influenced by its physiological state. Optimal conditions for spider mite infestation involve high temperatures and limited precipitation. Previous interactions with bacteria affect Arabidopsis thaliana's response to mite infestation under optimal conditions, even when disease symptoms are not visible. The plant's response is compromised even under suboptimal conditions for bacterial growth.
JOURNAL OF PLANT INTERACTIONS
(2023)
Article
Plant Sciences
Gara Romero-Hernandez, Manuel Martinez
Summary: The study demonstrates the opposite roles of MAPKKK17 and MAPKKK21 in the plant response to mite attack. MAPKKK17 acts as a positive regulator, while MAPKKK21 is a negative regulator. The expression of these two kinases is interdependent and they are coexpressed with different sets of genes.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Marta Boter, Isabel Diaz
Summary: Plants and phytophagous arthropods have coevolved in a battle for survival, with plants producing antiherbivore chemicals and herbivores adapting to their hosts. Cyanogenic glucosides are defense chemicals produced by cyanogenic plants, while the Brassicaceae family has evolved an alternative pathway to produce cyanohydrin. When a plant tissue is damaged, cyanogenic substrates come into contact with degrading enzymes, releasing toxic cyanide and derived compounds. This review focuses on the plant metabolic pathways linked to cyanogenesis and highlights its role as a defense mechanism against herbivores, discussing the potential of cyanogenesis-derived molecules for pest control strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Kristie Bruinsma, Cristina Rioja, Vladimir Zhurov, Maria Estrella Santamaria, Vicent Arbona, Marie Navarro, Marc Cazaux, Philippe Auger, Alain Migeon, Nicky Wybouw, Thomas Van Leeuwen, Isabel Diaz, Aurelio Gomez-Cadenas, Miodrag Grbic, Maria Navajas, Vojislava Grbic
Summary: The mechanisms underlying host adaptation and specialization in tomato-adapted spider mites were compared, revealing that although both mites use similar mechanisms to counteract tomato defenses, the specialist mite is better equipped to cope with these defenses.