Article
Biochemistry & Molecular Biology
Shiyun Han, Rongbin Wang, Xin Hong, Cuilian Wu, Sijia Zhang, Xianzhao Kan
Summary: This study explores the phylogeny of Bletilla using plastomic markers and reveals the non-monophyletic status of the genus. It also identifies potential molecular markers for species identification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Zhuang Zhao, Meng-Yao Zeng, Yu-Wei Wu, Jin-Wei Li, Zhuang Zhou, Zhong-Jian Liu, Ming-He Li
Summary: Epidendrum, an important genus in the Orchidaceae family, has significant horticultural and ornamental value and serves as a valuable research model. By sequencing and assembling the plastomes of five Epidendrum species, the characteristics and phylogenetic relationships of this genus were explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Marc Pignal, Christian Laudereau, Pierre-Louis Laudereau
Summary: A new species from New Caledonia, Pterostylis longilabia M.Pignal, sp. nov. is described and illustrated, with distinguishing morphological features such as a lip of the same length as the median sepal and a narrowly angled sinus between the synsepals. Due to threats to its locality, it is proposed to be classified as Endangered according to IUCN conservation status. An identification key is provided for New Caledonian Pterostylis species in English and French.
Article
Plant Sciences
Coyolxauhqui Figueroa, Teresa Terrazas, Patricia Davila, Gerardo A. Salazar
Summary: Through analysis of gynostemium development and morphology in 13 species of Spiranthinae, it was found that these plants share similarities in the early stages but exhibit differences in later developmental stages. Gynostemium development begins with the appearance of anther primordia, leading to the formation of pollen masses, with the entrance located between non-receptive lateral carpel apices and the receptive base of the median carpel apex.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Cheng-Yuan Zhou, Meng-Yao Zeng, Xuyong Gao, Zhuang Zhao, Ruyi Li, Yuhan Wu, Zhong-Jian Liu, Diyang Zhang, Ming-He Li
Summary: Trichoglottis is a valuable ornamental orchid genus with rich variations in colors and shapes of flower. Plastome data is found to be a valuable source for molecular identification and evolutionary studies of Trichoglottis and its related genera.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
P. Pablo Ferrer-Gallego
Summary: The typification of Ophrys apifera by Kunkele and Baumann was briefly discussed and superseded in this study, with a new lectotype being proposed based on an illustration from 1651. Although the new lectotype does not show key diagnostic characters to distinguish O. apifera from related species, an epitype is suggested for precise circumscription of the name.
Article
Biochemistry & Molecular Biology
Xiong-De Tu, Ding-Kun Liu, Shao-Wei Xu, Cheng-Yuan Zhou, Xu-Yong Gao, Meng-Yao Zeng, Sai Zhang, Jin-Liao Chen, Liang Ma, Zhuang Zhou, Ming-Zhong Huang, Shi-Pin Chen, Zhong-Jian Liu, Si-Ren Lan, Ming-He Li
Summary: Goodyerinae is a phylogenetically unresolved group within Orchidaceae. This study utilized large-scale phylogenomic data to compare plastome structure between two main clades, revealing unique features in plastome structure among different genera. The findings provide insights into orchid phylogenetics and plastome evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Plant Sciences
Sang-Hun Oh, Hwa-Jung Suh, Seon-Won Seo, Kyong-Sook Chung, Tomohisa Yukawa
Summary: This article describes a new terrestrial orchid species, Goodyera crassifolia, which is similar to G. schlechtendaliana but differs in flowering time and chromosome number.
JOURNAL OF PLANT BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Shu-Dong Zhang, Kai Yan, Li-Zhen Ling
Summary: In this study, the chloroplast genomes of ten Spiraea species were analyzed and compared with five previously reported genomes. The results showed that the genomes were highly conserved, but there were polymorphic sites and mutation hotspots that could be used as molecular markers for species identification.
Article
Plant Sciences
Lubna, Sajjad Asaf, Abdul Latif Khan, Rahmatullah Jan, Arif Khan, Adil Khan, Kyung-Min Kim, In-Jung Lee
Summary: Gymnosperms are a highly endangered group of plant species, with variable plastome size, structure, and gene order. Analysis of 167 gymnosperm plastomes revealed unique evolutionary scenarios for inverted repeats, and a positive correlation between simple sequence repeat abundance and plastome size. Time-calibrated plastid-based phylogenomic tree estimated the divergence between gymnosperms and angiosperms to be around 380 million years ago, providing insights into gymnosperm evolution.
Article
Multidisciplinary Sciences
Anna Victoria Silverio R. Mauad, Leila do Nascimento Vieira, Valter Antonio de Baura, Eduardo Balsanelli, Emanuel Maltempi de Souza, Mark W. Chase, Eric de Camargo Smidt
Summary: The study presented the first comparative plastome analysis of Pleurothallidinae, identifying ten highly variable regions for future phylogenetic studies. Despite some incongruence among different genetic markers, the results support a potential role for mitochondrial markers in Pleurothallidinae phylogenetics.
Article
Ecology
Yue Huang, Qing Ma, Jing Sun, Li-Na Zhou, Chan-Juan Lai, Pan Li, Xin-Jie Jin, Yong-Hua Zhang
Summary: This study conducted comparative genomic and evolutionary analyses on plastomes of 45 accepted Diospyros species, revealing a highly conserved genomic structure and identifying mutational hotspots in these species. Codon usage analysis showed the significant role of genetic pressure in shaping codon usage. Moreover, the study explored the selection pressure on genes in Diospyros. Overall, this study provides a meaningful foundation for the genetic architecture and taxonomy of Diospyros, contributing to the understanding of genetic diversity and conservation of genetic resources.
ECOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
Victoria A. Scobeyeva, Ilya V. Artyushin, Anastasiya A. Krinitsina, Pavel A. Nikitin, Maxim I. Antipin, Sergei V. Kuptsov, Maxim S. Belenikin, Denis O. Omelchenko, Maria D. Logacheva, Evgenii A. Konorov, Andrey E. Samoilov, Anna S. Speranskaya
Summary: Amaryllidaceae is a large plant family with diverse habitats. Chloroplast genes serve as phylogenetic markers, but also show signs of positive selection.
FRONTIERS IN GENETICS
(2021)
Article
Multidisciplinary Sciences
Md Salik Noorani, Mirza Sarwar Baig, Jawaid Ahmad Khan, Alam Pravej
Summary: The whole genome of PNRSV-infecting apricot was obtained and described in this study using RT-PCR and computational approaches. The size of the three RNAs was determined, and the sequence analysis revealed high identity among different PNRSV strains from around the world. This study provides important insights into the molecular evolution of PNRSV and will aid in the diagnosis and management of PNRSV-caused diseases.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Hashim B. Ali, Aleksei L. Lulla, Alex Nicholson, Jack C. Hankinson, Elizabeth E. Wignall-Fleming, Rhian O'Connor, Diem-Lan Vu, Stephen Graham, Janet Deane, Susana Guix, Valeria Lulla
Summary: During the last decade, there has been a significant increase in the detection of neurotropic astroviruses. These astroviruses, known as the MLB genogroup, are genetically distinct from other zoonotic astroviruses and are associated with gastroenteritis and severe neurological complications. Researchers have identified regions in the capsid-coding region of MLB astroviruses responsible for attenuation and have developed methods to create recombinant viruses with these deletions. This approach could be used to develop vaccines using attenuated astroviruses that infect humans, livestock animals, and poultry.
Article
Plant Sciences
Edlley M. Pessoa, Joel M. P. Cordeiro, Leonardo P. Felix, Priscila Lemes, Juan Viruel, Marccus Alves, Mark W. Chase, Cassio Van den Berg
Summary: In this study, we investigated the past connections between Amazonian and Atlantic forests using the Epidendrum latilabre complex. Our results showed that climatic shifts during the Pleistocene played a major role in promoting speciation. We also found that sister species within the complex had distinct climate niche spaces, and speciation was mainly driven by vicariance and peripheral isolation. Evidence suggested that the south-east/north-west bridge and the northern/north-eastern coastal route were occupied by the ancestors of the complex. Further research is needed to understand the dynamics of historical connections between Amazonian and Atlantic forests for other Neotropical epiphytic taxa.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Plant Sciences
Mark W. Chase, Rosabelle Samuel, Andrew R. Leitch, Maite S. Guignard, John G. Conran, Felipe Nollet, Paul Fletcher, Aljaz Jakob, Luiz A. Cauz-Santos, Gabriel Vignolle, Steven Dodsworth, Maarten J. M. Christenhusz, Maria Teresa Buril, Ovidiu Paun
Summary: This study on 46 species of allotetraploid Nicotiana in arid Australia found that decreases in genome size and chromosome number occur in parallel until the chromosome number threshold of 20, below which genome size increases. This phenomenon may be explained by decreasing rates of recombination over fewer chromosomes.
Article
Plant Sciences
Felipe Nollet, Enoque Medeiros Neto, Joel M. P. Cordeiro, Maria Teresa Buril, Mark W. Chase, Leonardo P. Felix
Summary: In Epidendrum subgenus Amphiglottium, high levels of chromosome modification are observed, and the study suggests that hybridization and introgression play a role in generating chromosome variation and heterochromatin diversification.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Biochemical Research Methods
Erick Parize, Edileusa C. M. Gerhardt, Ana C. M. Oliveira, Fabio O. Pedrosa, Emanuel M. Souza, Luciano F. Huergo, Maria B. R. Steffens
Summary: The study successfully heterologously expressed and purified the Rho protein from the diazotrophic environmental bacterium Azospirillum brasilense, showing its similarity to the E. coli orthologue. The purified AbRho protein exhibited correctly folded and active characteristics, indicating it is a RNA-dependent NTPase enzyme.
PROTEIN EXPRESSION AND PURIFICATION
(2022)
Article
Plant Sciences
Miguel Campos, Emma Kelley, Barbara Gravendeel, Frederic Medail, J. M. Maarten Christenhusz, Michael F. Fay, Pilar Catalan, Ilia J. Leitch, Felix Forest, Paul Wilkin, Juan Viruel
Summary: This study investigates taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data. The results confirm the monophyly of the two previously accepted species, D. communis and D. orientalis, in the Tamus clade. Three subclades with distinctive geographic patterns were identified within D. communis, which were also identifiable from morphometric and climatic data. It shows that integrated genomic, spatial and morphological approaches allow a more accurate definition of species boundaries and identification of previously undiscovered species.
Article
Plant Sciences
Francisco Javier Jimenez-Lopez, Montserrat Arista, Maria Talavera, Leonor Patricia Cerdeira Morellato, John R. Pannell, Juan Viruel, Pedro L. Ortiz Ballesteros
Summary: The genetic divergence between species depends on reproductive isolation (RI) caused by traits reducing interspecific mating (prezygotic isolation) or reduced hybrid fitness (postzygotic isolation). Prezygotic barriers were found to be generally stronger than postzygotic barriers, but previous studies mostly examined F-1 hybrid fitness in early life cycle stages. This study combined field and experimental data to assess the strength of 17 prezygotic and postzygotic reproductive barriers between co-occurring Lysimachia species. The results showed near complete RI between the two species, with prezygotic barriers contributing more in reducing gene flow in allopatry, while their contributions were more similar in sympatry. The strength of postzygotic RI was underestimated when effects on late stages of the life cycle were disregarded.
Article
Plant Sciences
Natalie Garrett, Juan Viruel, Nathaniel Klimpert, Marybel Soto Gomez, Vivienne K. Y. Lam, Vincent S. F. T. Merckx, Sean W. Graham
Summary: Thismiaceae species have lost the ability to photosynthesize and instead obtain carbon from soil fungi. This study analyzes the plastid genomes of Thismiaceae and reveals that most gene losses occurred early in their evolution, with occasional inversions and losses of the plastid inverted repeat region. Despite these changes, retained plastid genes are still under strong purifying selection.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Geysla Da Costa Fernandes, Naedja K. Luna, Elmary Fraga, Maria Claudene Barros, Mark W. Chase, Edlley M. Pessoa
Summary: Our study provides a new classification for neotropical Maranta based on molecular evidence. Our results confirm that the previous classification was incorrect and propose a new taxonomic scheme.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Evolutionary Biology
Roberta Gargiulo, Robin S. Waples, Adri K. Grow, Richard P. Shefferson, Juan Viruel, Michael F. Fay, Tiiu Kull
Summary: Estimating effective population size (N-e) is important, but it remains challenging for organisms with complex life-history traits. In this study, we examined how clonal versus sexual reproduction affected N-e in two populations of the orchid Cypripedium calceolus. The results showed that N-e in partially clonal plants cannot be predicted solely based on the number of genets generated by sexual reproduction.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Mycology
Nickolas Menezes da Silva, Guilherme Fonseca Reis, Flavia de Fatima Costa, Maria Eduarda Grisolia, Marlon Roger Geraldo, Bruno Paulo Rodrigues Lustosa, Bruna Jacomel Favoreto de Souza Lima, Vinicius Almir Weiss, Emanuel Maltempi de Souza, Ruoyu Li, Yinggai Song, Mariana Machado Fidelis Nascimento, Diogo Robl, Renata Rodrigues Gomes, G. Sybren de Hoog, Vania Aparecida Vicente
Summary: This study focused on the sequencing, assembly, and description of the whole genome of Cladophialophora exuberans, a black yeast related fungus, with an emphasis on genes and pathways related to carbon and toxin management, tolerance and bioremediation of lead and copper, and metal homeostasis. The results showed that the strain exhibited growth inhibition at minimum inhibitory and fungicidal concentrations of copper and lead, and could grow at higher concentrations in agar tests. In addition, the strain demonstrated uptake capacities of copper and lead in heavy metal bioremediation assays. This study contributed to the annotation of genes involved in heavy metal homeostasis and provided insights into the mechanisms of tolerance and adaptation to extreme conditions.
Article
Plant Sciences
Bhathiya Gopallawa, Amila Perera, Indrakheela Madola, Deepthi Yakandawala, Pankaj Kumar, Harsha Jayawickrama, Mark W. Chase
Article
Plant Sciences
Yohan Pillon, Pauline Majourau, Karine Gotty, Sandrine Isnard, Bruno Fogliani, Mark W. Chase, Gael J. Kergoat
Summary: The assembly of island plant communities is influenced by immigration, speciation, and extinction. This study focused on the origin of the New Caledonian Grevillea, a largely Australian genus. The analysis of plastid genes and a low-copy nuclear gene revealed that the New Caledonian Grevillea are allotetraploids resulting from hybridization events between two or three distinct parents. The study also highlighted the ecological and morphological differences between the two groups of New Caledonian Grevillea.
Article
Chemistry, Analytical
Gustavo Martins, Helena R. Galeski, Gabrielle A. Andrade, Marcia G. P. Valenga, Maria K. Ramos, Aldo J. G. Zarbin, Bruno C. Janegitz, Marcelo Mueller-Santos, Emanuel M. de Souza, Luiz Humberto Marcolino-Junior, Marcio F. Bergamini
Summary: Researchers proposed a new method for assembling an electrochemical immunosensor based on a one-step approach for selective layer formation, which is crucial for rapid and reliable diagnostic tests for new viruses and diseases. This method successfully detected SARS-CoV-2 nucleocapsid protein in different matrices with low detectable values, and demonstrated selectivity against interferents. The proposed assembly strategy reduces cost, analysis time, and waste generation, making it a suitable and reliable alternative for healthcare diagnostics.
ANALYTICA CHIMICA ACTA
(2023)
Article
Soil Science
Jessica Pereira de Souza, Fabiane Machado Vezzani, Tatiana Suzin Lazeris, Glaciela Kaschuk, Emanuel Maltempi de Souza, Eduardo Balsanelli, Deborah Pinheiro Dick, Helio Antonio Wood Joris, Cimelio Bayer
Summary: Crop system plays a crucial role in shaping soil microbial communities and organic matter content. This study investigates the long-term effects of different crop systems on soil composition and microbial diversity in subtropical soil. The results show that the current crop species significantly influence microbial community structure and diversity, while the long-term history of crop rotation has a relatively smaller impact. Crop rotation increases the proportion of carbohydrate-derived organic matter, while crop succession increases the proportion of alkyl-C and N/O alkyl-C. Crop species richness in rotation maintains soil functions and enhances the formation of biochemically labile organic matter, contributing to soil ecosystem functioning.
SOIL & TILLAGE RESEARCH
(2023)
Article
Environmental Sciences
Ricardo Belmonte-Lopes, Carlos E. R. Barquilha, Caroline Kozak, Demian S. Barcellos, Barbara Z. Leite, Fernanda J. O. Gomes da Costa, William L. Martins, Pamela E. Oliveira, Edy H. R. A. Pereira, Cesar R. Mota Filho, Emanuel M. de Souza, Gustavo R. C. Possetti, Vania A. Vicente, Ramiro G. Etchepare
Summary: The COVID-19 pandemic led to the collapse of healthcare systems and the emergence of wastewater-based epidemiology. This study conducted SARS-CoV-2 wastewater surveillance in Curitiba, Brazil, and found a correlation between viral loads and reported cases. The approach used proved to be a robust early warning system that can aid public decision-making and health interventions.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)