Article
Horticulture
Guangxin Liu, Yue Lan, Lianwei Qu, Yilian Zhao, Haoyang Xin, Mengli Xi
Summary: Through our research on wild species and cultivars, we have clarified the genetic relationships between different sections of tulips, as well as the differences and variations in the 5S rDNA sequences. Our findings provide clearer and more stable evidence for the classification of tulips.
SCIENTIA HORTICULTURAE
(2022)
Article
Plant Sciences
Simone Cardoni, Roberta Piredda, Thomas Denk, Guido W. Grimm, Aristotelis C. Papageorgiou, Ernst-Detlef Schulze, Anna Scoppola, Parvin Salehi Shanjani, Yoshihisa Suyama, Nobuhiro Tomaru, James R. P. Worth, Marco Cosimo Simeone
Summary: The process of plant speciation is more complex than standard models suggest, involving factors such as isolation, lineage mixing, and intra-genomic competition. Modern species are genetic mosaics, representing a striking case of ongoing reticulate evolution over the past 55 million years.
Article
Plant Sciences
Anna Scoppola, Simone Cardoni, Thomas Marcussen, Marco Cosimo Simeone
Summary: Viola sect. Melanium, also known as the pansy, is a morphologically well-defined allopolyploid group consisting of approximately 110 perennial and annual species in the northern hemisphere. Italy has four morphologically similar annual pansies belonging to the 'V. tricolor species complex', which are difficult to distinguish in the field and have resulted in uncertain records in field inventories and European herbaria. The lack of comprehensive intra- and interspecific comparative studies, appropriate genetic markers, and clear cytological descriptions have hindered the clear circumscription and phylogenetic inferences within this group. In this study, the researchers used DNA sequence variation of three plastid markers and High-Throughput Sequencing (HTS) to investigate species identity, genome organization, and evolution within the V tricolor species complex. The results revealed close relationships within this group, provided reliable molecular resolution for V. tricolor, and demonstrated the common ancestry of V. arvensis, V. kitaibeliana, and V. hymettia. The researchers also found evidence of significant geographic divergence within V. tricolor and V. arvensis, suggesting the presence of different eco-cytotypes within these species. The overall diversity patterns and the occurrence of multiple diverging 5S-IGS lineages are discussed in relation to the taxonomy and genomic evolution of Viola sect. Melanium.
Article
Forestry
Charalambos Neophytou, Devrim Semizer-Cuming, Hans-Gerhard Michiels, Antoine Kremer, Simon Jansen, Barbara Fussi
Summary: This study investigates the autochthony and genetic structure of Central European white oaks using chloroplast and nuclear microsatellite markers. The results show that the autochthony of oaks was preserved throughout historical times and still reflects the post-glacial recolonization in both relict and old managed stands. Significant admixture of haplotypes was only observed in stands established after the Second World War, indicating human interference. There were marked differences in nuclear genetic variation among species, with Quercus pubescens exhibiting a pronounced genetic structure.
FOREST ECOLOGY AND MANAGEMENT
(2024)
Article
Plant Sciences
Yurij O. Tynkevich, Antonina Y. Shelyfist, Liudmyla Kozub, Vera Hemleben, Irina I. Panchuk, Roman A. Volkov
Summary: This study evaluates the molecular organization and diversity of the intergenic spacer region (IGS) in the Solanum genus. The study finds that the main mechanism of IGS molecular evolution is the step-wise accumulation of single base substitution or short indels. The study also reconstructs the phylogeny of the Solanum genus using IGS sequences but identifies certain species that differ from previous results and require further clarification.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Yue Wang, Sheng Zhao, Peng Chen, Yongkang Liu, Zhigang Ma, Waqar Afzal Malik, Zhenghang Zhu, Zhenyu Peng, Haorong Lu, Yanli Chen, Yuxiao Chang
Summary: By studying 162 hollyhock accessions from China, extensive variation and strong correlations among quantitative traits were found. Whole-genome re-sequencing of 32 accessions identified 10,468,760 core single-nucleotide polymorphisms and calculated the average nucleotide diversity to be 0.00397. The results provide valuable information for hollyhock breeding.
Article
Multidisciplinary Sciences
Deden Derajat Matra, Muh Agust Nur Fathoni, Muhammad Majiidu, Hanif Wicaksono, Agung Sriyono, Gunawan Gunawan, Hilda Susanti, Rismita Sari, Fitmawati Fitmawati, Iskandar Zulkarnaen Siregar, Winarso Drajad Widodo, Roedhy Poerwanto
Summary: Research on the mango plant Mangifera casturi Kosterm. from South Kalimantan, Indonesia, focused on genetic variation and phylogeny, revealing broad genetic diversity and indicating the hybridization of multiple ancestors in its origin. This genetic information will be valuable for breeding improvement and conservation studies.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Rachel A. Swenie, Brian P. Looney, Yi-Hong Ke, Jorge A. Rojas, Marc A. Cubeta, Gitta J. Langer, Rytas Vilgalys, Patrick B. Matheny
Summary: In this study, a multi-locus pooled sequencing method using PacBio long-read high-throughput sequencing was developed and evaluated. The method successfully recovered multiple sequence variants of fungi species, providing accurate multi-locus sequence data. The method also allowed for the recovery of alleles from polymorphic samples and multi-organism specimens.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Microbiology
Zhipeng Guo, Tingting Zhang, Zhao Chen, Junpeng Niu, Xuewen Cui, Yue Mao, Mahmood Ul Hassan, Hafiz Abdul Kareem, Nan Xu, Xin Sui, Shuanghong Gao, Momi Roy, Jian Cui, Quanzhen Wang
Summary: This study detected seven main viruses infecting alfalfa in China's Gansu, Henan, Inner Mongolia, and Shaanxi provinces using high-throughput sequencing. The findings provide a basis for future research on the genetic evolution of alfalfa viruses in China and strategies for preventing diseases in alfalfa caused by these viruses.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Hanli Dang, Tao Zhang, Yuanyuan Li, Guifang Li, Li Zhuang, Xiaozhen Pu
Summary: This study evaluated the leaf nutrient concentration and photosynthetic chlorophyll index of Glycyrrhiza uralensis in different habitats to understand its growth physiology. Through genome-wide re-sequencing and analysis, the genetic diversity and structure of G. uralensis were revealed, and key genes related to its growth and metabolism were identified. These findings provide valuable information for the development and optimization of breeding programs for G. uralensis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Obstetrics & Gynecology
Wanwisa van Dijk, Kasper Derks, Marion Drusedau, Jeroen Meekels, Rebekka Koeck, Rick Essers, Joseph Dreesen, Edith Coonen, Christine de Die-Smulders, Servi J. C. Stevens, Han G. Brunner, Arthur van den Wijngaard, Aimee D. C. Paulussen, Masoud Zamani Esteki
Summary: The study found that using ETS-PGT can reduce the risk of sample switching while increasing detection efficiency and scalability.
HUMAN REPRODUCTION
(2022)
Article
Food Science & Technology
Qiu Qin Zhang, Dian Li, Wei Zhang, Mei Jiang, Xiao Hong Chen, Ming Sheng Dong
Summary: Chinese dry fermented sausages exhibit diverse microbial compositions, with similar phylum distributions but significant variations at the genus level. Factory origin has a stronger influence on bacterial diversity composition than product type, and potentially pathogenic and spoilage bacteria can be detected using high-throughput sequencing technology.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Irshad Ahmad Sofi, Irfan Rashid, Javaid Yousuf Lone, Sandhya Tyagi, Zafar A. Reshi, Reyazul Rouf Mir
Summary: The study focused on the genetic diversity and population structure of the clonal endemic plant species Sambucus wightiana in the Himalayan region, detecting two sub-populations and significant variability among different genotypes. The moderate to high genetic diversity observed may provide insurance against climate change and support further spread of S. wightiana.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
Yan-Qiu Yang, Su-Fang Deng, You-Quan Yang, Zhao-Yang Ying
Summary: The diversity and composition of endophytic bacterial communities in the phyllosphere of different Azolla species were investigated. A total of 1150 operational taxonomic units (OTUs) were detected, and the dominant bacteria belonged to Proteobacteria. The diversity and similarity of bacterial communities varied among different Azolla species.
Article
Veterinary Sciences
Tong Qin, Mingjie Shi, Meina Zhang, Zhitong Liu, Hao Feng, Yi Sun
Summary: Metagenomic sequencing was used to investigate the viromes in three tick species (Haemaphysalis concinna, Dermacentor silvarum, and Ixodes persulcatus) in North China. A total of 28 RNA viruses belonging to different viral families were identified. Ixodes persulcatus ticks had a higher diversity of viral species compared to the other two tick species. The study highlights the importance of studying tick-borne viruses for viral taxonomy and understanding tick-transmitted viral zoonotic diseases.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Plant Sciences
Roberta Piredda, Diana Sarno, Daniele De Luca, Wiebe H. C. F. Kooistra
Summary: The study analyzed the biogeography of six species of the diatom genus Bacteriastrum, revealing that these species are widely distributed in temperate and tropical oceans, with a few species only found in specific locations. The actual distribution of some species is more extensive than reported in official records, likely due to recent descriptions, inconspicuous characteristics, and possible misidentification in routine plankton counting.
EUROPEAN JOURNAL OF PHYCOLOGY
(2022)
Article
Plant Sciences
Simone Cardoni, Roberta Piredda, Thomas Denk, Guido W. Grimm, Aristotelis C. Papageorgiou, Ernst-Detlef Schulze, Anna Scoppola, Parvin Salehi Shanjani, Yoshihisa Suyama, Nobuhiro Tomaru, James R. P. Worth, Marco Cosimo Simeone
Summary: The process of plant speciation is more complex than standard models suggest, involving factors such as isolation, lineage mixing, and intra-genomic competition. Modern species are genetic mosaics, representing a striking case of ongoing reticulate evolution over the past 55 million years.
Article
Food Science & Technology
Roberta Piredda, Anna Mottola, Giulia Cipriano, Roberto Carlucci, Giuseppina Ciccarese, Angela Di Pinto
Summary: The multi-species fish products market is growing rapidly due to urbanization, modern lifestyles, and new technologies. These products lack species-related morphological traits and may contain fish waste, making them susceptible to substitution fraud. New molecular tools, such as metabarcoding, can be used to trace species in complex food matrices.
Article
Microbiology
Benjawan Tanunchai, Simon Andreas Schroeter, Li Ji, Sara Fareed Mohamed Wahdan, Shakhawat Hossen, Ann-Sophie Lehnert, Hagen Gruenberg, Gerd Gleixner, Francois Buscot, Ernst-Detlef Schulze, Matthias Noll, Witoon Purahong
Summary: This study used high-throughput sequencing techniques to explore the diversity and composition of lichenized fungi on the leaves and needles of 12 temperate tree species. The study highlights the importance of coniferous trees for maintaining the biodiversity of foliicolous lichens and emphasizes the significance of host species in shaping lichenized fungal communities. The discovery of red list lichens adds valuable information for conservation efforts.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Benjawan Tanunchai, Li Ji, Simon Andreas Schroeter, Sara Fareed Mohamed Wahdan, Panadda Larpkern, Ann-Sophie Lehnert, Eliane Gomes Alves, Gerd Gleixner, Ernst-Detlef Schulze, Matthias Noll, Francois Buscot, Witoon Purahong
Summary: Despite abundant observations of foliar pathogens, our knowledge about the structure and assembly processes of potential fungal pathobiome is limited. In this study, we analyzed the potential fungal pathobiome associated with senescing leaves and needles of 12 temperate tree species and found diverse and distinct fungal plant pathogens even in healthy-looking leaves/needles. Our study provides the first insights into the community assembly, networks, and complete taxonomy of the foliar fungal pathobiome in senescing leaves and needles.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Marine & Freshwater Biology
Albert Rene, Natalia Timoneda, Diana Sarno, Roberta Piredda, Gianpaolo Zampicinini, Adriana Zingone, Marina Montresor, Esther Garces
Summary: The presence and interactions of phytoplankton parasites, particularly Chytridiomycota, in the water column and sediments of the Gulf of Naples were investigated. Diatoms were found to dominate the upper layers of the water column, and Chytridiomycota were predominantly present in these layers, coinciding with diatom distribution. Laboratory incubations confirmed parasitic interactions between Chytridiomycota and diatoms. A 3-year metabarcoding time-series analysis revealed the recurrent presence of chytrids, but no clear patterns of co-occurrence with diatoms were observed. The chytrid community in sediments showed higher diversity compared to the water column samples. Overall, parasites were found to be a common component of the marine protist communities and understanding their interactions is crucial for understanding phytoplankton dynamics.
MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE
(2023)
Article
Plant Sciences
Thomas Denk, Johannes M. Bouchal, H. Tuncay Guner, Mario Coiro, Rainer Butzmann, Kathleen B. Pigg, Bruce H. Tiffney
Summary: Previous research suggested that the sclerophyllous subhumid vegetation in western Eurasia and western North America during the Paleogene period was endemic to these disjunct regions, implying isolation between the southern areas of the Holarctic flora. However, a recent study discovered the presence of Vauquelinia, which is currently endemic to western North America, in Cenozoic strata of western Eurasia. The fossil record suggests that Vauquelinia and other dry-adapted plants potentially migrated across the Paleogene North Atlantic land bridge during the Eocene.
Article
Geography, Physical
Manuel Vieira, Reinhard Zetter, Fridgeir Grimsson, Thomas Denk
Summary: The study revealed a high diversity of Fagaceae, including both extant and extinct lineages, in Late Pliocene Portugal. The pollen records suggest the presence of Himalayan-Southeast Asian groups in western Eurasia and the survival of cold-tolerant groups being more complex.
QUATERNARY SCIENCE REVIEWS
(2023)
Article
Multidisciplinary Sciences
Sandra Diaz, Jens Kattge, Johannes H. C. Cornelissen, Ian J. Wright, Sandra Lavorel, Stephane Dray, Bjoern Reu, Michael Kleyer, Christian Wirth, I. Colin Prentice, Eric Garnier, Gerhard Boenisch, Mark Westoby, Hendrik Poorter, Peter B. Reich, Angela T. Moles, John Dickie, Amy E. Zanne, Jerome Chave, S. Joseph Wright, Serge N. Sheremetiev, Herve Jactel, Christopher Baraloto, Bruno E. L. Cerabolini, Simon Pierce, Bill Shipley, Fernando Casanoves, Julia S. Joswig, Angela Guenther, Valeria Falczuk, Nadja Rueger, Miguel D. Mahecha, Lucas D. Gorne, Bernard Amiaud, Owen K. Atkin, Michael Bahn, Dennis Baldocchi, Michael Beckmann, Benjamin Blonder, William Bond, Ben Bond-Lamberty, Kerry Brown, Sabina Burrascano, Chaeho Byun, Giandiego Campetella, Jeannine Cavender-Bares, F. Stuart Chapin, Brendan Choat, David Anthony Coomes, William K. Cornwell, Joseph Craine, Dylan Craven, Matteo Dainese, Alessandro Carioca de Araujo, Franciska T. de Vries, Tomas Ferreira Domingues, Brian J. Enquist, Jaime Fagundez, Jingyun Fang, Fernando Fernandez-Mendez, Maria T. Fernandez-Piedade, Henry Ford, Estelle Forey, Gregoire T. Freschet, Sophie Gachet, Rachael Gallagher, Walton Green, Greg R. Guerin, Alvaro G. Gutierrez, Sandy P. Harrison, Wesley Neil Hattingh, Tianhua He, Thomas Hickler, Steven I. Higgins, Pedro Higuchi, Jugo Ilic, Robert B. Jackson, Adel Jalili, Steven Jansen, Fumito Koike, Christian Koenig, Nathan Kraft, Koen Kramer, Holger Kreft, Ingolf Kuehn, Hiroko Kurokawa, Eric G. Lamb, Daniel C. Laughlin, Michelle Leishman, Simon Lewis, Frederique Louault, Ana C. M. Malhado, Peter Manning, Patrick Meir, Maurizio Mencuccini, Julie Messier, Regis Miller, Vanessa Minden, Jane Molofsky, Rebecca Montgomery, Gabriel Montserrat-Marti, Marco Moretti, Sandra Mueller, UElo Niinemets, Roma Ogaya, Kinga Oellerer, Vladimir Onipchenko, Yusuke Onoda, Wim A. Ozinga, Juli G. Pausas, Begona Peco, Josep Penuelas, Valerio D. Pillar, Clara Pladevall, Christine Roemermann, Lawren Sack, Norma Salinas, Brody Sandel, Jordi Sardans, Brandon Schamp, Michael Scherer-Lorenzen, Ernst-Detlef Schulze, Fritz Schweingruber, Satomi Shiodera, Enio Sosinski, Nadejda Soudzilovskaia, Marko J. Spasojevic, Emily Swaine, Nathan Swenson, Susanne Tautenhahn, Ken Thompson, Alexia Totte, Rocio Urrutia-Jalabert, Fernando Valladares, Peter van Bodegom, Francois Vasseur, Kris Verheyen, Denis Vile, Cyrille Violle, Betsy von Holle, Patrick Weigelt, Evan Weiher, Michael C. Wiemann, Mathew Williams, Justin Wright, Gerhard Zotz
Summary: The 'Global Spectrum of Plant Form and Function Dataset' provides species mean values for six vascular plant traits on a global scale. Based on a large number of trait records, the dataset is the largest and most accurate compilation of vascular plant species mean traits to date, with comprehensive quality control.
Letter
Ecology
Fons van der Plas, Thomas Schroeder-Georgi, Alexandra Weigelt, Kathryn Barry, Sebastian Meyer, Adriana Alzate, Romain L. Barnard, Nina Buchmann, Hans de Kroon, Anne Ebeling, Nico Eisenhauer, Christof Engels, Markus Fischer, Gerd Gleixner, Anke Hildebrandt, Eva Koller-France, Sophia Leimer, Alexandru Milcu, Liesje Mommer, Pascal A. Niklaus, Yvonne Oelmann, Christiane Roscher, Christoph Scherber, Michael Scherer-Lorenzen, Stefan Scheu, Bernhard Schmid, Ernst-Detlef Schulze, Vicky Temperton, Teja Tscharntke, Winfried Voigt, Wolfgang Weisser, Wolfgang Wilcke, Christian Wirth
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Marine & Freshwater Biology
Iole Di Capua, Roberta Piredda, Rosa D'Angiolo, Carmen Minucci, Andrea Montalbano, Ferdinando Boero, Ylenia Carotenuto, Marco Uttieri
Summary: Molecular tools are used to refine identification of zooplankton organisms based on phenotypic features, revealing hidden diversity and facilitating detection of rare and non-indigenous species. The study focuses on key taxa from the Gulf of Naples, providing new molecular references and uncovering genetic diversification of zooplankton species in Mediterranean coastal waters.
MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE
(2023)
Article
Marine & Freshwater Biology
Solenn Mordret, Roberta Piredda, Gianpaolo Zampicinini, Wiebe H. C. F. Kooistra, Adriana Zingone, Marina Montresor, Diana Sarno
Summary: This study examined the diversity and seasonal distribution of dinoflagellates in the Gulf of Naples using a 3-year DNA dataset. The results revealed that there is still limited knowledge about many dinoflagellate species. It was found that dinoflagellates have a diverse community in winter, which was previously overlooked. This study provides new insights into the ecology and distribution of this important component of the plankton.
MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE
(2023)
Article
Environmental Sciences
Benjawan Tanunchai, Li Ji, Olaf Schroeder, Susanne Julia Gawol, Andreas Geissler, Sara Fareed Mohamed Wahdan, Francois Buscot, Stefan Kalkhof, Ernst-Detlef Schulze, Matthias Noll, Witoon Purahong
Summary: This study investigated the degradation of Poly(butylene succinate-co-adipate) (PBSA) and its plastisphere microbiome in forest ecosystems. The results showed that forest type significantly affected the richness and fungal community composition of the plastisphere microbiome. Bacterial community composition was mainly governed by stochastic processes, while fungal community composition was influenced by both stochastic and deterministic processes. Potential keystone taxa involved in PBSA degradation, such as fungal PBSA decomposers (Tetracladium) and N2-fixing bacteria, were identified.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Forestry
Pascal Edelmann, Wolfgang W. Weisser, Didem Ambarli, Claus Baessler, Francois Buscot, Martin Hofrichter, Bjorn Hoppe, Harald Kellner, Cynthia Minnich, Julia Moll, Derek Persoh, Sebastian Seibold, Claudia Seilwinder, Ernst-Detlef Schulze, Stephan Woellauer, Werner Borken
Summary: A long-term experiment in Germany suggests that climate, soil traits, and forest structure have significant impacts on the decay process and mass loss of deadwood. Soil nutrient content and precipitation have negative effects on mass loss, while temperature has a positive effect. Forest structure has a small influence on mass loss. The results indicate that at the regional scale, organismic diversity and microbial activity have a stronger impact on the decay process than exogenous factors.
FOREST ECOLOGY AND MANAGEMENT
(2023)