Article
Plant Sciences
Widad S. Al-Juhani, Kadry Ne Abdel Khalik
Summary: The study aimed to determine the phylogenetic relationships between Arabis alpina L. in Afro-Alpina Mountains of southwestern Saudi Arabia and its closely related species using DNA barcode, ITS2, matK and rbcL. The results indicated high success rates for DNA amplification and sequencing with ITS2 and matK, showing variations between A. alpina of Saudi Arabia and specimens from different geographical origins.
PAKISTAN JOURNAL OF BOTANY
(2021)
Article
Plant Sciences
Zhi Chao, Xiaoxi Hong, Xuena Xie, Rong Huang, Enwei Tian
Summary: A comparative analysis of chloroplast genomes and nuclear ribosomal DNA, as well as a phylogenomic study, were conducted on six closely related species of the genus Bupleurum. The study found that the chloroplast genomes of the six species were highly similar, while the highly variable regions showed no advantage in species resolution.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Khalid Mushwan, Shaikh Bokhtear Uddin, Amam Zonaed Siddiki, Mohammad Omar Faruque
Summary: The effectiveness of plant-based therapies relies on accurate identification of plant species. However, due to limited scientific knowledge, tribal communities and practitioners sometimes misidentify medicinal plants. This research utilized DNA sequencing to identify ethnomedicinal plants in Bangladesh, proving that partial genome sequencing using specific DNA markers is a feasible and efficient method for authentication.
GENETIC RESOURCES AND CROP EVOLUTION
(2023)
Article
Plant Sciences
Jianli Wang, Zhenfei Yan, Peng Zhong, Zhongbao Shen, Guofeng Yang, Lichao Ma
Summary: This study evaluated the utility of four candidate DNA barcoding regions in seven genera of Gramineae. It found that matK and ITS showed the highest discriminatory power, while rbcL and trnL-F were less effective. The study also demonstrated the feasibility of establishing a technical system for rapid and reliable identification of these seven genera, and provided crucial reference for analyzing the genetic diversity of grass germplasm resources.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ranjana K. Negi, Pooja Nautiyal, Rajneesh Bhatia, Rakesh Verma
Summary: This study evaluated the discriminatory potential of the rbcL region as a DNA barcode marker for authenticating Himalayan Aconites, which could be helpful in combating illicit trade of these valuable medicinal plants.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Plant Sciences
Joan Pere Pascual-Diaz, Sonia Garcia, Daniel Vitales
Summary: Plastid genomes in Asteraceae are generally highly conserved, with specific rearrangements being phylogenetically informative. This study provided a comprehensive plastome-based phylogeny of Asteraceae, revealing structural information, genetic diversity, and repeat composition. Despite the presence of a double inversion in most species, there are exceptions in basal tribes lacking a specific pseudogene. The phylogenomic analysis based on protein-coding genes, transfer RNA genes, and ribosomal RNA genes showed consistency with the family's general consensus, while also highlighting some incongruences between nuclear and plastid DNA data at the tribe level.
Article
Forestry
Behrouz Moradi Ashour, Mohammad Rabiei, Behrouz Shiran
Summary: The combination of nuclear and chloroplast barcode regions is effective for distinguishing pomegranate genotypes. The use of molecular, biochemical, and morphological markers has complementary functions. Exclusion of similar genotypes based on different markers helps to reduce collection size, especially when building a core collection.
TREES-STRUCTURE AND FUNCTION
(2023)
Article
Plant Sciences
Shoukat Hussain, Rehana Asghar, Muhammad Ajaib, Imran Ali, Muhammad Faheem Siddiqui, Samma Ain, Muhammad Sufian
Summary: The current research effort used DNA barcode analysis to confirm and authenticate the identity and interrelationship of Morus species. Chloroplast DNA of specimens were evaluated through PCR, sequence homology, and NJ clustering. The results showed that rbcL and matK markers can efficiently distinguish between species, and the research could be useful for identifying other species of Morus and contribute to the taxonomy of the genus.
PAKISTAN JOURNAL OF BOTANY
(2023)
Article
Plant Sciences
Xue-Min Xu, Zhen Wei, Jun-Zhe Sun, Qing-Fei Zhao, Yang Lu, Zhen-Long Wang, Shi-Xin Zhu
Summary: This study analyzed the chloroplast genomes of 43 Leontopodium and closely related genera. It found that the chloroplast genomes of Filago, Gamochaeta, and Leontopodium were well-conserved, but differed in terms of length and certain regions. The molecular phylogenetic results were inconsistent with the previous taxonomic system based on morphology.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Almuthanna K. Alkaraki, Maisam A. Aldmoor, Jamil N. Lahham, Mohammed Awad
Summary: The study aimed to develop a DNA barcoding method to identify and characterize Daphne mucronata Royle and Thymelaea hirsuta plant species. The research found that DNA barcoding successfully identified the two plant species using chloroplast genes.
Article
Plant Sciences
Wen-Pan Dong, Jia-Hui Sun, Yan-Lei Liu, Chao Xu, Yi-Heng Wang, Zhi-Li Suo, Shi-Liang Zhou, Zhi-Xiang Zhang, Jun Wen
Summary: The study used phylogenomic data to resolve relationships within the genus Olea and identify molecular markers for species identification. The results showed that the genus Olea is not monophyletic and provided insights into DNA barcodes for accurate species identification.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2022)
Article
Biology
Awad A. Algarni
Summary: This study is the first to document the rare plant Aloe shadensis using genomic markers. It found that the matK gene and ITS region sequences were effective in identifying the plant.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Plant Sciences
Sampath Perumal, Nomar Espinosa Waminal, Jonghoon Lee, Hyun-Jin Koo, Boem-soon Choi, Jee Young Park, Kyounggu Ahn, Tae-Jin Yang
Summary: The study utilized whole-genome shogun sequence (WGS) data to analyze nuclear and chloroplast diversity in 44 Brassica oleracea breeding lines, identifying genetic variations such as SNPs and indels. The phylogenetic tree grouped different morphotypes of B. oleracea based on nuclear and chloroplast genomes, revealing the evolutionary history and cytoplasm features of the crop. The research highlighted the importance of low-coverage NGS data in understanding genetic diversity and evolution in diverse Brassica oleracea morphotypes.
HORTICULTURAL PLANT JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Wen Zhang, Yuzhe Sun, Jia Liu, Chao Xu, Xinhui Zou, Xun Chen, Yanlei Liu, Ping Wu, Xueying Yang, Shiliang Zhou
Summary: Phylogenomics was applied to clarify the concept of rice species and identify rice germplasms, revealing 21 Oryza species and a 17% mislabeling rate of seed accessions. The study aims to support rice biodiversity by aiding in species identification and germplasm utilization.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Plant Sciences
Kaihui Zhao, Lianqiang Li, Hong Quan, Junbo Yang, Zhirong Zhang, Zhihua Liao, Xiaozhong Lan
Summary: This study sequenced and analyzed six Zanthoxylum chloroplast genomes, identifying specific genomic characteristics and mutational hotspots, with seven DNA barcode sequences for species differentiation. The phylogenetic analysis supported the existence of the Fagara subgenus within Zanthoxylum and proposed the potential for a new subgenus. The availability of these genomes provides valuable information for species identification, molecular breeding, and evolutionary analysis of Zanthoxylum.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Charles Pouchon, Jeremy Gauthier, Camille Pitteloud, Cyrille Claudel, Nadir Alvarez
Summary: This study provides insights into the evolutionary history and phylogenetic relationships of the Amorphophallus genus through genome sequencing. It identifies four main clades and explores their relationships with morphological characteristics, climate dynamics, and bird migration during the Oligocene/Miocene transition.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Ecology
Ian R. McFadden, Agnieszka Sendek, Morgane Brosse, Peter M. Bach, Marco Baity-Jesi, Janine Bolliger, Kurt Bollmann, Eckehard G. Brockerhoff, Giulia Donati, Friederike Gebert, Shyamolina Ghosh, Hsi-Cheng Ho, Imran Khaliq, J. Jelle Lever, Ivana Logar, Helen Moor, Daniel Odermatt, Loiec Pellissier, Luiz Jardim de Queiroz, Christian Rixen, Nele Schuwirth, J. Ryan Shipley, Cornelia W. Twining, Yann Vitasse, Christoph Vorburger, Mark K. L. Wong, Niklaus E. Zimmermann, Ole Seehausen, Martin M. Gossner, Blake Matthews, Catherine H. Graham, Florian Altermatt, Anita Narwani
Summary: Human impacts such as habitat loss, climate change, and biological invasions are drastically changing biodiversity. We propose an integrative approach to explain the differences in impacts between terrestrial and freshwater ecosystems by linking them to four fundamental processes that structure communities. Through this approach, we aim to provide insights into why human impacts and responses to them may differ across ecosystem types, using a mechanistic, eco-evolutionary framework.
Article
Ecology
Ao Luo, Xiaoting Xu, Yunpeng Liu, Yaoqi Li, Xiangyan Su, Yichao Li, Tong Lyu, Dimitar Dimitrov, Markku Larjavaara, Shijia Peng, Yongsheng Chen, Qinggang Wang, Niklaus E. Zimmermann, Loic Pellissier, Bernhard Schmid, Zhiheng Wang
Summary: The aim of this study is to demonstrate the global spatio-temporal patterns in angiosperm woodiness and their relationship with environmental factors. Using data on the growth forms and distributions of around 300,000 angiosperm species and an angiosperm phylogeny, the researchers mapped the current global geographical patterns in angiosperm woodiness and reconstructed ancestral states of growth forms. They found that temperature was the best predictor of the spatio-temporal decline in woodiness and was positively correlated with woodiness. The study highlights the role of temperature in maintaining the growth form composition of ecosystems and calls for attention to growth form transitions in temperate drylands.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Biodiversity Conservation
Antoine Adde, Pierre-Louis Rey, Philipp Brun, Nathan Kuelling, Fabian Fopp, Florian Altermatt, Olivier Broennimann, Anthony Lehmann, Blaise Petitpierre, Niklaus E. E. Zimmermann, Loic Pellissier, Antoine Guisan
Summary: Predicting species distributions is crucial, but existing modelling tools have limitations. To address this, we developed N-SDM, an SDM platform that combines various techniques and allows scalable high-resolution predictions. N-SDM is designed for biodiversity assessments and facilitates the use of species occurrence data at different scales. It integrates state-of-the-art features, such as covariate selection, multiple algorithms, hyperparameter optimization, and parallel processing.
Article
Ecology
Vanessa Cutts, Dagmar M. Hanz, Martha Paola Barajas-Barbosa, Franziska Schrodt, Manuel J. Steinbauer, Carl Beierkuhnlein, Pierre Denelle, Jose Maria Fernandez-Palacios, Pierre Gauzere, Matthias Grenie, Severin D. H. Irl, Nathan Kraft, Holger Kreft, Brian Maitner, Francois Munoz, Wilfried Thuiller, Cyrille Violle, Patrick Weigelt, Richard Field, Adam C. Algar
Summary: Current models of island biogeography treat endemic and non-endemic species as if they were functionally equivalent, focussing primarily on species richness. Thus, the functional composition of island biotas in relation to island biogeographical variables remains largely unknown.
Article
Ecology
Robert Spitzer, Eric Coissac, Joris P. G. M. Cromsigt, Annika M. Felton, Christian Fohringer, Marietjie Landman, Wiebke Neumann, David Raubenheimer, Navinder J. Singh, Pierre Taberlet, Fredrik Widemo
Summary: Differences in botanical diet compositions correlated with nutritional differences in moose faecal samples collected during winter. Moose mixed Scots pine and Vaccinium spp. as complementary foods to reach a nutritional target resembling Salix spp. twigs and selected for Salix spp. browse. Available protein and total non-structural carbohydrates showed significant correlation in observed diets.
FUNCTIONAL ECOLOGY
(2023)
Article
Ecology
Kuiling Zu, Jonathan Lenoir, Jingyun Fang, Zhiyao Tang, Zehao Shen, Chengjun Ji, Chengyang Zheng, Ao Luo, Wenqi Song, Niklaus E. Zimmermann, Loic Pellissier, Zhiheng Wang
Summary: This study assessed changes in species' elevational centroids and their drivers in 29 Chinese mountains using historical specimen records and recent field observations for 735 seed plant species. The results showed that 54% of the species shifted upward while 46% shifted downhill. The study also found that precipitation changes, species' climatic adaptations, functional traits, and mountain size all contributed to the magnitude of species' centroid elevational range shifts.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Ecology
Zdenka Lososova, Irena Axmanova, Milan Chytry, Gabriele Midolo, Sylvain Abdulhak, Dirk Nikolaus Karger, Julien Renaud, Jeremie Van Es, Pascal Vittoz, Wilfried Thuiller
Summary: This study compiled a comprehensive dataset of seed dispersal distance classes and predominant dispersal modes for most European vascular plants. The seed dispersal dataset can be used in functional biogeography, dynamic vegetation modelling, and ecological studies at local to continental scales.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Ecology
Lucie Mahaut, Philippe Choler, Pierre Denelle, Eric Garnier, Wilfried Thuiller, Jens Kattge, Servane Lemauviel-Lavenant, Sandra Lavorel, Francois Munoz, Delphine Renard, Josep M. Serra-Diaz, Nicolas Viovy, Cyrille Violle
Summary: The productivity of grasslands is influenced by both environmental factors and biodiversity, while the temporal stability of grasslands can display both positive and negative covariations with productivity. It is crucial to consider the multiple components of stability and the interaction between environment and biodiversity for sustainable grassland management.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Ecology
Giovanni Poggiato, Pierre Gauzere, Camille Martinez-Almoyna, Gabrielle Deschamps, Julien Renaud, Cyrille Violle, Tamara Munkemueller, Wilfried Thuiller
Summary: Understanding how combinations of ecological traits at the community-level vary with environmental conditions is crucial for addressing the biodiversity crisis. However, most previous studies have overlooked the inherent correlations between these traits, leading to unrealistic predictions. We propose a framework that incorporates joint trait distribution models to account for these correlations and provide more accurate predictions. Our framework enhances the understanding and prediction of trait distributions, moving functional biogeography towards a more predictive science. Overall, this framework has a high level of importance and would receive a score of 8 out of 10.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Biochemistry & Molecular Biology
Dana Suteu, Mihai Puscas, Ioan Bacila, Mihai Miclaus, Zoltan Robert Balazs, Philippe Choler
Summary: Microsatellite primers were developed and tested to genotype different populations of Carex curvula and to infer the phylogeographic relationships within the species and between its two subspecies. The results showed that the developed markers were efficient in distinguishing between the subspecies and populations, making them promising tools for evolutionary studies.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Multidisciplinary Sciences
Yunpeng Liu, Xiaoting Xu, Dimitar Dimitrov, Loic Pellissier, Michael K. Borregaard, Nawal Shrestha, Xiangyan Su, Ao Luo, Niklaus E. Zimmermann, Carsten Rahbek, Zhiheng Wang
Summary: By integrating global distributions and a phylogeny of 12,664 angiosperm genera, the study updates global floristic regions and explores their temporal changes. Most floristic realms have formed since the Paleogene, primarily due to geographic isolation induced by plate tectonics.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Kevin M. Andre, Nathalie Giordanengo Aiach, Veronica Martinez-Fernandez, Leo Zeitler, Adriana Alberti, Arach Goldar, Michel Werner, Cyril Denby Wilkes, Julie Soutourina
Summary: Chromatin organization is crucial for transcriptional regulation. Mediator and RSC contribute to chromatin remodeling and transcriptional regulation by establishing physical contact and coordinating their functions.
Article
Ecology
Clement Valle, Giovanni Poggiato, Wilfried Thuiller, Frederic Jiguet, Karine Prince, Isabelle Le Viol
Summary: The study examines the influence of data type, resolution, and sampling size on the species associations identified by joint species distribution models (jSDM). It finds that the associations are mainly affected by resolution and sampling size, rather than data type. The study also reveals a positive correlation between species associations and functional similarity, challenging the expectation of negative biotic interactions. Furthermore, the high-resolution residual species associations are shown to contain valuable information for enhancing predictive performance through conditional predictions.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Plant Sciences
Yaquan Chang, Katrina Gelwick, Sean D. Willett, Xinwei Shen, Camille Albouy, Ao Luo, Zhiheng Wang, Niklaus E. Zimmermann, Loic Pellissier
Summary: The geographic distribution of plant diversity matches the gradient of habitat heterogeneity. The associations between species richness and habitat heterogeneity were investigated at the scales of Eurasia and the Hengduan Mountains in China using species distribution models. High environmental heterogeneity provides suitable conditions for the diversification of lineages in the Hengduan Mountains, but other mechanisms, such as the complex geological history, may have contributed to shaping the exceptional biodiversity hotspot.