Article
Ecology
Nicole R. Foster, Kor-jent van Dijk, Ed Biffin, Jennifer M. Young, Vicki A. Thomson, Bronwyn M. Gillanders, Alice R. Jones, Michelle Waycott
Summary: Metabarcoding has greatly improved our understanding of plants in the environment, with applications in ecology, conservation, and invasive species management. This study presents a targeted capture approach using OZBaits_CP V1.0 to create a reference database for coastal temperate plant species. The approach achieved a high recovery rate of target genes in all specimens and demonstrated the importance of generating reference sequences across multiple chloroplast gene regions.
ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Xiangyu Tian, Luye Shi, Jia Guo, Liuyang Fu, Pei Du, Bingyan Huang, Yue Wu, Xinyou Zhang, Zhenlong Wang
Summary: The study reveals that peanuts can be divided into two lineages, with cultivated species primarily having AABB and AA genome types, while wild species exhibit diverse genome types. It is suggested that all allotetraploid cultivated peanuts may have originated from a maternal hybridization event, with a wild species potentially serving as a sub-genome ancestor. This research provides insight into the taxonomic status and evolutionary relationships of various Arachis species/accessions, aiding in the efficient use of germplasm resources for peanut breeding.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Le Zhang, Yi-Wei Huang, Jia-Lin Huang, Ji-Dong Ya, Meng-Qing Zhe, Chun-Xia Zeng, Zhi-Rong Zhang, Shi-Bao Zhang, De-Zhu Li, Hong-Tao Li, Jun-Bo Yang
Summary: In this study, DNA barcoding was conducted for species identification of Cymbidium using plastomes. A comprehensive DNA barcode reference library for Cymbidium species identification was established. The plastome showed improved species identification rates compared to standard DNA barcodes, but still had limitations. Nuclear genome data were also explored for species identification and showed potential as next-generation nuclear barcodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Amanda K. Broz, Alexandra Keene, Matheus Fernandes Gyorfy, Mychaela Hodous, Iain G. Johnston, Daniel B. Sloan
Summary: The study of the fate of new mitochondrial and plastid mutations is crucial for understanding plant evolution and breeding, shedding light on the transmission of heteroplasmies across generations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Yuri Yamazaki, Tadashi Kajita, Koji Takayama
Summary: Long-distance dispersal of seeds is crucial for plant migration and maintaining gene flow among isolated populations. Pantropical plants with sea-drifted seeds have achieved global distribution through long-distance dispersal. However, the processes and role of long-distance dispersal in achieving wide distribution have not yet been explained.
Article
Evolutionary Biology
Tian-Chu Li, Yan-Kun Wang, Zhuo-Xiao Sui, Tao Wang, Jing-Zi Nian, Jin-Zhuang Jiang, Ting Tang, Feng-Song Liu, Jin-Hua Xiao, Da-Wei Huang
Summary: The prevalence of multiple haplotypes within individual specimens may have an important impact on DNA barcode-based species identification and biodiversity assessment.
SYSTEMATIC ENTOMOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Bikash Shrestha, Lawrence E. Gilbert, Tracey A. Ruhlman, Robert K. Jansen
Summary: Plastid inheritance in Passiflora plants shows diverse patterns depending on different subgenera, with some predominantly maternal, paternal or biparental. The study suggests that plastid retention in later stages of plant development may not reflect the inheritance patterns in embryos, indicating complexity and diversity in plastid inheritance in Passiflora plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Mariano Martinez, Lars Harms, Doris Abele, Christoph Held
Summary: The species delimitation of Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. Different data sources suggest that cross-Drake populations belong to different species, but the situation is not clear within Antarctic populations. Standard barcoding procedures lead to amplification bias and overestimate the species richness. Nuclear SNPs show no differentiation, suggesting that the Antarctic populations represent a single species. Multiple data sources and quality control measures are important to increase the accuracy of species delimitation.
Article
Plant Sciences
Mengting Wang, Wenhui Yu, Jiapeng Yang, Zhenyu Hou, Chao Li, Zhitao Niu, Benhou Zhang, Qingyun Xue, Wei Liu, Xiaoyu Ding
Summary: Our study focuses on the Dendrobium orchids, which have large morphological divergence and difficulties in species taxonomy. We assembled the complete mitogenomes of two Dendrobium species and compared them with other orchids. The results reveal extensive variations in repetitive and chloroplast-derived sequences in Dendrobium mitogenomes, and the intergenic content has undergone expansion during evolution. We also sequenced the mitogenomes of 26 Dendrobium species and reconstructed their phylogenetic relationships based on mitochondrial and plastid data. The mitochondrial phylogeny shows partial characteristics of the plastid phylogeny and provides new insights into the phylogenetic relationships of Dendrobium species.
Article
Plant Sciences
Li-Jun Yan, Zhi-Guo Zhu, Pei Wang, Chao-Nan Fu, Xi-Jin Guan, Philip Kear, Chun-Zhi Zhang, Guang-Tao Zhu
Summary: In this study, the phylogenetic relationship of potato and its relatives was investigated by analyzing the plastid genomes. The results confirmed existing species boundaries and provided new insights into species classification and hybrid origin. The plastid genome performed best in species discrimination, but had limited discriminatory power for all species.
JOURNAL OF SYSTEMATICS AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Eun-Kyeong Han, Won-Bum Cho, Ichiro Tamaki, In-Su Choi, Jung-Hyun Lee
Summary: This study assembled the mitochondrial genomes of six Damnacanthus indicus plants, revealing gene and intron characteristics, as well as variations in genome structure and sequence divergence. The size and gene content of D. indicus mitochondria differed from other angiosperms, with two distinct genome structures identified within the Rubioideae. The study proposed a two-step direct repeat-mediated recombination model to explain structural changes between the two identified genome types.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Zhiqiang Ye, Chaoxian Zhao, R. Taylor Raborn, Man Lin, Wen Wei, Yue Hao, Michael Lynch
Summary: Genetic variants of mitochondrial DNA play important roles in cellular and evolutionary processes, with extensive heteroplasmy observed in some populations and remarkably low mitochondrial effective population sizes in D. pulex. Levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, likely due to the effects of deleterious mutations in the mitochondrial genome.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Agronomy
V. S. Bulgakova (Bogdanova), N. V. Shatskaya, O. E. Kosterin, G. V. Vasiliev
Summary: A case of paternal inheritance of mitochondrial DNA and natural heteroplasmy and recombination of mitochondrial genomes were observed in pea, shedding light on the microevolutionary processes that shape diversity in this important crop.
Article
Plant Sciences
Anchittha Satjarak, Linda E. Graham, Marie T. Trest, Patricia Arancibia-Avila
Summary: In this study, the complete chloroplast genome of the giant species Equisetum xylochaetum was assembled and compared with two other Equisetum species. The analysis revealed conserved traits in chloroplast genome structure and protein-coding regions among Equisetum species. Phylogenetic analysis confirmed the monophyly of Equisetum and provided insights into the relationships among different species. Single-gene phylogenetic estimation and haplotype analysis also shed light on the genetic diversity and mutation rate in Equisetum species.
Article
Multidisciplinary Sciences
Mohammed Dashti, Hussain Alsaleh, Juan L. Rodriguez-Flores, Muthukrishnan Eaaswarkhanth, Fahd Al-Mulla, Thangavel Alphonse Thanaraj
Summary: The study revealed that individuals with mitochondrial haplogroup J in the Qatari population have an increased risk of obesity, while individuals with haplogroup X have a lower risk of obesity. Additionally, a set of 38 mitochondrial variants were found to be associated with obesity.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Maria Victoria Diaz-Galiana, Magdalena Torres, Jose David Sanchez-Pagan, Pedro J. Navarro, Julia Weiss, Marcos Egea-Cortines
Summary: The study found that increasing red and blue light has a positive impact on strawberry production and quality, improving flowering rate and fruit quality. Supplementary lighting within a 13-hour light cycle can achieve fruit production and enhance quality.
SOUTH AFRICAN JOURNAL OF BOTANY
(2021)
Article
Plant Sciences
Marta Terry, Victoria Ruiz-Hernandez, Diego J. Aguila, Julia Weiss, Marcos Egea-Cortines
Summary: The quality of Narcissus flowers' scent is influenced by different light and temperature conditions, with the most complex scent profile achieved under a 15 degrees-5 degrees C thermoperiod and a 12:12 Light Dark photoperiod. Environmental factors play a critical role in scent emission and some volatiles are consistently dependent on light or thermoperiod. Additionally, scent emission changes significantly during the day and between different light and temperature treatments.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Environmental Sciences
Pedro J. Navarro, Leanne Miller, Alberto Gila-Navarro, Maria Victoria Diaz-Galian, Diego J. Aguila, Marcos Egea-Cortines
Summary: A new deep learning architecture named 3DeepM was developed for multispectral image classification, achieving superior performance in accuracy, number of classes, number of parameters, and training time. Additionally, a flexible and reconfigurable computer vision system was introduced to support the validation of the 3DeepM architecture for acquiring multispectral images.
Article
Biochemistry & Molecular Biology
Fernando Perez-Sanz, Victoria Ruiz-Hernandez, Marta Terry, Sara Arce-Gallego, Julia Weiss, Pedro J. Navarro, Marcos Egea-Cortines
Summary: Metabolomes consist of constitutive and non-constitutive metabolites produced due to physiological, genetic, or environmental effects. The tool gcProfileMakeR is developed for automatic data analysis in large datasets to define differences in metabolites.
Article
Agronomy
Jessica Cuartero, Onurcan Ozbolat, Virginia Sanchez-Navarro, Marcos Egea-Cortines, Raul Zornoza, Loredana Canfora, Luigi Orru, Jose Antonio Pascual, Juana-Maria Vivo, Margarita Ros
Summary: Long-term organic farming aims to reduce synthetic fertilizer and pesticide use to improve soil quality. Different cropping systems have varying effects on soil microbial communities, with organic cultivation leading to changes in bacterial communities.
Article
Plant Sciences
Victoria Ruiz-Hernandez, Lize Joubert, Amador Rodriguez-Gomez, Silvia Artuso, Jonathan G. Pattrick, Perla A. Gomez, Sarah Eckerstorfer, Sarah Sophie Brandauer, Carolina G. I. Trcka-Rojas, Luis Martinez-Reina, Josh Booth, Alex Lau-Zhu, Julia Weiss, Pablo Bielza, Beverley J. Glover, Robert R. Junker, Marcos Egea-Cortines
Summary: Research found that humans and bumblebees prefer flowers of parental species, while thrips prefer recombinant inbred lines. In flower selection, color and floral scent are important features that all organisms pay attention to, with bumblebees being more sensitive to visual traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Jessica Cuartero, Onurcan Ozbolat, Virginia Sanchez-Navarro, Julia Weiss, Raul Zornoza, Jose Antonio Pascual, Juana-Maria Vivo, Margarita Ros
Summary: Significant differences in microbial community and functionality were observed between organic and conventional farming systems. Organic farming showed higher negative interactions and modularity, leading to the increase of generalist species and improved response to adverse conditions. Long-term compost amendment application can benefit farmers and the environment by reducing fertilizer and pesticide use and enhancing soil stability against climate change.
Article
Agriculture, Multidisciplinary
Jessica Cuartero, Jose Antonio Pascual, Juana-Maria Vivo, Onurcan Ozbolat, Virginia Sanchez-Navarro, Marcos Egea-Cortines, Raul Zornoza, Maria Martinez Mena, Eloisa Garcia, Margarita Ros
Summary: The melon/cowpea intercropping system can optimize land use, increase melon yield, and benefit soil microbial community and environment.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2022)
Editorial Material
Plant Sciences
Ruslan Kalendar, Vladimir Orbovic, Marcos Egea-Cortines, Guo-qing Song
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Soil Science
Onurcan Ozbolat, Virginia Sanchez-Navarro, Raul Zornoza, Marcos Egea-Cortines, Jessica Cuartero, Margarita Ros, Jose A. Pascual, Carolina Boix-Fayos, Maria Almagro, Joris de Vente, Elvira Diaz-Pereira, Maria Martinez-Mena
Summary: This study aimed to assess the impact of reduced tillage and green manure on soil properties and bacterial community structure in a rainfed Mediterranean almond orchard. The results showed that a combination of reduced tillage and green manure increased soil organic matter and total nitrogen content, as well as the presence of beneficial bacteria associated with soil productivity.
Article
Plant Sciences
Raquel Alcantud, Julia Weiss, Marta I. Terry, Nuria Bernabe, Fuensanta Verdu-Navarro, Jesualdo Tomas Fernandez-Breis, Marcos Egea-Cortines
Summary: Short term experiments have identified heat shock and cold response elements in many biological systems, but the impact of long-term low or high temperatures is not well documented. To address this, Antirrhinum majus plants were grown under control, cold, and hot conditions for two years. Results showed that flower size, petal anthocyanin content, and pollen viability were higher in cold conditions and decreased in middle and high temperatures. Leaf chlorophyll content was higher in cold conditions, while pedicel length increased under hot conditions. The control conditions were optimal for scent emission and seed production.
FRONTIERS IN PLANT SCIENCE
(2023)
Editorial Material
Plant Sciences
Ruslan Kalendar, Kioumars Ghamkhar, Pietro Franceschi, Marcos Egea-Cortines
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Environmental Sciences
Jesus Aguilera-Huertas, Jessica Cuartero, Margarita Ros, Jose Antonio Pascual, Luis Parras-Alcantara, Manuel Gonzalez-Rosado, Onurcan Ozbolat, Raul Zornoza, Marcos Egea-Cortines, Maria Hurtado-Navarro, Beatriz Lozano-Garcia
Summary: Intercropping systems have a significant impact on microbial communities and soil properties. In particular, the Crocus sativus cropping system can increase soil organic carbon and total nitrogen, which are correlated with bacterial communities and improve soil functionality.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Biology
Pedro J. Navarro, Leanne Miller, Maria Victoria Diaz-Galian, Alberto Gila-Navarro, Diego J. Aguila, Marcos Egea-Cortines
Summary: This study developed the first public dataset of grape ground truth multispectral images. The dataset includes measurements of weight, anthocyanins, and Brix index associated with each multispectral image. This dataset should be useful for developing deep learning algorithms for classification, dimensionality reduction, regression, and prediction analysis.