Article
Plant Sciences
Jiao Zhang, Xiulian Chi, Juying Zhong, Alisdair Fernie, Saleh Alseekh, Luqi Huang, Dan Qian
Summary: This study found non-concerted evolution of internal transcribed spacer (ITS) sequences in the genus Lycium, showing high levels of polymorphism. The ITS paralogues were identified as pseudogenes or functional copies, with distinct differences from their corresponding functional copies. The results suggest a link between the non-concerted evolution of ITS and recent divergence of tandem repeats within the Lycium genome and hybridization between species.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Li Gong, Wei Shi, Min Yang, Hairong Luo
Summary: This study revealed a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in Cynoglossus melampetalus genome, indicating a non-concerted evolution manner. The presence of multiple types of rDNA sequences with differences in length, GC content, secondary structure stability, and minimum free energy challenges the previous assumption of homogeneity within species.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Microbiology
Fernando Martinez-Hernandez, Fabiola Sanchez-Aguillon, Joel Martinez-Ocana, Nelly Raquel Gonzalez-Arenas, Mirza Romero-Valdovinos, Eduardo Lopez-Escamilla, Pablo Maravilla, Guiehdani Villalobos
Summary: This study evaluated the genetic variability of the ITS region and pfor A gene of Trichomonas vaginalis from female patients and explored its implications in the host-parasite relationship. Results showed two main clusters in the ITS haplotypes and suggested that pfor A could be used as a marker for confirming trichomonads genus and species.
Article
Microbiology
Aisha Umar
Summary: Laccases have high biotechnological potential in industries due to their ability to catalyze the oxidation of various compounds. This study screened 10 Trichoderma species for laccase production, with T. atroviride showing the highest laccase production among them. Further analysis included purification, molecular weight determination, amino acid sequence confirmation, and phylogenetic tree construction of the laccase from T. atroviride.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Food Science & Technology
Alice Giusti, Enrica Ricci, Laura Gasperetti, Marta Galgani, Luca Polidori, Francesco Verdigi, Roberto Narducci, Andrea Armani
Summary: This study aimed to build an ITS gene dataset to aid the Italian Health Service in mushroom identification. By retrieving and filtering ITS sequences from GenBank and BOLD databases, as well as collecting wild specimens, a dataset of 5977 sequences was successfully established to support regional poisoning cases.
Article
Plant Sciences
Claudia Gonzalez-Toral, Herminio S. Nava, Jose Antonio Fernandez Prieto, Eduardo Cires
Summary: Bromus picoeuropeanus is a recently described species of grasses found in stony soils at heights ranging from 1600 to 2200 m in Picos de Europa, Spain. Phylogenetic analyses based on nuclear and chloroplastic markers suggest that B. picoeuropeanus is a separate species with a larger distribution than previously thought. However, more research is needed to understand its susceptibility to temperature rises.
Article
Immunology
Celine Nourrisson, Samia Hamane, Julie Bonhomme, Marie-Fleur Durieux, Jean-Baptiste Foulquier, Sophie Lesthelle, Maxime Moniot, Marie-Elisabeth French microsporidiosis network, Marie-Elisabeth Bougnoux, Philippe Poirier
Summary: This study reports 11 cases of intestinal microsporidiosis caused by E. hellem in non-HIV patients in France. All patients were immunocompromised and experienced diarrhea, with nearly 50% also experiencing weight loss. Treatment included discontinuation or decrease in immunosuppressive therapy for some patients, and albendazole administration for others. All patients recovered. Five different genotypes were identified based on the rRNA ITS sequence.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Mycology
Junichiro Hiruma, Honoka Nojo, Hitoshi Tsuchihashi, Hiromitsu Noguchi, Masataro Hiruma, Kazutoshi Harada, Rui Kano
Summary: In this study, T. interdigitale isolates were obtained from Japanese patients and their ITS types were investigated. The results showed that all 29 isolates belong to ITS type II, while one clinical isolate of T. mentagrophytes was similar to ITS type II*. Additionally, a terbinafine-resistant strain of T. interdigitale also belonged to ITS type II.
Article
Biochemistry & Molecular Biology
Qing Xian, Suyin Wang, Yanyan Liu, Shenglong Kan, Wei Zhang
Summary: The GC content of the ribosomal internal transcribed spacer 2 (ITS2) undergoes GC-biased evolution, with higher GC content than the adjacent 5.8S regions. The GCs are distributed in a heterogeneous manner in the ITS2 secondary structure, with paired regions being larger than unpaired regions, indicating selection for thermodynamic stability. Homogeneous ITS2 sequences are always GC-rich, supporting GC-biased gene conversion (gBGC) and concerted evolution of ITS2.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Gobena Ameni, Alebachew Messele Kebede, Aboma Zewude, Musse Girma Abdulla, Rahel Asfaw, Mesfin Mamo Gobena, Martina Kyalo, Francesca Stomeo, Balako Gumi, Teshale Sori
Summary: This study conducted a phylogenetic analysis of Histoplasma capsulatum isolated from cases of epizootic lymphangitis (EL) in horses in central Ethiopia and evaluated their relationship with isolates from other countries and clades. By analyzing the internal transcribed spacer (ITS) region of rRNA genes, the study identified different clades of H. capsulatum and revealed that the Ethiopian isolates were closely related to isolates from Latin America and Eurasia, but distantly related to isolates from North America.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Plant Sciences
Nikolai Friesen, Lisa Grutzmacher, Mikhail Skaptsov, Polina Vesselova, Vladimir Dorofeyev, Alexander N. Luferov, Nazgul Turdumatova, Georgii Lazkov, Sergei Smirnov, Alexander Shmakov, Herbert Hurka
Summary: The polymorph Allium pallasii s.l. from monotypic A. sect. Pallasia was studied using various methods, and it was found to be divided into two distinct species based on morphology, geography, cytology, and genetics. A. pallasii s. str. is found in North-East Kazakhstan, Western Siberia, and the Altai Mountains, while A. caricifolium is found in Kyrgyzstan, Northwest China, South-East Kazakhstan, and Zaysan Lake. Despite significant genetic differences, both species are sisters and are related to species of the A. sect. Codonoprasum (Subg. Allium). Allium caricifolium differs from A. pallasii s. str. in terms of taller stems, dense inflorescence, and longer filaments. The possible phylogenetic reasons for the separation of these species are discussed, and a nomenclature analysis of synonyms was conducted.
Article
Agronomy
Mostafa Nafaa, Samah Mohamed Rizk, Tahany Abdel-Ghafar Ahmed Aly, Mohamed Abdel-Salam Rashed, Diaa Abd El-Moneim, Abir Ben Bacha, Mona Alonazi, Mahmoud Magdy
Summary: In this study, fungal diversity in newly reclaimed land in Egypt was investigated. The results showed that these fungi can enhance nutrient availability in the soil and produce the plant growth hormone IAA. The findings suggest the potential of developing fungal biofertilizers for improving agriculture reclamation processes and practices.
Article
Horticulture
Majda El Amri, Moez Amri, El Mostafa Kadir, Zine El Abidine Triqui, Slimane Khayi, Rachid Mentag
Summary: In this study, the broomrape species attacking fennel in Morocco was identified as Phelipanche schultzii through morphological and molecular analysis. This is the first record of P. schultzii parasitizing fennel in Morocco, highlighting the need for urgent control measures to prevent its further spread.
Article
Agronomy
Pingping Lin, Xuguang Hu, Li Xue, Xinyi Li, Ping Wang, Xinwang Zhao, Muqing Zhang, Zuhu Deng, Fan Yu
Summary: The study analyzed the relationship and ploidy of wild sugarcane using DNA sequencing and fluorescence in situ hybridization. The results showed that rDNA sequences can be used as a useful marker for identifying the relationship and ploidy of wild sugarcane in sugarcane breeding.
Article
Microbiology
Shuqian Hu, Xiang Li, Xin Yin, Runmeng Li, Ruiyang Zhang, Junhao Zang, Yin Liu
Summary: This study developed a species-specific method for identification and classification of Pseudomonas based on ITS sequences combined with next-generation sequencing (NGS).
Article
Biotechnology & Applied Microbiology
Junbei Ni, Yuan Zhao, Ruiyan Tao, Lei Yin, Ling Gao, Ake Strid, Minjie Qian, Juncai Li, Yuanjun Li, Jiaqi Shen, Yuanwen Teng, Songling Bai
PLANT BIOTECHNOLOGY JOURNAL
(2020)
Article
Plant Sciences
Apekshika T. Premathilake, Junbei Ni, Jiaqi Shen, Songling Bai, Yuanwen Teng
Article
Plant Sciences
Ruiyan Tao, Wenjie Yu, Yuhao Gao, Junbei Ni, Lei Yin, Xiao Zhang, Hongxu Li, Dongsheng Wang, Songling Bai, Yuanwen Teng
Article
Plant Sciences
Apekshika T. Premathilake, Junbei Ni, Songling Bai, Ruiyan Tao, Mudassar Ahmad, Yuanwen Teng
Article
Plant Sciences
Junbei Ni, Apekshika T. Premathilake, Yuhao Gao, Wenjie Yu, Ruiyan Tao, Yuanwen Teng, Songling Bai
Summary: Ethylene induces anthocyanin biosynthesis in most fruits, but inhibits it in pears. The transcription factor PpERF105 activated the expression of PpMYB140, which then inhibited the anthocyanin biosynthesis in pears. The competition between PpMYB140 and PpMYB114 led to the formation of a complex that further inhibited anthocyanin biosynthesis.
Article
Plant Sciences
Jianzhao Li, Xinhui Yan, Mudassar Ahmad, Wenjie Yu, Zhizhong Song, Junbei Ni, Qinsong Yang, Yuanwen Teng, Hongxia Zhang, Songling Bai
Summary: The study found that alternative splicing of the PpDAM1 gene may play a crucial role in the pear flower bud dormancy process in 'Dangshansu' pear tree.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Plant Sciences
Qinsong Yang, Yuhao Gao, Xinyue Wu, Takaya Moriguchi, Songling Bai, Yuanwen Teng
Summary: This review focuses on the molecular regulation of endodormancy induction, maintenance, and release in floral buds of deciduous fruit trees, as well as recent advances in quantitative trait loci analysis of chilling requirements. The discussion includes phytohormones, epigenetic regulation, and the molecular network controlling endodormancy, centered on SVP and DAM genes. Understanding endodormancy can help in creating new cultivars with different chilling requirements.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Yuhao Gao, Qinsong Yang, Xinhui Yan, Xinyue Wu, Feng Yang, Jianzhao Li, Jia Wei, Junbei Ni, Mudassar Ahmad, Songling Bai, Yuanwen Teng
Summary: Dormancy-associated MADS-box (DAM) genes play a crucial role in regulating the endodormancy cycle in rosaceous plants. A high-quality genome assembly for the 'Cuiguan' pear (Pyrus pyrifolia) was constructed using PacBio and Hi-C technologies, revealing the differential expression of pear DAM genes and their repressive effects on bud break. Novel genes potentially involved in endodormancy release regulation were identified through RNA and chromatin immunoprecipitation sequencing analyses.
HORTICULTURE RESEARCH
(2021)
Article
Plant Sciences
Qinsong Yang, Xinyue Wu, Yuhao Gao, Junbei Ni, Jinjin Li, Ziqi Pei, Songling Bai, Yuanwen Teng
Summary: This study reveals the mechanism of how H3K4me3 marks are added to dormancy-related genes in perennial woody plants and uncovers a novel mechanism by which ABF3 integrates abscisic acid signaling and gibberellic acid catabolism during bud dormancy maintenance.
Article
Plant Sciences
Jia Wei, Qinsong Yang, Junbei Ni, Yuhao Gao, Yinxin Tang, Songling Bai, Yuanwen Teng
Summary: This study investigates the effect of defoliation on pear trees and finds that defoliation-induced auxin efflux from buds accelerates bud paradormancy release, leading to out-of-season flowering. The findings are important for understanding the mechanism of bud dormancy and developing methods to inhibit early defoliation-induced out-of-season flowering.
Article
Plant Sciences
Ahmed Alabd, Mudassar Ahmad, Xiao Zhang, Yuhao Gao, Lin Peng, Lu Zhang, Junbei Ni, Songling Bai, Yuanwen Teng
Summary: This study identified and functionally characterized a light-inducing WRKY transcription factor, PpWRKY44, in pear. PpWRKY44 promotes anthocyanin accumulation in pear and regulates its transcription by binding to the PpMYB10 promoter. These results reveal the mechanism of PpWRKY44 in the transcriptional regulation of fruit peel coloration in red pears.
HORTICULTURE RESEARCH
(2022)
Article
Agriculture, Multidisciplinary
Junbei Ni, Yifei Liao, Manman Zhang, Chen Pan, Qinsong Yang, Songling Bai, Yuanwen Teng
Summary: This study analyzed the effects of blue light on the appearance and internal quality of mango fruit, revealing the underlying mechanisms behind the regulation of anthocyanin, carotenoid, and sucrose biosynthesis pathways. Key blue light signaling-related genes and phytohormones were found to be involved in these pathways. The study provides new insights into the regulatory effects of light on the appearance and internal quality of mango fruit.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Plant Sciences
Ahmed Alabd, Haiyan Cheng, Mudassar Ahmad, Xinyue Wu, Lin Peng, Lu Wang, Shulin Yang, Songling Bai, Junbei Ni, Yuanwen Teng
Summary: Salinity treatment induces malate accumulation in pear fruit, calli, and plantlets. PpWRKY44 and PpABF3 transcription factors play crucial roles in promoting malate accumulation in response to salinity. This research provides insights into the molecular mechanism of salinity-induced malate accumulation and its impact on fruit quality.
Proceedings Paper
Agronomy
Y. Teng, P. Yu, S. Bai, S. Jiang
Summary: The classification and origin of Asian pear species have been clarified in this study, with DNA marker research revealing the genetic relationships between ussuriensis pear, pyrifolia pear, and bretschneideri pear varieties. New nomenclature and origin hypotheses have been proposed based on these findings.
PROCEEDINGS OF THE II INTERNATIONAL SYMPOSIUM ON FRUIT CULTURE ALONG SILK ROAD COUNTRIES - FRUITS FOR THE FUTURE
(2021)
Proceedings Paper
Agronomy
Y. Teng
Summary: Pyrus species are widespread throughout the Eurasian continent and are divided into occidental and oriental pears. Elucidating phylogenetic relationships in Pyrus is challenging due to lack of distinguishing characters and frequent hybridization. Recent studies suggest that reticulate evolution caused by hybridization is a major evolutionary strategy in Pyrus species.
XIII INTERNATIONAL PEAR SYMPOSIUM
(2021)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
