Article
Plant Sciences
Yang Zhang, Yingying Liu, Xueying Wang, Ruiqi Wang, Xuebing Chen, Shuang Wang, Hairong Wei, Zhigang Wei
Summary: In this study, a plant-specific transcription factor PtrWOX13A was identified and characterized for its role in secondary cell wall formation in Populus trichocarpa. Overexpression of PtrWOX13A resulted in enhanced growth potential and increased secondary cell wall thickness, fiber length, and lignin and hemicellulose contents. PtrWOX13A directly activated its target genes through binding to specific cis-elements in their promoter regions. Furthermore, PtrWOX13A was found to be responsive to gibberellin signaling and could regulate genes involved in GA homeostasis. The discovery of PtrWOX13A's role in secondary cell wall formation and its regulatory functions has important implications for improving wood quality through genetic engineering.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Jing Yu, Chenguang Zhou, Danning Li, Shuang Li, Ying-Chung Jimmy Lin, Jack P. Wang, Vincent L. Chiang, Wei Li
Summary: In this study, the formation mechanism of tension wood in Populus trichocarpa was analyzed using laser capture microdissection and full transcriptome RNA-sequencing. It was found that PtrLBD39 and PtrLBD22 are key regulatory genes controlling tension wood formation by regulating a set of tension wood-related genes.
PLANT COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Pei-Liang Wu, Xiao Chun Ling, Eugene Yu-Chuan Kang, Kuan-Jen Chen, Nan-Kai Wang, Laura Liu, Yen-Po Chen, Yih-Shiou Hwang, Chi-Chun Lai, Shun-Fa Yang, Wei-Chi Wu
Summary: The study found that TIMP-2 gene polymorphisms are associated with the risk and severity of retinopathy of prematurity (ROP). Individuals with rs12600817 gene polymorphism are more likely to develop ROP and have a higher risk. Individuals with rs2889529 gene polymorphism are correlated with the treatment response of ROP.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yingying Liu, Ruiqi Wang, Jiajie Yu, Shan Huang, Yang Zhang, Hairong Wei, Zhigang Wei
Summary: This study systematically investigated the PtrARF gene family and provided comprehensive information on their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics. The expression patterns of PtrARF genes were analyzed, and it was found that certain genes were preferentially expressed in primary stems and participated in different phases of wood formation. Some PtrARF genes showed different responses to exogenous IAA and ABA treatment. Three PtrARF proteins were characterized and their interactions with other proteins were demonstrated. This study lays the foundation for future research on PtrARF genes in tree development and growth, especially wood formation, in response to cellular signaling and environmental cues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Ruiqi Wang, Mengxuan Reng, Shuanghui Tian, Cong Liu, He Cheng, Yingying Liu, Huaxin Zhang, Muhammad Saqib, Hairong Wei, Zhigang Wei
Summary: This study utilized miRNA expression profiling to investigate the regulation of miRNA species on lignocellulosic synthesis in Populus trichocarpa stems at three different developmental stages. The results revealed differential expression of miRNAs and their candidate target genes, as well as the involvement of miRNAs in regulating processes such as cell division, wall modification, and lignification. Overall, the findings advance understanding of individual miRNAs and their diverse roles in the dynamic regulation of secondary growth in woody tree species.
G3-GENES GENOMES GENETICS
(2021)
Article
Immunology
Xiaohua Liang, Jian Wang, Yongshi Liu, Lin Wei, Feng Tian, Jianyong Sun, Guoliang Han, Yan Wang, Chao Ding, Zhaolei Guo
Summary: SNPs of COX/PGE2 pathway-related genes are associated with an elevated risk of lung cancer, providing new clues for understanding the pathogenesis and personalized treatment of the disease.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Abdou Rahmane Wade, Harold Durufle, Leopoldo Sanchez, Vincent Segura
Summary: Using 241 poplar genotypes, this study generated large datasets of phenotypic, genomic, and transcriptomic information, and built prediction models for traits based on SNPs and transcripts. Integration analysis revealed a negative correlation between changes in predictability and predictor ranking for trans eQTLs. This study provides a novel method to explore data integration.
Article
Genetics & Heredity
Marcos Calderon, Manuel J. More, Gustavo A. Gutierrez, Federico Abel Ponce de Leon
Summary: The project aimed to develop an alpaca single nucleotide polymorphism (SNP) microarray to improve the economic benefits and quality of life for small farm producers. The incorporation of molecular marker technology overcame current limitations for genetic improvement programs.
Article
Multidisciplinary Sciences
Ishtiaque Ahammad, Tabassum Binte Jamal, Arittra Bhattacharjee, Zeshan Mahmud Chowdhury, Suparna Rahman, Md Rakibul Hassan, Mohammad Uzzal Hossain, Keshob Chandra Das, Chaman Ara Keya, Md Salimullah
Summary: GRIN2A is a gene encoding NMDA receptors in the central nervous system, playing a crucial role in synaptic transmission, plasticity, and excitotoxicity. Variants in this gene, particularly the I463S variant, are predicted to have deleterious effects on protein structure and function. Bioinformatics tools were used to assess the impact of these variants, providing valuable insights for future research on GRIN2A-related diseases.
Article
Multidisciplinary Sciences
Yaxin Xu, Wentao Xue, Hongwei Gao, Jiabo Cui, Lingzhi Zhao, Chongge You
Summary: Studies have shown that TLRs gene polymorphisms may play a significant role in HBV and HCV infections, with certain SNPs affecting disease progression and prognosis. However, the exact mechanism of action still requires further exploration.
Article
Neurosciences
Qing Tian, Xiaohui Sun, Chengqian Li, Yong Yang, Binghui Hou, Anmu Xie
Summary: This study evaluates the link between CD33 single nucleotide polymorphisms (SNPs) and vulnerability to Parkinson's disease among the northern Chinese Han population. The findings suggest that CD33 SNPs are associated with Parkinson's disease and may contribute to genetic risk. The study recommends further research with larger sample sizes and diverse populations to explore the relationship between CD33 polymorphisms and Parkinson's disease.
NEUROSCIENCE LETTERS
(2023)
Article
Materials Science, Paper & Wood
Donata Krutul, Jan Szadkowski, Andrzej Antczak, Michal Drozdzek, Andrzej Radomski, Stanislaw Karpinski, Janusz Zawadzki
Summary: The study examined the changes in concentration of selected heavy metals in Populus trichocarpa wood before and after steam explosion and liquid hot water pretreatments, finding that except for iron, the concentration of other elements changed minimally after pretreatment. During the pretreatment process, wood biomass absorbed iron emitted from the equipment at high temperatures.
Article
Biotechnology & Applied Microbiology
Zixue Xuan, Yiwen Zhang, Jinying Jiang, Xiaowei Zheng, Xiaoping Hu, Xiuli Yang, Yanfei Shao, Guobing Zhang, Ping Huang
Summary: This study identified m(6)A-SNPs associated with breast cancer and explored their potential functions. The SNPs rs4829 and rs9610915 were found to potentially be associated with breast cancer due to having eQTL signals, altered gene expression, and proximity to m(6)A modification sites. Further research is needed to clarify how genetic variation affects epigenetic modification and its functions in breast cancer pathogenesis.
Article
Genetics & Heredity
Milena Neira-Goulart, Nathalia Beatriz Ramos de Sa, Marcelo Ribeiro-Alves, Hugo Perazzo, Kim Mattos Geraldo, Maria Pia Diniz Ribeiro, Sandra Wagner Cardoso, Beatriz Grinsztejn, Valdilea G. Veloso, Larissa Rodrigues Gomes, Andressa da Silva Cazote, Dalziza Victalina de Almeida, Carmem Beatriz Wagner Giacoia-Gripp, Fernanda Heloise Cortes, Mariza Goncalves Morgado
Summary: This study explores the impact of genetic variations in inflammasome genes on the clinical course of COVID-19. The findings suggest that certain genetic variations may influence the progression to critical outcomes, such as mechanical ventilation support or death, in individuals with COVID-19.
Article
Biochemistry & Molecular Biology
Laura Massarenti, Christina Aniol-Nielsen, Christian Enevold, Henrik Toft-Hansen, Claus Henrik Nielsen
Summary: Single nucleotide polymorphisms (SNPs) in insulin and insulin receptor genes may influence the interaction between the two molecules, and anti-insulin antibodies (IAs) may be associated with insulin treatment in patients with diabetes. This study found that two SNPs in the human insulin gene and two SNPs in the insulin receptor gene were associated with type 1 diabetes and glycaemic control.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Ecology
Marissa Lee, Jeff R. Powell, Brad Oberle, Faride Unda, Shawn D. Mansfield, Rhiannon Dalrymple, Jessica Rigg, William K. Cornwell, Amy E. Zanne
Summary: Microbial communities, wood traits, and environmental filtering all play important roles in the decay process. This study found that initial wood attributes have a greater influence on decay trajectories than the composition of microbial communities. Wood with smaller size, lower density, higher water content, lower nitrogen content, and lower lignin concentration decomposes faster and more consistently.
FUNCTIONAL ECOLOGY
(2022)
Article
Plant Sciences
Yingxuan Ma, Colleen P. MacMillan, Lisanne de Vries, Shawn D. Mansfield, Pengfei Hao, Julian Ratcliffe, Antony Bacic, Kim L. Johnson
Summary: This study suggests that FLA11 and FLA12 may act as cell surface sensors in plant xylem cells, allowing them to sense mechanical stimuli and regulate secondary cell wall (SCW) development. Overexpression of FLA11 promotes earlier SCW development, while overexpression of FLA12 increases cellulose content. These proteins play a role in modulating SCW responses to mechanical stress.
Article
Multidisciplinary Sciences
J. Stejskal, J. Klapste, J. Cepl, Y. A. El-Kassaby, M. Lstiburek
Summary: This study assessed the accuracies of breeding values and response to selection using traditional pedigree and genomic-based evaluation methods in forest tree breeding. The results showed that clonal replication in progeny testing improved selection accuracy, but the use of genomic information did not significantly enhance genetic gains.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Yaseen Mottiar, Rebecca A. Smith, Steven D. Karlen, John Ralph, Shawn D. Mansfield
Summary: This study identified a eudicot species, kenaf, that naturally contains p-coumaroylated lignin. A novel acyltransferase HcPMT was also identified and heterologous expression of this enzyme in hybrid poplar trees resulted in the incorporation of pCA in lignin.
Article
Biotechnology & Applied Microbiology
Yaseen Mottiar, Steven D. Karlen, Robyn E. Goacher, John Ralph, Shawn D. Mansfield
Summary: This study demonstrated the potential of producing more p-hydroxybenzoate in transgenic poplar trees, which could be used in the production of high-value bioproducts. The study also emphasized the importance of substrate supply in lignin engineering.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Shuai Nie, Shi-Wei Zhao, Tian-Le Shi, Wei Zhao, Ren-Gang Zhang, Xue-Chan Tian, Jing-Fang Guo, Xue-Mei Yan, Yu-Tao Bao, Zhi-Chao Li, Lei Kong, Hai-Yao Ma, Zhao-Yang Chen, Hui Liu, Yousry A. El-Kassaby, Ilga Porth, Fu-Sheng Yang, Jian-Feng Mao
Summary: This study compares two parental species with different flower colors and finds that the increase in long terminal repeat retrotransposons has led to an increase in genome size and specific gene regulatory changes resulting in different flower pigmentation. The study employs a multi-omics strategy to unravel the complex divergence between two important azaleas and provides references for further functional genetics and molecular breeding.
HORTICULTURE RESEARCH
(2023)
Article
Agronomy
Jaco-Pierre van der Merwe, Tongli Wang, Charlie Clarke, Shawn D. Mansfield
Summary: This study developed temperature and rainfall models for specific plantations in South Africa, considering global position, altitude, slope, aspect, and topographic position indices. The local climate models were found to be more accurate than global models and improved the understanding of the impact of terrain features on regional climate and tree growth.
AGRICULTURAL AND FOREST METEOROLOGY
(2023)
Review
Biodiversity Conservation
Myriam Heuertz, Silvia B. Carvalho, Juan Galindo, Baruch Rinkevich, Piotr Robakowski, Tsipe Aavik, Ilhan Altinok, Julia M. I. Barth, Helena Cotrim, Roos Goessen, Santiago C. Gonzalez-Martinez, Tine Grebenc, Sean Hoban, Alexander Kopatz, Barry J. McMahon, Ilga Porth, Joost A. M. Raeymaekers, Sabrina Traeger, Alejandro Valdecantos, Adriana Vella, Cristiano Vernesi, Pauline Garnier-Gere
Summary: Conserving biodiversity at genetic and community levels is crucial for the provision of ecosystem services. However, the application of genomics in biodiversity conservation and ecosystem service management is currently limited, primarily focusing on flagship species. To bridge this gap, a framework is proposed to guide genomics applications in management, including population supplementation, assisted migration, delimitation of conservation areas, and solving conservation trade-offs. Effective implementation of genomics-informed management actions requires collaboration between scientists and ecosystem service managers along with standardized workflows and training for managers.
BIOLOGICAL CONSERVATION
(2023)
Article
Plant Sciences
Shuai Nie, Xue-Chan Tian, Lei Kong, Shi-Wei Zhao, Zhao-Yang Chen, Si-Qian Jiao, Yousry A. El-Kassaby, Ilga Porth, Fu-Sheng Yang, Wei Zhao, Jian-Feng Mao
Summary: This study reveals the origin and evolutionary history of Ericales, uncovering its ancient complex allopolyploid origin and detecting extensive gene loss following polyploidization. This finding provides a new explanation for genetic variation and adaptive diversity in Ericales.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Microbiology
Anna Fijarczyk, Louis Bernier, Monique L. Sakalidis, Carmen M. Medina-Mora, Ilga Porth
Summary: Vascular wilts are important diseases caused by plant pathogenic fungi that cause rapid death of plants. Genetic mechanisms of pathogenesis in wilt-causing fungi have been investigated, but not compared to wilt-causing fungi causing oak wilt or Dutch elm disease. In this study, 20 whole genome assemblies of wilt-causing fungi were analyzed, together with 56 other species, to trace expansions and contractions of pathogenicity-related genes. Wilt-causing pathogens evolved seven times, with changes in different classes of genes. Common gains and losses of genes in secondary metabolite clusters were found in groups of wilt pathogens. Carbohydrate metabolic genes were enriched in gene family expansions of wilt pathogen groups. The study highlights the importance of pathogenicity-related genes and carbohydrate metabolism in wilt-causing fungi.
Article
Plant Sciences
Wen-Bo Wang, Xiang-Feng He, Xue-Mei Yan, Bo Ma, Cun-Fu Lu, Jing Wu, Yi Zheng, Wen-He Wang, Wen-Bo Xue, Xue-Chan Tian, Jing-Fang Guo, Yousry A. A. El-Kassaby, Ilga Porth, Ping-Sheng Leng, Zeng-Hui Hu, Jian-Feng Mao
Summary: Quercus dentata Thunb., a dominant tree species in northern China, has ecological and ornamental value due to its adaptability and beautiful autumn coloration. This study investigates the genes and mechanisms involved in leaf color transition and provides a high-quality genome assembly and metabolome resources. The MYB-bHLH-WD40 transcription activation complex and QdNAC and QdMYB transcription factors are identified as key regulators in anthocyanin biosynthesis and leaf senescence. These findings enrich the knowledge of Quercus genomics and contribute to the understanding of its ornamental and adaptive characteristics.
Article
Multidisciplinary Sciences
Shi-Wei Zhao, Jing-Fang Guo, Lei Kong, Shuai Nie, Xue-Mei Yan, Tian-Le Shi, Xue-Chan Tian, Hai-Yao Ma, Yu-Tao Bao, Zhi-Chao Li, Zhao-Yang Chen, Ren-Gang Zhang, Yong-Peng Ma, Yousry A. El-Kassaby, Ilga Porth, Wei Zhao, Jian-Feng Mao
Summary: In this study, a haplotype-resolved chromosome-scale genome assembly for Coriaria nepalensis was obtained using PacBio HiFi sequencing and Hi-C scaffolding techniques. The assembly has a size of approximately 620 Mb with a contig N50 of 11 Mb and 99.9% of the sequences anchored to 40 pseudochromosomes. A total of 60,862 protein-coding genes, 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs were predicted. This chromosome-scale genome provides a valuable resource for studying the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis in C. nepalensis.
Article
Plant Sciences
Xue-Mei Yan, Shan-Shan Zhou, Hui Liu, Shi-Wei Zhao, Xue-Chan Tian, Tian-Le Shi, Yu-Tao Bao, Zhi-Chao Li, Kai-Hua Jia, Shuai Nie, Jing-Fang Guo, Lei Kong, Ilga M. Porth, Jian-Feng Mao
Summary: Terpenes and terpenoids play a crucial role in plant defense, development, and oil composition. Understanding the differentiation of terpene synthase (TPS) genes provides valuable insights for genetic improvement of oil-producing plants. This study investigates the origin and evolution of TPS genes, revealing potential gene fusion events in the ancestor of land plants and mutual transfer between microbes and plants.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biodiversity Conservation
Roos Goessen, Nathalie Isabel, Christian Wehenkel, Nathalie Pavy, Lisa Tischenko, Lyne Touchette, Isabelle Giguere, Marie-Claude Gros-Louis, Jerome Laroche, Brian Boyle, Raju Soolanayakanahally, Karen Mock, Javier Hernandez-Velasco, Sergio Leonel Simental-Rodriguez, Jean Bousquet, Ilga M. Porth
Summary: This study investigates the genetic structure, reproductive type, and adaptive responses of aspen populations. The findings reveal the patterns of genetic variation as well as the selection responses to temperature and precipitation variations. The study uncovers the untapped adaptive potential of aspen populations, providing a basis for climate-resilient revegetation.
PLANTS PEOPLE PLANET
(2022)
Article
Forestry
Jie Xu, Hang Luo, Shan-Shan Zhou, S. Qian Jiao, Kai-Hua Jia, Shuai Nie, Hui Liu, Wei Zhao, Xiao-Ru Wang, Yousry A. El-Kassaby, Ilga Porth, Jian-Feng Mao
Summary: This study evaluated the physiological and transcriptomic responses of Pinus tabuliformis Carr. to high-irradiance UV-B and UV-C waves, revealing both communalities and differences in the plant's responses to the two types of UV radiation. The research found that both UV-B and UV-C significantly inhibited photosynthesis while enhancing antioxidant capacity, flavonoid production, and stress resistance pathways in pine, indicating a shift towards enhanced defensive metabolism. The study isolated distinct subnetworks related to photoreceptor-mediated signal transduction, Fv/Fm regulation, and flavonoid biosynthesis in response to UV-B and UV-C radiation.