Article
Plant Sciences
Raul Castanera, Pol Vendrell-Mir, Amelie Bardil, Marie-Christine Carpentier, Olivier Panaud, Josep M. Casacuberta
Summary: Transposable elements (TEs) are important genetic elements with MITEs being a subset that are highly present in plant genomes and closely linked to genes. A portion of MITE insertions have become fixed in rice during domestication while others remain at low frequencies. MITE TIP-GWAS studies reveal that MITEs may have greater impact on agronomically important traits than SNPs, showcasing evidence of replicative amplification.
Article
Plant Sciences
Hiroki Nagata, Akemi Ono, Kaoru Tonosaki, Taiji Kawakatsu, Yutaka Sato, Kentaro Yano, Yuji Kishima, Tetsu Kinoshita
Summary: DNA methylation is necessary for maintaining genome integrity, but under certain circumstances, transposable elements (TEs) can escape from this repression and reactivate transcription. This study investigated the expression patterns of TE transcripts during rice endosperm development and found dynamic regulation of TE activity, particularly for miniature inverted-repeat TEs (MITEs).
Review
Plant Sciences
Joseph L. L. Pegler, Jackson M. J. Oultram, Christopher W. G. Mann, Bernard J. J. Carroll, Christopher P. L. Grof, Andrew L. L. Eamens
Summary: The miniature inverted-repeat transposable elements (MITEs) have contributed significantly to expanding the miRNA repertoire of angiosperms by transposing within gene-rich regions and producing noncoding RNA (ncRNA) that can be processed into miRNA.
Article
Plant Sciences
Lianyu Lin, Anupma Sharma, Qingyi Yu
Summary: This study identified and characterized MITEs in the pineapple genome, revealing that Ac-mMITEs are the most abundant and likely derived from Mutator-like DNA transposon. Ac-mMITEs exhibit preference for insertion in (TA) n microsatellite regions, potentially as a damage-limiting strategy during co-evolution. The differential impact on gene expression between mt-MITEs and ml-MITEs suggests a potential mechanism for the amplification of mt-MITEs.
Article
Horticulture
Hyeonju Jeong, Young Bok Yun, Seung Yong Jeong, Younsup Cho, Sunggil Kim
Summary: Nucellar embryony, an important trait in citrus breeding, is caused by the transposition of a MITE in the CitRWP gene promoter. An MITE family called DTM10 was identified, which had the highest homology among 110 citrus MITE families. Analysis of DTM10 elements in different Citrinae species revealed common ancestors for the transposed MITEs in CitRWP. In addition, DNA secondary structures and polymerase jumping were predicted and observed in the study. Three complementary molecular markers based on MITE insertion and single nucleotide polymorphism were developed for reliable genotyping in citrus.
SCIENTIA HORTICULTURAE
(2023)
Review
Cell Biology
Syed Farhan Ahmad, Worapong Singchat, Thitipong Panthum, Kornsorn Srikulnath
Summary: Snakes have unique biological features and evolutionary characteristics, making them fascinating model systems for studying genomic evolution and the relationship between variation at the genomic level and phenotypic-level evolution. Snake genomes, similar to other eukaryotic genomes, are composed of a large proportion of repetitive DNA, including transposable elements and satellite repeats. The significance of repetitive DNA in snake genomes, particularly its structural and functional roles, remains unclear. The study highlights the diversity and composition of repetitive DNA in snake genomes, presenting snakes as an emerging and important model system for understanding the impact of repetitive DNA under sex and microchromosome evolution. Certain repetitive elements in snakes are found to be transcriptionally active and show highly dynamic lineage-specific patterns as repeat sequences, suggesting that they may trigger genomic mechanisms contributing to adaptive evolution in snakes. New approaches are reviewed for studying the expression of repetitive elements in complex genomes, such as snakes, to further explore the role of genomic repeats in shaping snake evolution.
Article
Biochemistry & Molecular Biology
Xiaowei Wu, Yan Liang, Hengbin Gao, Jiyao Wang, Yan Zhao, Lekai Hua, Yundong Yuan, Ahong Wang, Xiaohui Zhang, Jiafan Liu, Jie Zhou, Xiangbing Meng, Dahan Zhang, Shaoyang Lin, Xuehui Huang, Bin Han, Jiayang Li, Yonghong Wang
Summary: The study identified a previously unrecognized regulatory gene OsREM20 that controls grain number per panicle (GNP) in rice, and revealed that genetic variation in the IR sequence of the OsREM20 promoter affects its expression level and contributes to GNP variation among rice varieties. The findings suggest a promising strategy for improving rice production by manipulating the cis-regulatory element-containing IR sequence in the OsREM20 promoter.
Article
Entomology
Khouloud Klai, Marwa Zidi, Benoit Chenais, Francoise Denis, Aurore Caruso, Nathalie Casse, Maha Mezghani Khemakhem
Summary: MITEs are ubiquitous, non-autonomous class II transposable elements. The moths Helicoverpa armigera and Helicoverpa zea are recognized as the two most serious pest species within the genus. Moreover, these pests have the ability to develop insecticide resistance. In this study, a genome-wide analysis of MITEs present in H. armigera and H. zea genomes was conducted using the bioinformatics tool MITE tracker. A total of 3570 and 7405 MITE sequences were identified in the H. armigera and H. zea genomes, respectively. Comparative analysis of the identified MITE sequences led to the identification of 18 families, comprising 140 MITE members in H. armigera and 161 MITE members in H. zea. The analysis of MITE insertion sites in defensome genes showed intronic insertions of 11 MITEs in H. armigera and one MITE in H. zea. These insertions could be involved in the insecticide resistance observed in these pests.
Article
Plant Sciences
Benjamin Ewa Ubi, Yasir Serag Alnor Gorafi, Beery Yaakov, Yuki Monden, Khalil Kashkush, Hisashi Tsujimoto
Summary: Transposable elements make up a large portion of the bread wheat genome and play a significant role in wheat evolution and adaptation. This study examined the efficiency of TE insertion polymorphism markers as genetic markers in wheat and related species. The results showed variation in MITE insertions based on ploidy, and the phylogenetic trees constructed were consistent with the evolutionary history of the species. The study also demonstrated the stability of MITE insertions, making them promising markers for genomic studies in wheat.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Sonia Campo, Ferran Sanchez-Sanuy, Rosany Camargo-Ramirez, Jorge Gomez-Ariza, Patricia Baldrich, Lidia Campos-Soriano, Mauricio Soto-Suarez, Blanca San Segundo
Summary: miR812w is a newly identified member of the rice miRNA family that plays a role in disease resistance, synthesized by DCL3 and loaded into AGO4 protein. Overexpression of miR812w enhances resistance to rice blast fungus, while CRISPR/Cas9-mediated editing of MIR812w increases disease susceptibility.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Plant Sciences
Xizhi Luo, Shiyu Chen, Yu Zhang
Summary: This study re-annotated repeats of 459 plant genomes and released a new database called PlantRep. PlantRep sheds light on repeat evolution and provides fundamental data for in-depth exploration of genomes.
PLANT CELL REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Thomas M. Beckermann, Wentian Luo, Catherine M. Wilson, Ruth Ann Veach, Matthew H. Wilson
Summary: The study found that there is restricted cross-species transposition activity within the piggyBac family, with PGBD5 unable to mobilize piggyBac transposons and bind piggyBac terminal repeats.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Haidong Yan, David C. Haak, Song Li, Linkai Huang, Aureliano Bombarely
Summary: Transposable elements (TEs) are a major force in the production of new alleles during domestication, but their complexity has limited their use in association studies. A TE genotyping pipeline (TEmarker) was developed and applied to a whole-genome GWAS study on Oryza sativa subsp. japonica to identify genetic elements associated with agronomic traits. TE markers were able to recover a large proportion of SNP-based GWAS peaks and reduce false positives associated with SNP marker linkage disequilibrium. The study also revealed positive selection on TEs associated with agronomic traits and identified insertion and deletion variants potentially resulting from the direct action of TEs.
PLANT COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Brandon Weissbourd, Tsuyoshi Momose, Aditya Nair, Ann Kennedy, Bridgett Hunt, David J. Anderson
Summary: Jellyfish are radially symmetric organisms without a brain, achieving organismal behaviors through coordinated interactions between autonomously functioning body parts. The Clytia hemisphaerica model introduced in this study revealed a previously unrecognized level of structured neural organization, providing a platform for studies of neural function, behavior, and evolution within a clade of marine organisms of ecological and economic importance.
Article
Agronomy
Huanhuan Wang, Zhenyang Liao, Yingying Gao, Lingge Zhang, Wenlong Lei, Hantang Huang, Siru Lei, Mengwei Jiang, Shuai Chen, Longqing Shi
Summary: Through the identification of transposon insertion sites in susceptible and resistant rice varieties, six possible candidate insect resistance genes were potentially located. Quantitative analysis showed a significant difference in gene expression between insect-resistant and insect-susceptible varieties. This study provides insights into the functional analysis of transposons and population transposon polymorphisms, and offers a theoretical foundation for the development of insect-resistant rice varieties.
News Item
Plant Sciences
Z. Y. Sun, Y. H. Zhang, Q. Q. Xu, Z. X. Chen, L. Xie, B. Z. Mao
Article
Chemistry, Applied
Dong Li, Xiaochen Zhang, Hongxia Qu, Li Li, Bizeng Mao, Yanqun Xu, Xingyu Lin, Zisheng Luo
Editorial Material
Plant Sciences
K. R. Yan, Y. H. Zhang, C. B. Yang, C. N. Ma, B. W. He, B. Z. Mao
Article
Multidisciplinary Sciences
Xinqiao Zhan, Jufeng Qi, Bin Zhou, Bizeng Mao
SCIENTIFIC REPORTS
(2020)
Article
Food Science & Technology
Juan Xu, CongMei Xiao, HaiShun Xu, ShengXiang Yang, ZheMing Chen, HongZhen Wang, BingSong Zheng, BiZeng Mao, XueQian Wu
Summary: Ganoderma lucidum sterols (GLS) exhibit anti-inflammatory effects by inhibiting cell polarization and the release of proinflammatory mediators. The anti-inflammatory activity of GLS is mediated through MAPK and NF-kappa B pathways, suggesting a synergistic effect with Ganoderma polysaccharides and triterpenes.
FOOD AND CHEMICAL TOXICOLOGY
(2021)
Article
Plant Sciences
Xinqiao Zhan, Yichun Qian, Bizeng Mao
Summary: In this study, eight DcaNGLS genes were identified from the genome of Dendrobium catenatum, consisting of three types of synthases. These genes showed high conservation during evolution. Gene expression analysis revealed that DcaNGLSs were highly expressed in specific tissues and growth stages, and were induced by freezing, salt stress, and drought.
Article
Agricultural Engineering
Chuanbao Yang, Keru Yan, Changnian Ma, Li Xie, Wei Wang, Weiliang Chen, Bizeng Mao
Summary: Plant virus elimination can greatly improve soil quality, bacterial diversity, and both aboveground and belowground productivity, leading to a shift in soil bacteria from oligotrophy to copiotrophy. This study highlights the potential of plant virus elimination as a new approach for future environmental breeding programs.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Plant Sciences
S. Ali Mirghasempour, David J. Studholme, Weiliang Chen, Dongzhu Cui, Bizeng Mao
Summary: This study reports the first occurrence of F. nirenbergiae causing C. sativus corm rot in China and worldwide. The whole genome sequences of highly virulent F. nirenbergiae strains were obtained, contributing to the understanding of genetic diversity, genomic information, and host determination. This research provides important insights for management measures against this hazardous disease.
Article
Plant Sciences
Xinqiao Zhan, Jufeng Qi, Qingwen Shen, Bowei He, Bizeng Mao
Summary: This study revealed the regulation of phenylpropanoid metabolism during freezing stress and post-freezing recovery in Dendrobium officinale. The results showed significant increases in anthocyanins and flavonols during post-freezing recovery. Transcriptomics analysis identified genes related to quercetin derivative production. In addition, hormone-related genes and specific genes associated with freezing stress and hormone responses were also identified. Overall, this study provides valuable insights into the phenylpropanoid metabolism in response to freezing stress and can contribute to enhancing freezing tolerance in D. officinale.
JOURNAL OF PLANT INTERACTIONS
(2022)
Article
Microbiology
Seyed Ali Mirghasempour, David J. Studholme, Weiliang Chen, Weidong Zhu, Bizeng Mao
Summary: This study isolated 261 Fusarium-like isolates from rotted saffron corms in China and identified the species using molecular analysis, revealing that F. nirenbergiae, F. commune, and F. annulatum are the causative agents of saffron corm rot. The research expands our knowledge about the diversity of Fusarium species associated with saffron corm rot.
Article
Biochemistry & Molecular Biology
Xinqiao Zhan, Yichun Qian, Bizeng Mao
Summary: This study investigated the distribution of terpene compounds and the characterization of terpene biosynthesis-related genes in Dendrobium catenatum. The results showed tissue-specific accumulation of terpene compounds and revealed the expression patterns of terpene biosynthesis-related genes in different organs. The study also identified the regulatory elements and environmental factors influencing terpene biosynthesis. These findings provide valuable insights for further functional investigation and regulation of terpene biosynthesis in Dendrobium.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Seyed Ali Mirghasempour, Themis Michailides, Weiliang Chen, Bizeng Mao
Summary: This study reports the first identification of Fusarium concentricum, Fusarium curvatum, Fusarium fujikuroi, Fusarium nirenbergiae, and Fusarium stilboides as the causal agents of dieback disease in Dendrobium officinale in China and worldwide. The study provides valuable data on the diversity and pathogenicity of Fusarium populations.
Article
Biology
Xinqiao Zhan, Yichun Qian, Bizeng Mao
Summary: This study identified 52 GELP genes in Dendrobium catenatum, revealing their crucial roles in plant growth and stress responses. Co-expression analysis of the transcriptome and lipidome identified a GELP gene positively correlated with lipids, and another gene specially induced by freezing.
Article
Biochemistry & Molecular Biology
Xinqiao Zhan, Yichun Qian, Bizeng Mao
Summary: This study used a multi-omics strategy to investigate the metabolic flow during freezing treatment and post-freezing recovery in Dendrobium catenatum. Proteome and lipidome assays revealed significant remodeling in the phospholipid category and upregulation of most sphingolipids during freezing. Integrated multi-omics analysis identified significant changes in the expression levels of mRNAs and encoding proteins associated with phospholipid editing and galactolipid remodeling. These findings provide insights into improving the freezing tolerance of D. catenatum through genetic engineering.
Article
Chemistry, Multidisciplinary
Zihan Zhang, Jiajin Song, Houpu Zhang, Zhiruo Zheng, Tongxin Li, Shenggan Wu, Bowei He, Bizeng Mao, Yunlong Yu, Hua Fang
Summary: Herbal medicines are at risk of contamination by pesticides and heavy metals, which can be harmful to human health. This study developed a modified QuEChERS pre-treatment method combined with HPLC/GC-MS/MS to determine pesticide residues in Dendrobium candidum. The study also used microwave digestion combined with ICP-MS to detect heavy metal residues in Dendrobium candidum. The results showed acceptable levels of pesticide and heavy metal residues in the samples, posing no significant health risk to the general population.
