Browsing by Person "Xi, Lin"

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Genome-wide development of simple sequence repeat (SSR) markers at 2-Mb intervals in lotus (Nelumbo Adans.)
(2025) Liu, Fengluan; Xi, Lin; Fu, Naifeng; Liu, Fengluan; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, No. 3888 Chenhua Road, Songjiang District, 201602, Shanghai, China; Xi, Lin; Department of Plant Systems Biology, University of Hohenheim, 70599, Stuttgart, Germany; Fu, Naifeng; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, No. 3888 Chenhua Road, Songjiang District, 201602, Shanghai, China
Background: Despite the rapid advancement of high-throughput sequencing, simple sequence repeats (SSRs) remain indispensable molecular markers for various applied and research tasks owing to their cost-effectiveness and ease of use. However, existing SSR markers cannot meet the growing demand for research on lotus ( Nelumbo Adans.) given their scarcity and weak connections to the lotus genome. Methods: Using whole-genome resequencing, active SSR loci were identified throughout the genomes of eight typical Asian lotus. After that, high polymorphism SSR molecular markers were mined from each 2n + 0.5 Mb site on each chromosome (e.g., Chr.1-2.5, 4.5, 6.5 Mb) through four steps: online primer design, primer pair evaluation, agarose gel electrophoresis testing using six Asian lotus, one American lotus, and two their hybrids, and DNA sequence alignment. Finally, the polymerase chain reaction (PCR) efficiency of several SSR markers was validated in 20 Asian temperate lotus, eight Asian tropical lotus, and one American lotus. Results: A total of 463 SSR markers were developed based on each 2n + 0.5 Mb site of the eight lotus chromosomes (totaling 821.29 Mb). These markers were evenly distributed throughout the lotus genome at a density of 1 SSR per 1.76 Mb. The chromosomal locations of the SSR markers were determined precisely, and the specificity of the primer pairs for each site was verified by sequencing the PCR products. We further provided a set of genome-wide SSR loci, covering 129 per Mb, identified from eight representative Asian lotus, allowing other researchers to independently discover specific SSR markers for particular experiments. Conclusion: These SSR markers, which have a density of 1 SSR marker per 1.76 Mb in this study, will act as a bridge connecting lotus phenotypes with the genome. This work reveals a novel and convenient strategy for developing highly polymorphic SSR markers at any location throughout the lotus genome, and it sheds light on the development of SSR molecular markers in other plant species.
A high‐confidence Physcomitrium patens plasmodesmata proteome by iterative scoring and validation reveals diversification of cell wall proteins during evolution
(2023) Gombos, Sven; Miras, Manuel; Howe, Vicky; Xi, Lin; Pottier, Mathieu; Kazemein Jasemi, Neda S.; Schladt, Moritz; Ejike, J. Obinna; Neumann, Ulla; Hänsch, Sebastian; Kuttig, Franziska; Zhang, Zhaoxia; Dickmanns, Marcel; Xu, Peng; Stefan, Thorsten; Baumeister, Wolfgang; Frommer, Wolf B.; Simon, Rüdiger; Schulze, Waltraud X.
Plasmodesmata (PD) facilitate movement of molecules between plant cells. Regulation of this movement is still not understood. Plasmodesmata are hard to study, being deeply embedded within cell walls and incorporating several membrane types. Thus, structure and protein composition of PD remain enigmatic. Previous studies of PD protein composition identified protein lists with few validations, making functional conclusions difficult. We developed a PD scoring approach in iteration with large‐scale systematic localization, defining a high‐confidence PD proteome of Physcomitrium patens (HC300). HC300, together with bona fide PD proteins from literature, were placed in Pddb. About 65% of proteins in HC300 were not previously PD‐localized. Callose‐degrading glycolyl hydrolase family 17 (GHL17) is an abundant protein family with representatives across evolutionary scale. Among GHL17s, we exclusively found members of one phylogenetic clade with PD localization and orthologs occur only in species with developed PD. Phylogenetic comparison was expanded to xyloglucan endotransglucosylases/hydrolases and Exordium‐like proteins, which also diversified into PD‐localized and non‐PD‐localized members on distinct phylogenetic clades. Our high‐confidence PD proteome HC300 provides insights into diversification of large protein families. Iterative and systematic large‐scale localization across plant species strengthens the reliability of HC300 as basis for exploring structure, function, and evolution of this important organelle.
Influence of rhizospheric symbiotic microorganisms on the behavioural effects of antimony in soil-plant system: insights from a proteomic perspective
(2024) Zhou, Min; Li, Hui; Xi, Lin; Shi, Feng; Li, Xinru; Wang, Fanfan; Liu, Xuesong; Su, Hailei; Wei, Yuan
Antimony (Sb) pollution in soil-rice systems can affect human health by enriching of food chains. Currently, the mechanism of the negative role underlying microorganisms in plant responses to Sb stress remains clear. The results of this study showed that the presence of arbuscular mycorrhizal (AM) fungi, a common symbiotic microorganism in rhizosphere soil, significantly enhanced Sb uptake by upland rice and inhibited its growth. Furthermore, we explained the reasons for the adverse effects of AM fungi mediation on upland rice growth under Sb stress from a molecular perspective. The results also showed that AM fungi affect the biological processes of the response of upland rice to oxidative stress and the functions of its antioxidant active molecules throughout the vegetative growth phase of upland rice, and that the phenylpropanoid biosynthesis pathway is significantly downregulated. At the same time, phenylalanine/tyrosine ammonia-lyase (PTAL) in the pathway was significantly expressed in the middle and late stages of vegetative growth of upland rice. Therefore, PTAL can act as a potential reference protein to investigate the response of upland rice to Sb stress mediated by AM fungi. These findings enrich our understanding of the impact of Sb pollution on soil-plant systems in real soil environments.