Integrated Transcriptomic and Metabolomic Analyses Reveal Organ-Specific Molecular and Metabolic Features in Nitraria sibirica
- 1International Sakharov Environmental Institute, Belarusian State University, 220070 Minsk, Belarus
- 2College of Life Science and Technology, Xinjiang Institute for Advanced Studies, Urumqi 830017, China
- 3College of Food Science and Engineering, Yangzhou University, Yangzhou 210095, China
Abstract
Background/Objectives: Nitraria sibirica Pall. is a halophytic shrub with ecological and phytochemical value, but its organ-level molecular organization remains poorly resolved. Methods: We integrated RNA sequencing and untargeted LC–MS metabolomics for matched roots, stems, leaves, and fruits collected from one field population. Results: We quantified 25,263 genes and 2143 annotated metabolite entries, and the four organs separated clearly in both omics datasets. Across six pairwise comparisons, 12,160 nonredundant differentially expressed genes and 1446 nonredundant differentially accumulated metabolites were identified; intersection screening further resolved 3955 organ-preferential genes and 539 organ-preferential metabolites. Leaves contained the largest and most diverse preferential metabolite set and showed photosynthetic, chloroplast, pigment, and carbon-fixation signatures. Stems were distinguished by secondary-cell-wall, cytoskeletal, carbohydrate-conversion, phenylpropanoid, and lignan-related patterns. Fruits preferentially accumulated organic acids, amino-acid-related metabolites, sugars, and glycosides and showed energy-metabolism and flavonoid-modification signatures. Roots contained fewer preferential metabolites and were characterized by signaling, protective responses, RNA processing, and surface-barrier metabolism. WGCNA identified one significant organ-associated module for each organ, and cross-omics analyses linked these modules to preferential metabolites while prioritizing candidate gene–metabolite associations. Conclusions: These data define matched four-organ molecular and metabolic partitioning in N. sibirica and provide testable candidates for functional and targeted-metabolite validation.
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BibTeX
@article{nie2026integrated,
title = {{Integrated Transcriptomic and Metabolomic Analyses Reveal Organ-Specific Molecular and Metabolic Features in Nitraria sibirica}},
author = {Yuhao Nie and Wenhui Guo and Yongqi Yin and Deju Zhang},
journal = {Metabolites},
year = {2026},
month = oct,
doi = {10.3390/metabo16110826},
url = {https://www.mdpi.com/2218-1989/16/11/826},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrated Transcriptomic and Metabolomic Analyses Reveal Organ-Specific Molecular and Metabolic Features in Nitraria sibirica
AU - Yuhao Nie
AU - Wenhui Guo
AU - Yongqi Yin
AU - Deju Zhang
PY - 2026
DA - 2026/10/29
JO - Metabolites
DO - 10.3390/metabo16110826
UR - https://www.mdpi.com/2218-1989/16/11/826
AB - Background/Objectives: Nitraria sibirica Pall. is a halophytic shrub with ecological and phytochemical value, but its organ-level molecular organization remains poorly resolved. Methods: We integrated RNA sequencing and untargeted LC–MS metabolomics for matched roots, stems, leaves, and fruits collected from one field population. Results: We quantified 25,263 genes and 2143 annotated metabolite entries, and the four organs separated clearly in both omics datasets. Across six pairwise comparisons, 12,160 nonredundant differentially expressed genes and 1446 nonredundant differentially accumulated metabolites were identified; intersection screening further resolved 3955 organ-preferential genes and 539 organ-preferential metabolites. Leaves contained the largest and most diverse preferential metabolite set and showed photosynthetic, chloroplast, pigment, and carbon-fixation signatures. Stems were distinguished by secondary-cell-wall, cytoskeletal, carbohydrate-conversion, phenylpropanoid, and lignan-related patterns. Fruits preferentially accumulated organic acids, amino-acid-related metabolites, sugars, and glycosides and showed energy-metabolism and flavonoid-modification signatures. Roots contained fewer preferential metabolites and were characterized by signaling, protective responses, RNA processing, and surface-barrier metabolism. WGCNA identified one significant organ-associated module for each organ, and cross-omics analyses linked these modules to preferential metabolites while prioritizing candidate gene–metabolite associations. Conclusions: These data define matched four-organ molecular and metabolic partitioning in N. sibirica and provide testable candidates for functional and targeted-metabolite validation.
SN - 2218-1989
ER -