ArticleBMC bioinformatics2013
Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 40 citations in OpenAlex.
- Advances in Soybean Genetic Improvement.Plants (Basel, Switzerland) · 2024Review
- Article
- Effect of High Temperature Stress During the Reproductive Stage on Grain Yield and Nutritional Quality of Lentil (Frontiers in nutrition · 2022Article
- Towards Developing Drought-smart Soybeans.Frontiers in plant science · 2021Review
- Intertwined signatures of desiccation and drought tolerance in grasses.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Phytohormones Regulate Accumulation of Osmolytes Under Abiotic Stress.Biomolecules · 2019Review
- Reduction in nutritional quality and growing area suitability of common bean under climate change induced drought stress in Africa.Scientific reports · 2018Article
- Water Deficit Affects Primary Metabolism Differently in Two Lolium multiflorum/Festuca arundinacea Introgression Forms with a Distinct Capacity for Photosynthesis and Membrane Regeneration.Frontiers in plant science · 2016Article
- Salinity and High Temperature Tolerance in Mungbean [Vigna radiata (L.) Wilczek] from a Physiological Perspective.Frontiers in plant science · 2016Review
- Identification of Leaf Proteins Differentially Accumulated between Wheat Cultivars Distinct in Their Levels of Drought Tolerance.PloS one · 2015Article
- Insights into genomics of salt stress response in rice.Rice (New York, N.Y.) · 2013Article
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDespite the importance of osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources.
methodsA curated set of osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome.
resultsThe workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo-inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs.
conclusionsSoybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.
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