Dataset Information

Transcriptomic analysis of the primary roots of Alhagi sparsifolia in response to water stress.

ABSTRACT:

Background

Alhagi sparsifolia is a typical desert phreatophyte and has evolved to withstand extreme dry, cold and hot weather. While A. sparsifolia represents an ideal model to study the molecular mechanism of plant adaption to abiotic stress, no research has been done in this aspect to date. Here we took advantage of Illumina platform to survey transcriptome in primary roots of A. sparsifolia under water stress conditions in aim to facilitate the exploration of its genetic basis for drought tolerance.

Methodology and principal findings

We sequenced four primary roots samples individually collected at 0, 6, 24 and 30h from the A. sparsifolia seedlings in the course of 24h of water stress following 6h of rehydration. The resulting 38,763,230, 67,511,150, 49,259,804 and 54,744,906 clean reads were pooled and assembled into 33,255 unigenes with an average length of 1,057 bp. All-unigenes were subjected to functional annotation by searching against the public databases. Based on the established transcriptome database, we further evaluated the gene expression profiles in the four different primary roots samples, and identified numbers of differently expressed genes (DEGs) reflecting the early response to water stress (6h vs. 0h), the late response to water stress (24h vs. 0h) and the response to post water stress rehydration (30h vs. 24h). Moreover, the DEGs specifically regulated at 6, 24 and 30h were captured in order to depict the dynamic changes of gene expression during water stress and subsequent rehydration. Functional categorization of the DEGs indicated the activation of oxidoreductase system, and particularly emphasized the significance of the 'Glutathione metabolism pathway' in response to water stress.

Conclusions

This is the first description of the genetic makeup of A. sparsifolia, thus providing a substantial contribution to the sequence resources for this species. The identified DEGs offer a deep insight into the molecular mechanism of A. sparsifolia in response to water stress, and merit further investigation.

SUBMITTER: Wu H

PROVIDER: S-EPMC4379016 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Publications

Transcriptomic analysis of the primary roots of Alhagi sparsifolia in response to water stress.

Wu Huanian H Zhang Yongqiang Y Zhang Wangbin W Pei Xinwu X Zhang Chao C Jia Shirong S Li Weimin W

PloS one 20150330 3

<h4>Background</h4>Alhagi sparsifolia is a typical desert phreatophyte and has evolved to withstand extreme dry, cold and hot weather. While A. sparsifolia represents an ideal model to study the molecular mechanism of plant adaption to abiotic stress, no research has been done in this aspect to date. Here we took advantage of Illumina platform to survey transcriptome in primary roots of A. sparsifolia under water stress conditions in aim to facilitate the exploration of its genetic basis for dro ...[more]

PMID: 25822368

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Project description:Alhagi sparsifolia Shap. is a perennial subshrub belonging to genus Alhagi, family Leguminosae. As a typical desert phreatophyte, this plant species has highly developed deep roots and displays a great capacity to withstand poor soil as well as extreme dry, cold and hot weather. A. sparsifolia is naturally distributed in the arid and salinized regions of northernwestern China and adjacent countries in Central Asia, and plays a fundamental role in maintaining the local ecosystem. In addition, this plant is usually used as a fodder for local animals due to its high protein content, and is important in the development of local livestock husbandry. Considering its great tolerance to harsh environments, A. sparsifolia represents an ideal species for deciphering the mechanism of plant adaption to abiotic stress, such as water deficit. However, understanding the stress adaption in this plant is limited. While a few studies were conducted on physiological responses of A. sparsifolia to water stress, research has never been done to explore the genomic basis for its drought-tolerance to date. In particular, as a non-model plant species, the genomic resource of A. sparsifolia is rather scarce, only one expressed sequence tag (EST) and one protein have been deposited in Genbank prior to Sept., 2014. In aim to explore the genetic basis underlying drought tolerance in this species, recently we took advantage of transcriptome sequencing to survey the water stress responsive genes in A. sparsifolia primary roots. Using Illumina HiSeq™ 2000 platform, we sequenced the primary root samples individually collected at four different time points (0, 6h, 24 and 30h) from A. sparsifolia seedlings during 24h of water stress following 6h of rehydration. The resulting 38,763,230, 67,511,150, 49,259,804 and 54,744,906 high quality reads were pooled and assembled into 33,255 unigenes with an average length of 1,057 bp. All-unigenes were subjected to functional annotation by searching against the public databases including NR, NT, Swiss-Prot, Pfamm, GO, KOG and KEGG. On the basis of the established transcriptome database, we evaluated the gene expression profiles in A. sparsifolia primary roots at 0, 6, 24 and 30h in the course of water stress and subsequent rehydration. An extensive repertoire of the differently expressed genes (DEGs) reflecting the early response to water stress (6h), the late response to water stress (24h) and the response to post stress rehydration (30h) were identified. In addition, to unravel the dynamic changes of gene expression during water stress and subsequent rehydration, we further captured the DEGs commonly or specifically regulated at 6, 24 and 30h. Functional categorization of the DEGs disclosed the activation of oxidoreductase system in A. sparsifolia primary roots upon water stress, and particularly emphasized the significance of the ‘Glutathione metabolism pathway’. To our knowledge, this is the first description of the genetic makeup of A. sparsifolia, thus providing a substantial contribution to the sequence resources for this species. The DEGs identified herein offers a deep insight into the molecular mechanism of A. sparsifolia in response to water stress, and merits further investigation.

Project description:The stoichiometry of carbon, nitrogen, and phosphorus (C:N:P) among leaves, stems, and roots reflects trade-offs in plants for acquiring resources and their growth strategy. The widely distributed plant Alhagi sparsifolia is an ideal species to study the ecological stoichiometry in different organs in response to the availability of nutrients and water in the desert ecosystem. However, which response of organs is most sensitive to environmental conditions is still unclear. To answer this question, we collected samples of plants and soils including not only aboveground leaves and stems, but also underground roots and soils from a wide range of arid areas during the growing season. The C, N, P, C:N, C:P, and N:P ratios in leaves, thorns, stems, and roots were derived to explore their relationship as well as their response mechanisms to nutrients and water spanning 1 m deep in the soil. The results showed that the order of N concentration was leaves > thorns > stems > roots, that the concentration of P in the leaves, thorns, and stems was similar, and that their values were higher than those in the roots. First, the C:N ratios in the leaves and stems were significantly positively correlated with the ratio in roots. The C:N ratios in each organ showed a significant relationship with the soil alkali hydrolyzable nitrogen (SAN) above a depth of 60 cm. In addition to SAN, soil available phosphorus (SAP) and soil organic carbon (SOC) affect the C:N ratio in the roots. Second, the C:P and N:P ratios in aboveground organs showed no correlations with the ratios in roots. The C:P and N:P ratios in the leaves and thorns have no relationship with soil nutrients, while the C:P ratio in roots was influenced by SAN and SOC in all soil layers. Finally, the N:P ratios in roots were also affected by nutrients in different soil depths at 0-20 and 60-80 cm. These results illustrate that the roots were more sensitive to soil nutrients than the aboveground parts. Our study of ecological stoichiometry also suggests a novel systematic approach for analyzing the sensitivity of responses of an organ to environmental conditions.

Dataset Information

Transcriptomic analysis of the primary roots of Alhagi sparsifolia in response to water stress.

Background

Methodology and principal findings

Conclusions

Publications

Transcriptomic analysis of the primary roots of Alhagi sparsifolia in response to water stress.

Similar Datasets

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