Dataset Information

Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis.

ABSTRACT: The desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn as trees develop to maturity. P. euphratica is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophylls, juvenile heterophylls were sampled individually, and then, the expression patterns of miRNAs, mRNAs, lncRNAs and circRNAs were analysed by small RNA sequencing and strand-specific RNA sequencing. We found that 1374 mRNAs, 19 miRNAs, 71 lncRNAs and 2 circRNAs were P. euphratica heterophyll morphogenesis-associated (PHMA) RNAs; among them, 17 PHMA miRNAs could alter the expression of 46 PHMA mRNAs. Furthermore, 11 lncRNAs and 2 circRNAs interacted with 27 PHMA mRNAs according to the ceRNA hypothesis. According to GO and KEGG pathway analysis, PHMA RNAs were mainly involved in metabolism, response to stimulus and developmental processes. Our results indicated that external environmental factors and genetic factors in P. euphratica co-regulated the expression of PHMA RNAs, repressed cell division, reinforced cell growth, and ultimately resulted in the morphogenesis of P. euphratica heterophylls.

SUBMITTER: Qin SW

PROVIDER: S-EPMC6250686 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis.

Qin Shao-Wei SW Jiang Ren-Jun RJ Zhang Na N Liu Zhan-Wen ZW Li Cai-Lin CL Guo Zhong-Zhong ZZ Bao Liang-Hong LH Zhao Li-Feng LF

Scientific reports 20181122 1

The desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn as trees develop to maturity. P. euphratica is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophylls, juvenile heterophylls were sampled individually, and then, the expression patterns of miRNAs, mRNAs, lncRNAs an ...[more]

PMID: 30467318

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Project description:De novo shoot regeneration is one of the important manifestations of cell totipotency in organogenesis, which reflects a survival strategy organism evolved when facing natural selection. Compared with tissue regeneration, and somatic embryogenesis, de novo shoot regeneration denotes a shoot regeneration process directly from detatched or injured tissues of plant. Studies on plant shoot regeneration had identified key genes mediating shoot regeneration. However, knowledge was derived from Arabidopsis; the regeneration capacity is hugely distinct among species. To achieve a comprehensive understanding of the shoot regeneration mechanism from tree species, we select four genetic lines of Populus euphratica from a natural population to be sequenced at transcriptome level. On the basis of the large difference of differentiation capacity, between the highly differentiated (HD) and low differentiated (LD) groups, the analysis of differential expression identified 4920 differentially expressed genes (DEGs), which were revealed in five groups of expression patterns by clustering analysis. Enrichment showed crucial pathways involved in regulation of regeneration difference, including "plant hormone signal transduction", "cell differentiation", "cellular response to auxin stimulus", and "auxin-activated signaling pathway". The expression of nine genes reported to be associated with shoot regeneration was validated using quantitative real-time PCR (qRT-PCR). For the specificity of regeneration mechanism with P. euphratica, large amount of DEGs involved in "plant-pathogen interaction", ubiquitin-26S proteosome mediated proteolysis pathway, stress-responsive DEGs, and senescence-associated DEGs were summarized to possibly account for the differentiation difference with distinct genotypes of P. euphratica. The result in this study helps screening of key regulators in mediating the shoot differentiation. The transcriptomic characteristic in P. euphratica further enhances our understanding of key processes affecting the regeneration capacity of de novo shoots among distinct species.

Project description:Populus euphratica Oliv. has a high tolerance for drought, salinity, and alkalinity. The main purpose of this study is to explore the effects of environments of different salinity intensities on endophytic community structure and the possible roles of endophytes in the tolerance of host plants. The characterization of endogenous bacteria in diversity has been investigated by using the Illumina high-throughput sequencing technique. The research showed that endophytic bacteria of P. euphratica in an extremely saline environment had low species diversity, especially in sap tissue. The dominant phyla in all groups were Proteobacteria, Actinobacteria, and Bacteroidetes. Notably, Firmicutes (relative abundance >5%) was a different dominant phylum in the samples from the high-saline environment compared with the relatively low-saline-environment group. The linear discriminant analysis effect size (LEfSe) analysis found that there were significant differences in different saline environments of Cytophagaceae (family), Rhodobacteraceae (family), and Rhodobacterales (order). These results indicated that the composition of the endogenous bacterial community was related to the growth environment of host plants. The predictive analysis of KEGG pathways and enzymes showed that the abundance of some enzymes and metabolic pathways of endophytes of P. euphratica increased with the increase of soil salinity, and most of the enzymes were related to energy metabolism and carbohydrate metabolism. These findings suggested that the endogenous bacteria of the host plant had different expression mechanisms under different degrees of stress, and this mechanism was very obvious in the distribution of endophytes, while the function of the endogenous bacteria needs to be further explored. IMPORTANCE Euphrates poplar (Populus euphratica Oliv.), as the only tree species that grows in the desert, has tenacious vitality with the characteristics of cold tolerance, drought tolerance, salt-alkali tolerance, and wind-sand resistance. P. euphratica has a long growth cycle and a high growth rate, which can break wind, fix sand, green the environment, and protect farmland, making it an important afforestation tree species in arid and semiarid areas. The area of P. euphratica in Xinjiang accounts for 91.1% of its area in China. Studying the endophytic bacteria of P. euphratica can give people a systematic understanding of it and the adaptability of the endogenous flora to the host and special environments. In this study, by analyzing the endophytic bacteria of P. euphratica in different saline-alkali regions of Xinjiang, it was found that the bacteria in different tissues of P. euphratica changed with the change of soil salinity. Especially in the sap tissue of P. euphratica under extremely high salinity, the diversity of endogenous bacteria was significantly lower than that in other tissues. These differential bacteria under different salinities were mostly related to the stress resistance of themselves and the host. Not only that, we also selected a strain of Bacillus with high stress resistance from the tissues of P. euphratica, which can survive under the extreme conditions of 10% NaCl and pH 11. We obtained a genome completion map of this strain, named it Bacillus haynesii P19 (GenBank accession no. PRJNA648288), and tried to use it for fermentation but in a different work, so as to develop it into a promising industrial fermentation chassis bacterium. Therefore, this study was of great significance for the understanding of endophytic bacteria in P. euphratica and the acquisition of extremophilic microbial resources.

Dataset Information

Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis.

Publications

Genome-wide analysis of RNAs associated with Populus euphratica Oliv. heterophyll morphogenesis.

Similar Datasets

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