Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq

Zhao, Xinpeng; Bai, Shenglong; Li, Lechen; Han, Xue; Li, Jia-hui; Zhu, Yumeng; Fang, Yuan; Zhang, Dale

doi:10.3390/ijms21103595

Cited by 23 publications

(21 citation statements)

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“…Although several molecular studies on abiotic mechanisms in Ae. tauschii have been conducted [20,21], validation of reference genes in this weed have been rarely reported. This study evaluated the stability of several reference genes and validated them under different abiotic conditions and developmental stages.…”

Section: Introductionmentioning

confidence: 99%

Selection and Validation of Reference Genes for RT-qPCR Analysis in Aegilops tauschii (Coss.) under Different Abiotic Stresses

Abbas

et al. 2021

IJMS

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Aegilops tauschii (Coss.) is an aggressive and serious annual grass weed in China. Its DD genome is a rich source of genetic material and performs better under different abiotic stress conditions (salinity, drought, temperature, etc.). Reverse-transcribed quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for reference gene selection and validation. This work aimed to evaluate the stability of reference gene expression in Ae. tauschii under different abiotic stresses (salinity, drought, hot, and cold) and developmental stages (seedling and development). The results show that the ubiquitin-conjugating enzyme E2 36-like (UBC36) and protein microrchidia 2-like (HSP) are the most stable genes under control and salinity conditions, respectively. Under drought stress conditions, UBC36 is more stable as compared with others. Glyceraldehyde-3-phosphate dehydrogenase (GADPH) is the most stable reference gene during heat stress conditions and thioredoxin-like protein (YLS) under cold stress condition. Phosphate2A serine/threonine-protein phosphatase 2A (PP2A) and eukaryotic translation initiation factor 3 (ETIF3) are the most stable genes at seedling and developmental stages. Intracellular transport protein (CAC) is recommended as the most stable gene under different abiotic stresses and at developmental stages. Furthermore, the relative expression levels of NHX1 and DREB under different levels of salinity and drought stress conditions varied with the most (HSP and UBC36) and least (YLS and ACT) stable genes. This study provides reliable reference genes for understanding the tolerance mechanisms in Ae. tauschii under different abiotic stress conditions.

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Section: Introductionmentioning

confidence: 99%

Selection and Validation of Reference Genes for RT-qPCR Analysis in Aegilops tauschii (Coss.) under Different Abiotic Stresses

Abbas

et al. 2021

IJMS

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“…Progenitors of bread wheat (T. aestivum) A. taushii (DD) and T. dicoccoides (AABB) showed different antioxidant capacity in response to dehydration (Suneja et al, 2017). Similarly, two different accession (XJ002 and XJ098) of A. tauschii (hexaploid wheat progenitor) showed differential gene expression in response to drought that was estimated by transcriptome analysis (Zhao et al, 2020). In this study, 6969 DEGs (differentially expressed genes) related to drought resistance were detected.…”

Section: Introductionmentioning

confidence: 68%

“…Also, progenitors of T. aestivum (A. tauschii (DD) and T. dicoccoides (AABB)) differed in their antioxidant activity after their exposure to drought (Suneja et al, 2017). In addition, upon exposure to drought, two accessions of A. tauschii (DD genome contributor) represented difference in gene expression of 6969 genes related to drought tolerance which was parallel to physiological changes correlated with drought resistance (Zhao et al, 2020). Interestingly, ancient and modern wheat varieties revealed various molecular differences including antioxidant and antiinflammatory capacities.…”

Section: Discussionmentioning

confidence: 99%

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Expression of Stress-Responsive Genes in Wheat (Triticum Aestivum) and its Progenitors Under Heat Stress

Elseehy

2021

Alexandria Science Exchange Journal

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Hexaploid wheat (Triticum aestivum, AABBDD) had developed from tetraploid and diploid progenitors with different genomic background. During evolution, changes in genome organization, gene expression, and genomic interactions occur. Real time PCR was employed to disclose changes in gene expression of three abiotic induced genes (DREB2, NAC6D, HSP17) in T. aestivum and four of its progenitors which had contributed in its development including Triticum turgidum (AABB), Triticum monococcum (AA), Aegilops spltoides (BB), and Aegilops taushii (DD) with different ploidy levels. Results showed that the three genes presented wide variations between T. aestivum and its progenitors as well as among its progenitors. Results suggested that T. aestivum could have inherited the high expression pattern of DREB2 from its progenitor A. speltoids, inherited its expression pattern of NAC6D form T. turgidum and/or A. taushii. The high expression pattern of HSP17 in T. aestivum could have been inherited from A. speltoides and/or T. turgidum. The obtained results support the notion that wheat progenitors have contributed in the gene expression profile of the hexaploid wheat. Results of this study will help detection of important genes in wheat progenitors that could be introduced into breeding programs for devolving new wheat varieties with desired characteristics.

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“…Independently, these protein sequences were given as input to KofamKOALA ( https://www.genome.jp/tools/kofamkoala/ ) with e-value default threshold 1e-2, which reports on top KEGG orthologs using an HMMsearch. E-value threshold was determined from previous studies [ 83 , 84 ]. Orthologs for genes linked to ANTAR-target RNAs, were mapped using EggNOG and/or KofamKOALA (Additional file 2 : Table S4).…”

Section: Methodsmentioning

confidence: 99%

Diversity and prevalence of ANTAR RNAs across actinobacteria

Mehta

Ramesh

2021

BMC Microbiol

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Background Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory system consists of a family of RNAs (the ANTAR-target RNAs) that selectively recruit ANTAR proteins. This protein-RNA complex together regulates genes at the level of translation or transcriptional elongation. Despite the widespread distribution of ANTAR proteins in bacteria, their target RNAs haven’t been identified in certain bacterial phyla such as actinobacteria. Results Here, by using a computational search model that is tuned to actinobacterial genomes, we comprehensively identify ANTAR-target RNAs in actinobacteria. These RNA motifs lie in select transcripts, often overlapping with the ribosome binding site or start codon, to regulate translation. Transcripts harboring ANTAR-target RNAs majorly encode proteins involved in the transport and metabolism of cellular metabolites like sugars, amino acids and ions; or encode transcription factors that in turn regulate diverse genes. Conclusion In this report, we substantially diversify and expand the family of ANTAR RNAs across bacteria. These findings now provide a starting point to investigate the actinobacterial processes that are regulated by ANTAR.

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Comparative Transcriptome Analysis of Two Aegilops tauschii with Contrasting Drought Tolerance by RNA-Seq

Cited by 23 publications

References 80 publications

Selection and Validation of Reference Genes for RT-qPCR Analysis in Aegilops tauschii (Coss.) under Different Abiotic Stresses

Selection and Validation of Reference Genes for RT-qPCR Analysis in Aegilops tauschii (Coss.) under Different Abiotic Stresses

Expression of Stress-Responsive Genes in Wheat (Triticum Aestivum) and its Progenitors Under Heat Stress

Diversity and prevalence of ANTAR RNAs across actinobacteria

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