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      Transcriptome Analysis of Jujube ( Ziziphus jujuba Mill.) Response to Heat Stress

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          Abstract

          Heat stress (HS) is a common stress influencing the growth and reproduction of plant species. Jujube ( Ziziphus jujuba Mill.) is an economically important tree with strong abiotic stress resistance, but the molecular mechanism of its response to HS remains elusive. In this study, we subjected seedlings of Z. jujuba cultivar “Hqing1-HR” to HS (45°C) for 0, 1, 3, 5, and 7 days, respectively, and collected the leaf samples (HR0, HR1, HR3, HR5, and HR7) accordingly. Fifteen cDNA libraries from leaves were constructed for transcriptomics assays. RNA sequencing and transcriptomics identified 1,642, 4,080, 5,160, and 2,119 differentially expressed genes (DEGs) in comparisons of HR1 vs. HR0, HR3 vs. HR0, HR5 vs. HR0, and HR7 vs. HR0, respectively. Gene ontology analyses of the DEGs from these comparisons revealed enrichment in a series of biological processes involved in stress responses, photosynthesis, and metabolism, suggesting that lowering or upregulating expression of these genes might play important roles in the response to HS. This study contributed to our understanding of the molecular mechanism of jujube response to HS and will be beneficial for developing jujube cultivars with improved heat resistance.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

            Summary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data. Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org). Contact: mrobinson@wehi.edu.au
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              HISAT: a fast spliced aligner with low memory requirements.

              HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments. HISAT uses an indexing scheme based on the Burrows-Wheeler transform and the Ferragina-Manzini (FM) index, employing two types of indexes for alignment: a whole-genome FM index to anchor each alignment and numerous local FM indexes for very rapid extensions of these alignments. HISAT's hierarchical index for the human genome contains 48,000 local FM indexes, each representing a genomic region of ∼64,000 bp. Tests on real and simulated data sets showed that HISAT is the fastest system currently available, with equal or better accuracy than any other method. Despite its large number of indexes, HISAT requires only 4.3 gigabytes of memory. HISAT supports genomes of any size, including those larger than 4 billion bases.
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                Author and article information

                Contributors
                Journal
                Int J Genomics
                Int J Genomics
                IJG
                International Journal of Genomics
                Hindawi
                2314-436X
                2314-4378
                2021
                2 December 2021
                : 2021
                : 3442277
                Affiliations
                1Department of Horticulture, College of Agriculture, Shihezi University, Shihezi, 832003 Xinjiang, China
                2Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, 832003 Xinjiang, China
                3Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 Xinjiang, China
                4Scientific Observing and Experimental Station of Pomology (Xinjiang), Urumqi, 830091 Xinjiang, China
                Author notes

                Academic Editor: Hengfu Yin

                Author information
                https://orcid.org/0000-0002-2434-9229
                https://orcid.org/0000-0003-1625-6177
                https://orcid.org/0000-0003-3268-8842
                https://orcid.org/0000-0003-4948-3229
                https://orcid.org/0000-0002-1086-0800
                Article
                10.1155/2021/3442277
                8660251
                34901262
                dcb315ae-e74e-4a6c-aacb-eb12bd0ac723
                Copyright © 2021 Lei Yang et al.

                This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 7 August 2021
                : 18 October 2021
                : 28 October 2021
                Funding
                Funded by: Xinjiang Jujube Industrial technology System
                Award ID: XJCYTX-01
                Funded by: China Agriculture Research System
                Award ID: CARS-30
                Funded by: National Natural Science Foundation of China
                Award ID: 31801815
                Funded by: Natural Science Foundation of Xinjiang Province
                Award ID: 2019D01A64
                Categories
                Research Article

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