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      Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

          Yoav Benjamini, Yosef Hochberg (1995)
          Article 0 comments Cited 24503 times – based on 0 reviews     Review now
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            HISAT: a fast spliced aligner with low memory requirements.

            Daehwan Kim, Ben Langmead, Steven L Salzberg (2018)
            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.
            Article 0 comments Cited 6132 times – based on 0 reviews     Review now
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              StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

              Mihaela Pertea, Geo M Pertea, Corina M Antonescu … (2016)
              Methods used to sequence the transcriptome often produce more than 200 million short sequences. We introduce StringTie, a computational method that applies a network flow algorithm originally developed in optimization theory, together with optional de novo assembly, to assemble these complex data sets into transcripts. When used to analyze both simulated and real data sets, StringTie produces more complete and accurate reconstructions of genes and better estimates of expression levels, compared with other leading transcript assembly programs including Cufflinks, IsoLasso, Scripture and Traph. For example, on 90 million reads from human blood, StringTie correctly assembled 10,990 transcripts, whereas the next best assembly was of 7,187 transcripts by Cufflinks, which is a 53% increase in transcripts assembled. On a simulated data set, StringTie correctly assembled 7,559 transcripts, which is 20% more than the 6,310 assembled by Cufflinks. As well as producing a more complete transcriptome assembly, StringTie runs faster on all data sets tested to date compared with other assembly software, including Cufflinks.
              Article 0 comments Cited 3491 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Frank M. You: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Int J Mol Sci
                Journal ID (iso-abbrev): Int J Mol Sci
                Journal ID (publisher-id): ijms
                Title: International Journal of Molecular Sciences
                Publisher: MDPI
                ISSN (Electronic): 1422-0067
                Publication date (Electronic): 11 March 2021
                Publication date Collection: March 2021
                Volume: 22
                Issue: 6
                Electronic Location Identifier: 2837
                Affiliations
                [1 ]Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA; venura@ 123456agri.pdn.ac.lk
                [2 ]Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
                Author notes
                [* ]Correspondence: jm.verchot@ 123456tamu.edu ; Tel.: +1-979-286-1788
                Author information
                https://orcid.org/0000-0003-2977-2787
                https://orcid.org/0000-0001-8789-3144
                Article
                Publisher ID: ijms-22-02837
                DOI: 10.3390/ijms22062837
                PMC ID: 8001266
                PubMed ID: 33799566
                SO-VID: 04e849f3-9df9-459a-95e1-8adcf3fc2391
                Copyright © © 2021 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 12 February 2021
                Date accepted : 09 March 2021
                Categories
                Subject: Article

                ScienceOpen disciplines: Molecular biology
                Keywords: pvx,gene expression regulation,rna-seq,solanum tuberosum,potato virology,virus movement,host-pathogen interactions,antiviral defense,potexvirus
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: pvx, gene expression regulation, rna-seq, solanum tuberosum, potato virology, virus movement, host-pathogen interactions, antiviral defense, potexvirus

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