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Physiological Characterization and Comparative Transcriptome Analysis of White and Green Leaves of Ananas comosus var. bracteatus

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      Abstract

      Leaf coloration is one of the most important and attractive characteristics of Ananas comosus var. bracteatus. The chimeric character is not stable during the in vitro tissue culturing. Many regenerated plants lost economic values for the loss of the chimeric character of leaves. In order to reveal the molecular mechanisms involved in the albino phenotype of the leaf cells, the physiological and transcriptional differences between complete white (CWh) and green (CGr) leaf cells of A. comosus var. bracteatus were analyzed. A total of 1,431 differentially expressed unigenes (DEGs) in CGr and CWh leaves were identified using RNA-seq. A comparison to the COG, GO and KEGG annotations revealed DEGs involved in chlorophyll biosynthesis, chloroplast development and photosynthesis. Furthermore, the measurement of main precursors of chlorophyll in the CWh leaves confirmed that the rate-limiting step in chlorophyll biosynthesis, and thus the cause of the albino phenotype of the white cells, was the conversion of pyrrole porphobilinogen (PBG) to uroporphyrinogen III (Uro III). The enzyme activity of porphobilinogen deaminase (PBGD) and uroporporphyrinogn III synthase (UROS), which catalyze the transition of PBG to Uro III, was significantly decreased in the CWh leaves. Our data showed the transcriptional differences between the CWh and CGr plants and characterized key steps in chlorophyll biosynthesis of the CWh leaves. These results contribute to our understanding of the mechanisms and regulation of pigment biosynthesis in the CWh leaf cells of A. comosus var. bracteatus.

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        High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.
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          Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.

          We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. Blast2GO is freely available via Java Web Start at http://www.blast2go.de. http://www.blast2go.de -> Evaluation.
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            Author and article information

            Affiliations
            [1 ]College of Landscape Architecture of Sichuan Agricultural University, Chengdu, Sichuan, China
            [2 ]Institute of Plant Protection, Agricultural Research Organization, The Volcani Center, Beit Dagan, Israel
            [3 ]Horticultural Biotechnology College of South China Agricultural University, Guangzhou, Guangdong, China
            NARO Institute of Fruit Tree Science, JAPAN
            Author notes

            Competing Interests: The authors have declared that no competing interests exist.

            • Conceptualization: JM YH.

            • Data curation: JM XL.

            • Formal analysis: XL XZ SY RL LS.

            • Funding acquisition: JM.

            • Investigation: XL XZ SY RL.

            • Methodology: JM YH.

            • Project administration: JM.

            • Resources: YH.

            • Supervision: JM YH.

            • Validation: XL XZ.

            • Visualization: JM SK.

            • Writing – original draft: XL JM SK.

            • Writing – review & editing: XL JM SK.

            Contributors
            Role: Editor
            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, CA USA )
            1932-6203
            17 January 2017
            2017
            : 12
            : 1
            28095462
            5240938
            10.1371/journal.pone.0169838
            PONE-D-16-42306
            (Editor)
            © 2017 Li et al

            This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

            Counts
            Figures: 6, Tables: 2, Pages: 17
            Product
            Funding
            Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
            Award ID: 31300585
            Award Recipient :
            The research was supported by the Natural Science Foundation of China (31300585; 31570698 ( http://www.nsfc.gov.cn/).The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
            Categories
            Research Article
            Biology and Life Sciences
            Plant Science
            Plant Anatomy
            Leaves
            Biology and Life Sciences
            Cell Biology
            Cellular Structures and Organelles
            Chloroplasts
            Chlorophyll
            Biology and Life Sciences
            Cell Biology
            Plant Cell Biology
            Chloroplasts
            Chlorophyll
            Biology and Life Sciences
            Plant Science
            Plant Cell Biology
            Chloroplasts
            Chlorophyll
            Biology and Life Sciences
            Cell Biology
            Cellular Types
            Plant Cells
            Chloroplasts
            Chlorophyll
            Biology and Life Sciences
            Cell Biology
            Plant Cell Biology
            Plant Cells
            Chloroplasts
            Chlorophyll
            Biology and Life Sciences
            Plant Science
            Plant Cell Biology
            Plant Cells
            Chloroplasts
            Chlorophyll
            Physical Sciences
            Materials Science
            Materials by Attribute
            Pigments
            Organic Pigments
            Chlorophyll
            Biology and Life Sciences
            Biochemistry
            Biosynthesis
            Biology and Life Sciences
            Computational Biology
            Genome Analysis
            Transcriptome Analysis
            Biology and Life Sciences
            Genetics
            Genomics
            Genome Analysis
            Transcriptome Analysis
            Biology and Life Sciences
            Biochemistry
            Plant Biochemistry
            Photosynthesis
            Biology and Life Sciences
            Plant Science
            Plant Biochemistry
            Photosynthesis
            Biology and Life Sciences
            Computational Biology
            Genome Analysis
            Gene Ontologies
            Biology and Life Sciences
            Genetics
            Genomics
            Genome Analysis
            Gene Ontologies
            Biology and life sciences
            Molecular biology
            Molecular biology techniques
            Sequencing techniques
            RNA sequencing
            Research and analysis methods
            Molecular biology techniques
            Sequencing techniques
            RNA sequencing
            Physical Sciences
            Materials Science
            Materials by Attribute
            Pigments
            Organic Pigments
            Carotenoids
            Custom metadata
            All relevant data are within the paper and its Supporting Information files.

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