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Analysis of expressed sequence tags from mulberry (Morus indica) roots and implications for comparative transcriptomics and marker identification

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Abstract

Mulberry (Morus indica) serves as the most commercially valuable plant of the sericulture industry and has the unrealized potential to influence rural economy directly. Despite the poised economic importance of mulberry, there is a dearth of genomic or transcriptomic data available for mulberry; therefore, in the present study, efforts were initiated to produce transcriptomic data about mulberry roots to aid selective breeding and biotechnology for stress tolerance in this important tree species of the sericulture industry. Knowledge of the mulberry root transcriptome is an important step and will contribute to a better understanding of molecular information of this important cash crop. A total of 2,400 expressed sequence tags were sequenced from the roots of M. indica cv. K-2 and assembled into 148 contigs and 1,420 singletons. Functional categorization of mulberry unigenes revealed conservation of genes involved in diverse cellular processes. Comparative transcriptomic studies undertaken from the leaf and root tissues of mulberry exposed to a variety of abiotic stress conditions revealed overlapping and specific patterns of transcript expression. The utility of expressed sequence tag (EST)-based simple sequence repeats (SSRs) prompted us to perform a bioinformatics analysis for SSR detection in the EST repertoires of mulberry leaf and root. The identification of expressed transcripts generated from this effort has the unrealized potential as cornerstones of functional genomics studies, and candidate genes relevant to the interest of the sericulture industry may represent important molecular tools to mulberry research groups.

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Acknowledgments

This work was financially supported by grants received from the Department of Biotechnology (DBT), Government of India, New Delhi. VGC and BS acknowledge the University Grants Commission (UGC) and Council of Scientific and Industrial Research (CSIR), respectively, for the award of research fellowships.

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Authors and Affiliations

  1. Department of Plant Molecular Biology, University of Delhi South Campus, Dhaula Kuan, New Delhi, 110021, India

    Vibha G. Checker, Bushra Saeed & Paramjit Khurana

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  1. Vibha G. Checker
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  2. Bushra Saeed
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  3. Paramjit Khurana
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Correspondence to Paramjit Khurana.

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Communicated by J. Dean

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Checker, V.G., Saeed, B. & Khurana, P. Analysis of expressed sequence tags from mulberry (Morus indica) roots and implications for comparative transcriptomics and marker identification. Tree Genetics & Genomes 8, 1437–1450 (2012). https://doi.org/10.1007/s11295-012-0531-6

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  • DOI: https://doi.org/10.1007/s11295-012-0531-6

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