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Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome

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Abstract

We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80 % of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37 %) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.

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  1. Jamil-ur-Rehman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan

    M. Kamran Azim & Ishtaiq A. Khan

  2. BGI-Shenzhen, Beishan Road, Yantian District, Shenzhen, 518083, China

    Yong Zhang

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  1. M. Kamran Azim
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Azim, M.K., Khan, I.A. & Zhang, Y. Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome. Plant Mol Biol 85, 193–208 (2014). https://doi.org/10.1007/s11103-014-0179-8

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