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The chloroplast genome sequence of Syzygium cumini (L.) and its relationship with other angiosperms

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Abstract

Only a few studies to date have conducted comparative genomics in the Myrtaceae family. Here, we report the complete sequence and bioinformatics analysis of the chloroplast genome of Syzygium cumini (L.), one of the family members. The size of S. cumini cp genome was within the range of reported angiosperm chloroplast genomes. Comparison of S. cumini cpDNA sequence with previously reported partial sequences of S. cumini revealed several SNPs that resulted in non-synonymous mutations in maturase K and NADH-plastoquinone oxidoreductase subunit-5. These polymorphic characters might serve as intra-specific markers to address whether lineage sorting from polymorphic ancestry has occurred. Comparison of the S. cumini chloroplast genome with related dicots revealed an expansion in the intergenic spacer located between IRA/large single copy (LSC) border and the first gene of LSC region, driven by sequence of 54 bp. This type of variation in the intergenic regions can be utilized in the development of species-specific vectors for chloroplast genetic engineering. Several of the longer (30–40 bp) repeats were found to be conserved in other dicot species, suggesting that they might be widespread in angiosperm chloroplast genomes.

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Acknowledgments

The authors are thankful to Masahiro Sugiura and Yukawa Yasushi (Nagoya City University, Nagoya, Japan) for their suggestions on manuscript. Huma Asif, Asif Iqbal and Ishtiaq Ahmad Khan acknowledged the financial support of Higher Education Commission, Pakistan under Indigenous PhD Fellowship Program.

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Authors and Affiliations

  1. H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan

    Huma Asif, Asifullah Khan, Asif Iqbal, Ishtiaq Ahmad Khan & M. Kamran Azim

  2. Department of Genetics, Federal Research Centre for Forests, Hauptstraße 7, 1140, Vienna, Austria

    Berthold Heinze

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  1. Huma Asif
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  2. Asifullah Khan
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  3. Asif Iqbal
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  4. Ishtiaq Ahmad Khan
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  5. Berthold Heinze
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  6. M. Kamran Azim
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Correspondence to M. Kamran Azim.

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Communicated by D. Grattapaglia

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Asif, H., Khan, A., Iqbal, A. et al. The chloroplast genome sequence of Syzygium cumini (L.) and its relationship with other angiosperms. Tree Genetics & Genomes 9, 867–877 (2013). https://doi.org/10.1007/s11295-013-0604-1

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  • DOI: https://doi.org/10.1007/s11295-013-0604-1

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