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Genome-Wide Comparative Analyses of Microsatellites in Papaya

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Abstract

Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic and universally distributed in eukaryotes. SSRs have been used extensively as sequence tagged markers in genetic studies. Recently, the functional and evolutionary importance of SSRs has received considerable attention. Here we report the mining and characterization of the SSRs in papaya genome. We analyzed SSRs from 277.4 Mb of whole genome shotgun (WGS) sequences, 51.2 Mb bacterial artificial chromosome (BAC) end sequences (BES), and 13.4 Mb expressed sequence tag (EST) sequences. The papaya SSR density was one SSR per 0.7 kb of DNA sequence in the WGS, which was higher than that in BES and EST sequences. SSR abundance was dramatically reduced as the repeat length increased. According to SSR motif length, dinucleotide repeats were the most common motif in class I, whereas hexanucleotides were the most copious in class II SSRs. The tri- and hexanucleotide repeats of both classes were greater in EST sequences compared to genomic sequences. In class I SSR, AT and AAT were the most frequent motifs in BES and WGS sequences. By contrast, AG and AAG were the most abundant in EST sequences. For SSR marker development, 9,860 primer pairs were surveyed for amplification and polymorphism. Successful amplification and polymorphic rates were 66.6% and 17.6%, respectively. The highest polymorphic rates were achieved by AT, AG, and ATG motifs. The genome wide analysis of microsatellites revealed their frequency and distribution in papaya genome, which varies among plant genomes. This complete set of SSRs markers throughout the genome will assist diverse genetic studies in papaya and related species.

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Acknowledgements

We thank Yinjun Li for technical assistance. This project was supported by a USDA T-STAR grant through the University of Hawaii (to R. P., R.M., P. M., and Q.Y), a USDA-ARS Cooperative Agreement (CA 58-3020-8-134) with the Hawaii Agriculture Research Center, the U. Hawaii (to M.A.), U.S. Department of Defense (W81XWH0520013 to M.A), and startup funds from the University of Illinois at Urbana-Champaign (to R.M)

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Authors and Affiliations

  1. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Jianping Wang, Cuixia Chen, Jong-Kuk Na & Ray Ming

  2. Hawaii Agriculture Research Center, Aiea, HI, 96701, USA

    Qingyi Yu

  3. Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, 96822, USA

    Shaobin Hou & Maqsudul Alam

  4. Department of Tropical Plant and Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA

    Robert E. Paull

  5. USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA

    Paul H. Moore

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  1. Jianping Wang
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Correspondence to Ray Ming.

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Supplementary Table 1

Comprehensive information of 9,860 SSR marker surveyed (DOC 3.04 MB)

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Wang, J., Chen, C., Na, JK. et al. Genome-Wide Comparative Analyses of Microsatellites in Papaya. Tropical Plant Biol. 1, 278–292 (2008). https://doi.org/10.1007/s12042-008-9024-z

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