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BMC Genomics. 2015 Feb 5;16:48. doi: 10.1186/s12864-015-1285-y.

Comparative whole-genome analyses of selection marker-free rice-based cholera toxin B-subunit vaccine lines and wild-type lines.

Author information

1
Division of Mucosal Immunology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. koji-kashima@asahikogyosha.co.jp.
2
Asahi Kogyosha Co., Ltd., Tokyo, Japan. koji-kashima@asahikogyosha.co.jp.
3
Division of Mucosal Immunology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. m-meji@ims.u-tokyo.ac.jp.
4
Division of Mucosal Immunology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. shiho-k@ims.u-tokyo.ac.jp.
5
Crop Development Division, NARO Agriculture Research Center, Niigata, Japan. kurodama@affrc.go.jp.
6
Division of Mucosal Immunology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. kiyono@ims.u-tokyo.ac.jp.
7
International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. kiyono@ims.u-tokyo.ac.jp.
8
Division of Mucosal Immunology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. yukiy@ims.u-tokyo.ac.jp.
9
International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. yukiy@ims.u-tokyo.ac.jp.

Abstract

BACKGROUND:

We have developed a rice-based oral cholera vaccine named MucoRice-CTB (Cholera Toxin B-subunit) by using an Agrobacterium tumefaciens-mediated co-transformation system. To assess the genome-wide effects of this system on the rice genome, we compared the genomes of three selection marker-free MucoRice-CTB lines with those of two wild-type rice lines (Oryza sativa L. cv. Nipponbare). Mutation profiles of the transgenic and wild-type genomes were examined by next-generation sequencing (NGS).

RESULTS:

Using paired-end short-read sequencing, a total of more than 300 million reads for each line were obtained and mapped onto the rice reference genome. The number and distribution of variants were similar in all five lines: the numbers of line-specific variants ranged from 524 to 842 and corresponding mutation rates ranged from 1.41 × 10(-6) per site to 2.28 × 10(-6) per site. The frequency of guanine-to-thymine and cytosine-to-adenine transversions was higher in MucoRice-CTB lines than in WT lines. The transition-to-transversion ratio was 1.12 in MucoRice-CTB lines and 1.65 in WT lines. Analysis of variant-sharing profiles showed that the variants common to all five lines were the most abundant, and the numbers of line-specific variant for all lines were similar. The numbers of non-synonymous amino acid substitutions in MucoRice-CTB lines (15 to 21) were slightly higher than those in WT lines (7 or 8), whereas the numbers of frame shifts were similar in all five lines.

CONCLUSIONS:

We conclude that MucoRice-CTB and WT are almost identical at the genomic level and that genome-wide effects caused by the Agrobacterium-mediated transformation system for marker-free MucoRice-CTB lines were slight. The comparative whole-genome analyses between MucoRice-CTB and WT lines using NGS provides a reliable estimate of genome-wide differences. A similar approach may be applicable to other transgenic rice plants generated by using this Agrobacterium-mediated transformation system.

PMID:
25653106
PMCID:
PMC4320824
DOI:
10.1186/s12864-015-1285-y
[Indexed for MEDLINE]
Free PMC Article

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