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Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana

Wang, Xuewen, Yang, Shuai, Chen, Yongdui, Zhang, Shumeng, Zhao, Qingshi, Li, Meng, Gao, Yulong, Yang, Long, Bennetzen, Jeffrey L.·2018·BMC Genomics
DOI 10.1186/s12864-018-4878-4PMC PMC6020451
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Fig. 1 Frequency distributions of different types of SSR repeat units in Nicotiana genomes. N. ben, N. syl, N. tom, N. oto, N. tab TN90, K326 and BX represent N. benthamiana, N. sylvestris, N. tomentosiformis, N. otophora, N. tabacum TN90, N. tabacum K326, and N. tabacum BX, respectively
Fig. 1 Frequency distributions of different types of SSR repeat units in Nicotiana genomes. N. ben, N. syl, N. tom, N. oto, N. tab TN90, K326 and BX represent N. benthamiana, N. sylvestris, N. tomentosiformis, N. otophora, N. tabacum TN90, N. tabacum K326, and N. tabacum BX, respectivelyCC BY · PubMed Central
Fig. 2 The locations of SSR in Nicotiana genome sequences. Plots show SSR locations in five large scaffolds of Nicotiana genome sequence. The top five largest sequences were extracted from seven Nicotiana genome assemblies, and SSR positions were mined using software GMATA®. The gi number shows the genome sequence ID at GenBank
Fig. 2 The locations of SSR in Nicotiana genome sequences. Plots show SSR locations in five large scaffolds of Nicotiana genome sequence. The top five largest sequences were extracted from seven Nicotiana genome assemblies, and SSR positions were mined using software GMATA®. The gi number shows the genome sequence ID at GenBankCC BY · PubMed Central
Fig. 3 Venn diagram showing the number of common and specific NIX markers in Nicotiana species and varieties (a), varieties of N. tab (b), N. tab K326 and putative progenitors (c). N. ben, N. syl, N. tom, N. oto, N. tab TN90, K326 and BX represent N. benthamiana, N. sylvestris, N. tomentosiformis, N. otophora, N. tabacum TN90, N. tabacum K326, and N. tabacum BX, respectively
Fig. 3 Venn diagram showing the number of common and specific NIX markers in Nicotiana species and varieties (a), varieties of N. tab (b), N. tab K326 and putative progenitors (c). N. ben, N. syl, N. tom, N. oto, N. tab TN90, K326 and BX represent N. benthamiana, N. sylvestris, N. tomentosiformis, N. otophora, N. tabacum TN90, N. tabacum K326, and N. tabacum BX, respectivelyCC BY · PubMed Central
Fig. 4 Experimental validations of NIX markers by amplification and allele scoring. Image shows the PCR fragments resolved by agarose gel (a) or DNA fragment analyzer ABI3730X (b). N. syl, N. tom, N. Tab HD, N. Tab K326, and N. ben represent N. sylvestris, N. tomentosiformis, N. tabacum HD, N. tabacum K326 (K), and N. benthamiana (B), respectively. The numbers in the image represent validated IDs for markers
Fig. 4 Experimental validations of NIX markers by amplification and allele scoring. Image shows the PCR fragments resolved by agarose gel (a) or DNA fragment analyzer ABI3730X (b). N. syl, N. tom, N. Tab HD, N. Tab K326, and N. ben represent N. sylvestris, N. tomentosiformis, N. tabacum HD, N. tabacum K326 (K), and N. benthamiana (B), respectively. The numbers in the image represent validated IDs for markersCC BY · PubMed Central
Fig. 5 The online tobacco markers and primers database TMPD. The TMPD database is freely available online at http://biodb.sdau.edu.cn/tmpd/index.html. Images a, b, c, and d show the TMPD interface, search function, Blast function and validation search function
Fig. 5 The online tobacco markers and primers database TMPD. The TMPD database is freely available online at http://biodb.sdau.edu.cn/tmpd/index.html. Images a, b, c, and d show the TMPD interface, search function, Blast function and validation search functionCC BY · PubMed Central

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Metadata

Authors
Wang, X., Yang, S., Chen, Y., Zhang, S., Zhao, Q., Li, M., Gao, Y., Yang, L., & Bennetzen, J. L.
ORCID
Wang, Xuewen
Venue
BMC Genomics
Publisher
Springer Science and Business Media LLC
Published
2018-06-27
Volume
19
Issue
1
ISSN
1471-2164
DOI
10.1186/s12864-018-4878-4
PMC
PMC6020451
Cited by
56
References
1
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (tdm)
Funders
the Kunming Institute of Botany, Chinese Academy of Sciences

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