Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology
Abstract
:1. Introduction
2. Previous Work in the Development of a DNA Microarray for Cronobacter Species Identity
3. Recent Work Describing the Use of the Cronobacter Microarray to Data Mine Specific Alleles
4. Future Directions
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Species and Strain | Number of Alleles from Each Strain | Number Present (% Present) b | Genome NCBI c Accession Numbers | Plasmid Name, NCBI Accession Numbers |
---|---|---|---|---|
C. sakazakii ATCC BAA-894 | 2035 | 1904 (93.5) | NC_009778 | pESA3, NC_009780.1; pESA2, NC_009779.1 |
4.01C | 139 | 132 (94.9) | AJLB00000000.1 | pESA3-like, AJLB00000000.1 |
2151 | 201 | 171 (85.0) | AJKT01000000.1 | pESA3- and pCSA2151, AJKT01000000.1 |
Es35 | 202 | 188 (93.0) | AJLC00000000.1 | pESA3- and pCTU3-like, AJLC00000000.1) |
Es764 | 304 | 266 (87.5) | AJLA00000000.1 | pESA3-like, AJLA00000000.1 |
C. turicensis LMG23827T | 4402 | 4039 (91.7) | NC_013282.2 | pCTU1, NC_013283.1; pCTU2, NC_013284.1; pCTU3, NC_013285 |
C. malonaticus | ||||
LMG23826T | 1582 | 1434 (90.6) | AJKV01000000.1 | pCMA1, NZ_CP013941.1/CP013941.1; pCMA2, NZ_CP013942.1/CP013942.1 |
CDC2193-01 | 257 | JXTD00000000.1 | pCTU1-like, JXTD00000000.1 | |
C. dublinensis | ||||
C. dublinensis subsp.d dublinensis LMG23823T | 781 | 745 (95.4) | AJKZ01000000.1 | pCTU1-like, AJKZ01000000.1 |
C. dublinensis subsp. lausannensis LMG23824T | 2580 | 2386 (92.5) | AJKY01000000.1 | pCTU1-like, AJKY01000000.1 |
C. muytjensii ATCC 51329T | 1754 | 1708 (97.3) | AJKU01000000.1 | No Plasmid |
C. universalis NCTC9529T | 1315 | 1201 (91.3) | AJKW01000000.1 | pEAS3-like, AJKW01000000.1 |
C. condimenti LMG26250T | 2611 | 2498 (95.7) | CAKW00000000.1 | pCTU1-like, CAKW00000000.1 |
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Tall, B.D.; Gangiredla, J.; Grim, C.J.; Patel, I.R.; Jackson, S.A.; Mammel, M.K.; Kothary, M.H.; Sathyamoorthy, V.; Carter, L.; Fanning, S.; et al. Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology. Microarrays 2017, 6, 6. https://doi.org/10.3390/microarrays6010006
Tall BD, Gangiredla J, Grim CJ, Patel IR, Jackson SA, Mammel MK, Kothary MH, Sathyamoorthy V, Carter L, Fanning S, et al. Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology. Microarrays. 2017; 6(1):6. https://doi.org/10.3390/microarrays6010006
Chicago/Turabian StyleTall, Ben D., Jayanthi Gangiredla, Christopher J. Grim, Isha R. Patel, Scott A. Jackson, Mark K. Mammel, Mahendra H. Kothary, Venugopal Sathyamoorthy, Laurenda Carter, Séamus Fanning, and et al. 2017. "Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology" Microarrays 6, no. 1: 6. https://doi.org/10.3390/microarrays6010006
APA StyleTall, B. D., Gangiredla, J., Grim, C. J., Patel, I. R., Jackson, S. A., Mammel, M. K., Kothary, M. H., Sathyamoorthy, V., Carter, L., Fanning, S., Iversen, C., Pagotto, F., Stephan, R., Lehner, A., Farber, J., Yan, Q. Q., & Gopinath, G. R. (2017). Use of a Pan–Genomic DNA Microarray in Determination of the Phylogenetic Relatedness among Cronobacter spp. and Its Use as a Data Mining Tool to Understand Cronobacter Biology. Microarrays, 6(1), 6. https://doi.org/10.3390/microarrays6010006