Development of a lab-made microarray for analyzing the genetic diversity of nitrogen fixing symbionts Sinorhizobium meliloti and Sinorhizobium medicae

Bailly, X., Olivieri, I., de Mita, S., Cleyet-Marel, J. C., Béna, G., in press. Recombination and selection shape the molecular diversity pattern of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Mol. Ecol. Bertucci, 1999, Sensitivity issues in DNA array-based expression measurements and performance of nylon microarrays for small samples, Hum. Mol. Genet., 8, 1715, 10.1093/hmg/8.9.1715 Bertucci, 2003, Gene expression profiling of breast carcinomas using nylon DNA arrays, C. R. Biol., 326, 1031, 10.1016/j.crvi.2003.09.010 Booth, 2003, Design of oligonucleotide arrays to detect point mutations: molecular typing of antibiotic resistant strains of Neisseria gonorrhoeae and hantavirus infected deer mice, Mol. Cell Probes, 17, 77, 10.1016/S0890-8508(03)00005-7 Breslauer, 1986, Predicting DNA duplex stability from the base sequence, Proc. Natl. Acad. Sci. U. S. A., 83, 3746, 10.1073/pnas.83.11.3746 Brumfield, 2003, The utility of single nucleotide polymorphisms in inferences of population history, Trends Ecol. Evol., 18, 249, 10.1016/S0169-5347(03)00018-1 Brunel, 1996, Comparison of nucleotide diversity and symbiotic properties of Rhizobium meliloti populations from annual Medicago species, FEMS Microbiol. Ecol., 19, 71, 10.1111/j.1574-6941.1996.tb00200.x Chang, 1974, Effects of microscopic and macroscopic viscosity on the rate of renaturation of DNA, Biopolymers, 13, 1847, 10.1002/bip.1974.360130915 Chen, 1993, A simple and rapid method for the preparation of gram-negative bacterial genomic DNA, Nucleic Acids Res., 21, 2260, 10.1093/nar/21.9.2260 Coenye, 2002, Multilocus restriction typing: a novel tool for studying global epidemiology of Burkholderia cepacia complex infection in cystic fibrosis, J. Infect. Dis., 185, 1454, 10.1086/340279 Drmanac, 2002, Sequencing by hybridization (SBH): advantages, achievements, and opportunities, Adv. Biochem. Eng. Biotechnol., 77, 75 Galibert, 2001, The composite genome of the legume symbiont Sinorhizobium meliloti, Science, 293, 668, 10.1126/science.1060966 Gevers, 2005, Opinion: re-evaluating prokaryotic species, Nat. Rev. Microbiol., 3, 733, 10.1038/nrmicro1236 Hacia, 1999, Resequencing and mutational analysis using oligonucleotide microarrays, Nat. Genet., 21, 42, 10.1038/4469 Hacia, 1996, Detection of heterozygous mutations in BRCA1 using high density oligonucleotide arrays and two-colour fluorescence analysis, Nat. Genet., 14, 441, 10.1038/ng1296-441 Held, 2003, Modeling of DNA microarray data by using physical properties of hybridization, Proc. Natl. Acad. Sci. U. S. A., 100, 7575, 10.1073/pnas.0832500100 Hutton, 1977, Renaturation kinetics and thermal stability of DNA in aqueous solutions of formamide and urea, Nucleic Acids Res., 4, 3537, 10.1093/nar/4.10.3537 Levicky, 2005, Physicochemical perspectives on DNA microarray and biosensor technologies, Trends Biotechnol., 23, 143, 10.1016/j.tibtech.2005.01.004 Lockhart, 1996, Expression monitoring by hybridization to high-density oligonucleotide arrays, Nat. Biotechnol., 14, 1675, 10.1038/nbt1296-1675 Maiden, 1998, Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms, Proc. Natl. Acad. Sci. U. S. A., 95, 3140, 10.1073/pnas.95.6.3140 Morin, 2004, SNPs in ecology, evolution and conservation, Trends Ecol. Evol., 19, 208, 10.1016/j.tree.2004.01.009 Nicholas, 1997, GeneDoc: analysis and visualization of genetic variation, EMBNEW. NEWS, 4, 14 Panjkovich, 2005, Comparison of different melting temperature calculation methods for short DNA sequences, Bioinformatics, 21, 711, 10.1093/bioinformatics/bti066 Panjkovich, 2005, dnaMATE: a consensus melting temperature prediction server for short DNA sequences, Nucleic Acids Res., 33, W570, 10.1093/nar/gki379 Pease, 1994, Light-generated oligonucleotide arrays for rapid DNA sequence analysis, Proc. Natl. Acad. Sci. U. S. A., 91, 5022, 10.1073/pnas.91.11.5022 Richmond, 1999, Genome-wide expression profiling in Escherichia coli K-12, Nucleic Acids Res., 27, 3821, 10.1093/nar/27.19.3821 Rome, 1996, Sinorhizobium medicae sp. nov., isolated from annual Medicago spp., Int. J. Syst. Bacteriol., 46, 972, 10.1099/00207713-46-4-972 Rose, 2002, Hybridization parameters revisited: solutions containing SDS, Biotechniques, 33, 54, 10.2144/02331st01 Schwartz, 1984, Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis, Cell, 37, 67, 10.1016/0092-8674(84)90301-5 Sekar, 2005, Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres, Nucleic Acids Res., 33, 366, 10.1093/nar/gki163 Southern, 1999, Molecular interactions on microarrays, Nat. Genet., 21, 5, 10.1038/4429 Sunnucks, 2000, SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology, Mol. Ecol., 9, 1699, 10.1046/j.1365-294x.2000.01084.x Thompson, 1997, The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876 Urakawa, 2003, Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays, Appl. Environ. Microbiol., 69, 2848, 10.1128/AEM.69.5.2848-2856.2003 Vincent, 1970, A manual for the practical study of root-nodule bacteria, vol. 15, 73 Vos, 1995, AFLP: a new technique for DNA fingerprinting, Nucleic Acids Res., 23, 4407, 10.1093/nar/23.21.4407 Wang, 1998, Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome, Science, 280, 1077, 10.1126/science.280.5366.1077 Wetmur, 1968, Kinetics of renaturation of DNA, J. Mol. Biol., 31, 349, 10.1016/0022-2836(68)90414-2 Williams, 1990, DNA polymorphisms amplified by arbitrary primers are useful as genetic markers, Nucleic Acids Res., 18, 6531, 10.1093/nar/18.22.6531 Wrobel, 2003, Optimization of high-density cDNA-microarray protocols by ‘design of experiments’, Nucleic Acids Res., 31, e67, 10.1093/nar/gng067 Zwick, 2005, Microarray-based resequencing of multiple Bacillus anthracis isolates, Genome Biol., 6, R10, 10.1186/gb-2004-6-1-r10