Isolation and analysis of high quality nuclear DNA with reduced organellar DNA for plant genome sequencing and resequencing

BMC Biotechnology

Volumn 11, Issue , 2011, Pages

  Lutz, Kerry A ^a,b   Wang, Wenqin ^a   Zdepski, Anna ^a   Michael, Todd P ^c  

^a RUTGERS UNIVERSITY   (United States)

^b FARMINGDALE STATE COLLEGE   (United States)

^c MONSANTO COMPANY   (United States)

Author keywords

Chloroplast DNA; High throughput sequencing; Mitochondrial DNA; Nuclear DNA isolation; Plant genome sequencing; Quantitative real time PCR (qPCR)

Indexed keywords

CHLOROPLAST DNA; HIGH THROUGHPUT; MITOCHONDRIAL DNA; NUCLEAR DNA; PLANT GENOMES; QUANTITATIVE REAL TIME PCR;

CHLOROPHYLL; DNA; MITOCHONDRIA; MOLECULAR WEIGHT; PHENOLS; PLANTS (BOTANY); POLYMERASE CHAIN REACTION; QUALITY CONTROL; THROUGHPUT;

GENE ENCODING;

CELL DNA; CELL NUCLEUS DNA; CHLOROPLAST DNA; MITOCHONDRIAL DNA; PLANT DNA;

ARTICLE; CELL NUCLEUS; COPY NUMBER VARIATION; DNA CONTAMINATION; DNA DETERMINATION; DNA ISOLATION; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; NONHUMAN; PLANT GENOME; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MAIZE; METHODOLOGY; PLANT; SORGHUM;

CELL NUCLEUS; DNA, PLANT; GENOME, PLANT; PLANTS; SEQUENCE ANALYSIS, DNA; SORGHUM; ZEA MAYS;

EID: 79956189425     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-11-54     Document Type: Article

References (36)

1. Varma A, Padh H, Shrivastava N. Plant genomic DNA isolation: An art or a science. Biotechnol J 2007, 2(3):386-392. 10.1002/biot.200600195, 17285676.
2. Zoschke R, Liere K, Borner T. From seedling to mature plant: Arabidopsis plastidial genome copy number, RNA accumulation and transcription are differentially regulated during leaf development. Plant J 2007, 50(4):710-722. 10.1111/j.1365-313X.2007.03084.x, 17425718.
3. Kato N, Reynolds D, Brown ML, Boisdore M, Fujikawa Y, Morales A, Meisel LA. Multidimensional fluorescence microscopy of multiple organelles in Arabidopsis seedlings. Plant Methods 2008, 4:9. 10.1186/1746-4811-4-9, 2424051, 18489765.
4. Warmke HE, Lee SL. Pollen abortion in T cytoplasmic male-sterile corn (Zea mays): A suggested mechanism. Science 1978, 200(4341):561-563. 10.1126/science.200.4341.561, 17839439.
5. De Paepe R, Forchioni A, Chetrit P, Vedel F. Specific mitochondrial proteins in pollen: Presence of an additional ATP synthase β subunit. Proc Natl Acad Sci USA 1993, 90(13):5934-5938. 10.1073/pnas.90.13.5934, 46841, 8327463.
6. Shaver JM, Oldenburg DJ, Bendich AJ. Changes in chloroplast DNA during development in tobacco, Medicago truncatula, pea, and maize. Planta 2006, 224(1):72-82. 10.1007/s00425-005-0195-7, 16362324.
7. Aguettaz P, Seyer P, Pesey H, Lescure A. Relations between the plastid gene dosage and the levels of 16S rRNA and rbcL gene transcripts during amyloplast to chloroplast change in mixotrophic spinach cell suspensions. Plant Mol Biol 1987, 8(2):169-177.
8. Rauwolf U, Golczyk H, Greiner S, Herrmann RG. Variable amounts of DNA related to the size of chloroplasts III. Biochemical determinations of DNA amounts per organelle. Mol Genet Genomics 2010, 283(1):35-47. 10.1007/s00438-009-0491-1, 2799680, 19911199.
9. Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D. Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res 2008, 18(12):2024-2033. 10.1101/gr.080200.108, 2593571, 18818371.
10. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, Fitzgerald LM, Vezzulli S, Reid J, et al. A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS One 2007, 2(12):e1326.. 2147077, 18094749.
11. Huang S, Li R, Zhang Z, Li L, Gu X, Fan W, Lucas WJ, Wang X, Xie B, Ni P, et al. The genome of the cucumber, Cucumis sativus L. Nat Genet 2009, 41(12):1275-1281. 10.1038/ng.475, 19881527.
12. Wicker T, Narechania A, Sabot F, Stein J, Vu GT, Graner A, Ware D, Stein N. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 2008, 9:518. 10.1186/1471-2164-9-518, 2584661, 18976483.
13. Initiative TIB. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463(7282):763-768. 10.1038/nature08747, 20148030.
14. Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 1980, 8(19):4321-4325. 10.1093/nar/8.19.4321, 324241, 7433111.
15. Gendrel AV, Lippman Z, Martienssen R, Colot V. Profiling histone modification patterns in plants using genomic tiling microarrays. Nat Methods 2005, 2(3):213-218. 10.1038/nmeth0305-213, 16163802.
16. Peterson DG TJ, Frisch DA, Wing RA, Paterson AH. Construction of plant bacterial artificial chromosome (BAC) libraries: An illustrated guide. J Agricult Genom 2000, 5.
17. Peterson DG, Kevin S, Stephen M. Isolation of milligram quantities of nuclear DNA from tomato (Lycopersicon esculentum), A plant containing high levels of polyphenolic compounds. Plant Mol Biol Rep 1997, 15(2):148-153.
18. Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker JR, et al. Regulation of flowering time in Arabidopsis by K homology domain proteins. Proc Natl Acad Sci USA 2004, 101(34):12759-12764. 10.1073/pnas.0404552101, 515126, 15310842.
19. Sasson A, Michael TP. Filtering error from SOLiD output. Bioinformatics 2010, 26(6):849-850. 10.1093/bioinformatics/btq045, 20207696.
20. Plachno BJ, Kozieradzka-Kiszkurno M, Swiatek P. Functional utrastructure of Genlisea (Lentibulariaceae) digestive hairs. Ann Bot 2007, 100(2):195-203. 10.1093/aob/mcm109, 2735322, 17550910.
21. Park DH, Somers DE, Kim YS, Choy YH, Lim HK, Soh MS, Kim HJ, Kay SA, Nam HG. Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 1999, 285(5433):1579-1582. 10.1126/science.285.5433.1579, 10477524.
22. Kidd AD, Francis D, Bennett MD. Replicon Size, Mean Rate of DNA Replication and the Duration of the Cell Cycle and its Component Phases in Eight Monocotyledonous Species of Contrasting DNA C Values. Ann Bot 1987, 59(6):603-609.
23. Miller TA, Muslin EH, Dorweiler JE. A maize CONSTANS-like gene, conz1, exhibits distinct diurnal expression patterns in varied photoperiods. Planta 2008, 227(6):1377-1388. 10.1007/s00425-008-0709-1, 18301915.
24. Miwa K, Serikawa M, Suzuki S, Kondo T, Oyama T. Conserved expression profiles of circadian clock-related genes in two Lemna species showing long-day and short-day photoperiodic flowering responses. Plant Cell Physiol 2006, 47(5):601-612. 10.1093/pcp/pcj027, 16524874.
25. Darwin C. Insectivorious plants 1875, London: John Murray.
26. Greilhuber J, Borsch T, Muller K, Worberg A, Porembski S, Barthlott W. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biol (Stuttg) 2006, 8(6):770-777.
27. Fleischmann A, Schaferhoff B, Heubl G, Rivadavia F, Barthlott W, Muller KF. Phylogenetics and character evolution in the carnivorous plant genus Genlisea A. St.-Hil. (Lentibulariaceae). Mol Phylogenet Evol 2010, 56(2):768-783. 10.1016/j.ympev.2010.03.009, 20226867.
28. Barthlott W, Porembski S, Fischer E, Gemmel B. First protozoa-trapping plant found. Nature 1998, 392(6675):447-447.
29. Loomis WD. Overcoming problems of phenolics and quinones in the isolation of plant enzymes and organelles. Methods Enzymol 1974, 31(Pt A):528-544.
30. Carrier G, Santoni S, Rodier-Goud M, Canaguier A, de Kochko A, Dubreuil-Tranchant C, This P, Boursiquot J-M, Cunff LL. An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods. Am J Bot 2011,
31. Fang G, Hammar S, Grumet R. A quick and inexpensive method for removing polysaccharides from plant genomic DNA. Biotechniques 1992, 13(1):52-54, 56.
32. Pandey R, Adams R, Flournoy L. Inhibitions of random amplified polymorphic DNAs (RAPDs) by plant polysaccharides. Plant Mol Biol Rep 1996, 14:17-22.
33. Do N, Adams RP. A simple technique for removing plant polysaccharide contaminants from DNA. Biotechniques 1991, 10(2):162, 164, 166.
34. Ye J, Sayre RT. Reduction of Chloroplast DNA Content in Solanum nigrum Suspension Cells by Treatment with Chloroplast DNA Synthesis Inhibitors. Plant Physiol 1990, 94(3):1477-1483. 10.1104/pp.94.3.1477, 1077402, 16667857.
35. Rowan BA, Oldenburg DJ, Bendich AJ. The demise of chloroplast DNA in Arabidopsis. Curr Genet 2004, 46(3):176-181.
36. Rowan BA, Oldenburg DJ, Bendich AJ. A multiple-method approach reveals a declining amount of chloroplast DNA during development in Arabidopsis. BMC Plant Biol 2009, 9:3. 10.1186/1471-2229-9-3, 2632658, 19128504.