Genome-wide microsatellite identification in the fungus anisogramma anomala using illumina sequencing and genome assembly

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Cai, Guohong ^a,b   Leadbetter, Clayton W ^a   Muehlbauer, Megan F ^a   Molnar, Thomas J ^a   Hillman, Bradley I ^a  

^a The State University of New Jersey   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASCOMYCOTA; DATABASES, GENETIC; GENETIC MARKERS; GENOME, FUNGAL; MICROSATELLITE REPEATS;

EID: 84894260881     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0082408     Document Type: Article

References (39)

1. Dutech C, Enjalbert J, Fournier E, Delmotte F, Barrès B et al. (2007) Challenges of microsatellite isolation in fungi. Fungal Genet Biol 44: 933-949. doi:10.1016/j.fgb.2007.05.003. PubMed: 17659989.
2. Castoe TA, Poole AW, Gu WJ, de Koning APJ, Daza JM et al. (2010) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Mol Ecol Resour 10: 341-347. doi:10.1111/j.1755-0998.2009.02750.x. PubMed: 21565030.
3. Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T et al. (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26: 403-404. doi:10.1093/bioinformatics/btp670. PubMed: 20007741.
4. Allentoft ME, Schuster SC, Holdaway RN, Hale ML, McLay E et al. (2009) Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. BioTechniques 46: 195-200. doi:10.2144/000113086. PubMed: 19317662.
5. Abdelkrim J, Robertson BC, Stanton JAL, Gemmell NJ (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques 46: 185-191. doi:10.2144/000113084. PubMed: 19317661.
6. Ji PF, Zhang Y, Li C, Zhao ZX, Wang J et al. (2012) High throughput mining and characterization of microsatellites from common carp genome. Int J Mol Sci 13: 9798-9807. doi:10.3390/ijms13089798. PubMed: 22949831.
7. Yu J-N, Won C, Jun J, Lim Y, Kwak M (2011) Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus. PLOS ONE 6: e26933. doi:10.1371/journal.pone. 0026933. PubMed: 22069476.
8. Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF et al. (2012) Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLOS ONE 7: e30953. doi:10.1371/journal.pone.0030953. PubMed: 22348032.
9. Peck CH (1875) Report of the botanist. Annual Report on the New York Museum of Natural History 28: 31-88.
10. Halsted BD (1892) A serious filbert disease. New Jersey State Agricultural Experiment Station Annual Report 13: 287-289.
11. Humphrey JE (1893) A hazel fungus. Massachusetts State Agricultural Experiment Station (Amherest) Annual Report 10: 242-243.
12. Morris RT (1920) Hazel nuts. American Nut Journal 12: 57.
13. Barss HP (1930) Eastern filbert blight. California Agriculture Department Bulletin 19: 489-490.
14. Mehlenbacher SA (1991) Hazelnuts (Corylus). In: JN MooreJR Jr. Ballington. Genetic resources of temperate fruit and nut crops. Wageningen, Netherlands: Int. Soc. Hort. Sci. pp. 789-836.
15. Gottwald TR, Cameron HR (1980) Disease increase and the dynamics of spread of canker caused by Anisogramma anomala in european filbert in the pacific Northwest. Phytopathology 70: 1087-1092. doi: 10.1094/Phyto-70-1087.
16. Johnson KB, Mehlenbacher SA, Stone JK, Pscheidt JW, Pinkerton JN (1996) Eastern filbert blight of European hazelnut: It's becoming a manageable disease. Plant Disease 80: 1308-1316. doi:10.1094/PD-80-1308.
17. Davidson AD, Davidson JRM (1973) Apioporthe and Monchaetia canker reported in western Washington. Plant Disease Reporter 57: 522-523.
18. Pinkerton JN, Johnson KB, Theiling KM, Griesbach JA (1992) Distribution and characteristics of the eastern filbert blight epidemic in western Oregon. Plant Disease 76: 1179-1182. doi:10.1094/PD-76-1179.
19. Mehlenbacher SA, Thompson MM, Cameron HR (1991) Occurrence and inheritance of resistance to eastern filbert blight in 'Gasaway' hazelnut. Hortscience 26: 410-411.
20. Mehlenbacher SA, Thompson MM (1991) Four Hazelnut pollenizers resistant to eastern filbert blight. Hortscience 26: 442-443.
21. Mehlenbacher SA, Smith DC (2004) Hazelnut pollenizers 'Gamma', 'Delta', 'Epsilon', and 'Zeta'. Journal of Hort-Science 39: 1498-1499.
22. Mehlenbacher SA, Azarenko AN, Smith DC, McCluskey R (2007) 'Santiam' hazelnut. Hortscience 42: 715-717.
23. Mehlenbacher SA, Smith DC, McCluskey RL (2009) 'Yamhill' hazelnut. Hortscience 44: 845-847.
24. Mehlenbacher SA, Smith DC, McCluskey RL (2012) 'Eta' and 'Theta' hazelnut pollenizers. Journal of Hort-Science 47: 1180-1181.
25. Molnar TJ, Goffreda JC, Funk CR (2010) Survey of Corylus resistance to Anisogramma anomala from different geographic locations. Journal of Hort-Science 45: 832-836.
26. Capik JM, Molnar TJ (2012) Assessment of Host (Corylus sp.) Resistance to eastern filbert blight in New Jersey. Journal of the American Society of Horticultural Science 137: 157-172.
27. Molnar TJ, Capik JM (2012) Advances in hazelnut research in North America. Acta Hort 940: 57-65.
28. Stone JK, Pinkerton JN, Johnson KB (1994) Axenic culture of Anisogramma anomala: evidence for self-Inhibition of ascospore germination and colony growth. Mycologia 86: 674-683. doi: 10.2307/3760539.
29. Li R, Zhu H, Ruan J, Qian W, Fang X et al. (2009) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research: -.
30. Gregory TR, Nicol JA, Tamm H, Kullman B, Kullman K et al. (2007) Eukaryotic genome size databases. Nucleic Acids Res 35: D332-D338. PubMed: 17090588.
31. Thiel, Michalek, Varshney Graner (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). TAG Theoretical and Applied Genetics 106: 411-422.
32. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: S KrawetzS Misener. Bioinformatics Methods and Protocols: Methods in Molecular Biology. Totowa, NJ: Humana Press. pp. 365-368.
33. Cavagnaro PF, Senalik DA, Luming Y, Simon PW, Harkins TT, et al. (2010) Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). Bmc Genomics 11: 569-586.
34. Yamaoka Y, Katsuya K (1984) Study on axenic cultures of Melampsora chelidonii-pierotii, Melampsora coleosporioides and Melampsoridium betulinum. Transactions of the Mycological Society of Japan 25. pp. 435-444.
35. Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18: 233-234. doi:10.1038/72708. PubMed: 10657137.
36. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21: 2128-2129. doi:10.1093/ bioinformatics/bti282. PubMed: 15705655.
37. Weir BS (1996) Genetic data analysis, II: Methods for discrete population genetic data. Sinauer Associates, Inc. Sunderland, Massachusetts.
38. Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331. PubMed: 6247908.
39. Chakraborty R, Jin L (1993) Determination of relatedness between individuals using DNA fingerprinting. Hum Biol 65: 875-895. PubMed: 8300084.