Meeting the challenges of non-referenced genome assembly from short-read sequence data

Acta Horticulturae

Volumn 859, Issue , 2010, Pages 323-332

  Parks, M ^a   Liston, A ^a   Cronn, R ^b  

^a OREGON STATE UNIVERSITY   (United States)

^b PACIFIC NORTHWEST RESEARCH STATION   (United States)

Author keywords

Illumina; Massively parallel sequencing; Next generation sequencing; Pinus

Indexed keywords

EMBRYOPHYTA; PINACEAE;

EID: 77957320601     PISSN: 05677572     EISSN: None     Source Type: Book Series    
DOI: 10.17660/ActaHortic.2010.859.38     Document Type: Conference Paper

References (25)

1. Ahn, S.-M., Kim, T.-H., Lee, S., Kim, D., Ghang, H., Kim, D.-S., Kim, B.-C., Kim, S.-Y., Kim, W.-Y., Kim, C. et al., 2009. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 19:1622-1629.
2. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al., 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53.
3. Collins, F.S., Lander, E.S., Rogers, J., Waterston, R.H. and Conso, I. 2004. Finishing the euchromatic sequence of the human genome. Nature 431:931-945.
4. Craig, D.W., Pearson, J.V., Szelinger, S., Sekar, A., Redman, M., Corneveaux, J.J., Pawlowski, T.L., Laub, T., Nunn, G. and Stephan, D.A. 2008. Identification of genetic variants using bar-coded multiplexed sequencing. Nature Meth 5:887-893.
5. Cronn, R., Liston, A., Parks, M., Gernandt, D.S., Shen, R. and Mockler, T. 2008. Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-bysynthesis technology. Nucleic Acids Res. 36:e122.
6. Gernandt, D.S., Magallon, S., Geada Lopez, G., Zeron Flores, O., Willyard, A. and Liston, A. 2008. Use of simultaneous analyses to guide fossil-based calibrations of Pinaceae phylogeny. Int. J. Plant Sci. 169:1086-1099.
7. Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E.M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S. and Russ, C. 2009. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotech. 27:182-189.
8. Gupta, P.K. 2009. Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol. 26:602-611.
9. Herman, D.S., Hovingh, G.K., Iartchouk, O., Rehm, H.L., Kucherlapati, R., Seidman, J.G. and Seidman, C.E. 2009. Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection. Nat. Methods 6:507-510.
10. Hillier, L.W., Marth, G.T., Quinlan, A.R., Dooling, D., Fewell, G., Barnett, D., Fox, P., Glasscock, J.I., Hickenbotham, M., Huang, W. et al. 2008. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5:183-188.
11. Holt, R.A. and Jones, S.J.M. 2008. The new paradigm of flow cell sequencing. Genome Res. 18:839.
12. Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., Devon, K., Dewar, K., Doyle, M. and FitzHugh, W. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
13. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. 2009. Ultrafast and memoryefficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
14. Ley, T.J., Mardis, E.R., Ding, L., Fulton, B., McLellan, M.D., Chen, K., Dooling, D., Dunford-Shore, B.H., McGrath, S. and Hickenbotham, M. 2008. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456:66-72.
15. Lidholm, J. and Gustafsson, P. 1991. The chloroplast genome of the gymnosperm Pinus contorta: a physical map and a complete collection of overlapping clones. Curr. Genet. 20:161-166.
16. Mardis, E.R., Ding, L., Dooling, D.J., Larson, D.E., McLellan, M.D., Chen, K., Koboldt, D.C., Fulton, R.S., Delehaunty, K.D., McGrath, S.D. et al. 2009. Recurring mutations found by sequencing an acute myeloid leukemia genome. New Engl. J. Med.: 361:1058-1066. NEJMoa0903840.
17. Meyers, S.C. and Liston, A. 2010. Characterizing the genome of wild relatives of Limnanthes alba (Meadowfoam) using massively parallel sequencing. Acta Hort. 859:309-314.
18. Pop, M. and Salzberg, S.L. 2008. Bioinformatics challenges of new sequencing technology. Trends Genet. 24:142-149.
19. Porreca, G.J., Zhang, K., Li, J.B., Xie, B., Austin, D., Vassallo, S.L., LeProust, E.M., Peck, B.J., Emig, C.J., Dahl, F. et al., 2007. Multiplex amplification of large sets of human exons. Nat. Methods 4:931-936.
20. Simon, S.A., Zhai, J., Nandety, R.S., McCormick, K.P., Zeng, J., Mejia, D. and Meyers, B.C. 2009. Short-read sequencing technologies for transcriptional analyses. Annu. Rev. Plant Biol. 60:305-333.
21. Venter, J.C., Adams, M.D., Myers, E.W., Li, P.W., Mural, R.J., Sutton, G.G., Smith, H.O., Yandell, M., Evans, C.A. and Holt, R.A. 2001. The sequence of the human genome. Science 291:1304-1351.
22. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J. and Zhang, J. 2008. The diploid genome sequence of an Asian individual. Nature 456:60-65.
23. Whiteford, N., Haslam, N., Weber, G., Prugel-Bennett, A., Essex, J.W., Roach, P.L., Bradley, M. and Neylon, C. 2005. An analysis of the feasibility of short read sequencing. Nucleic Acids Res. 33:e171.
24. Whittall, J.B., Syring, J., Parks, M., Buenrostro, J., Dick, C., Liston, A. and Cronn, R. 2009. Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines. Mol. Ecol. (in press)
25. Willyard, A., Syring, J., Gernandt, D.S., Liston, A. and Cronn, R. 2007. Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus. Mol. Biol. Evol. 24:90-101.