Rapid whole-genome mutational profiling using next-generation sequencing technologies

Douglas R. Smith, Aaron R. Quinlan, Heather E. Peckham, Kathryn Makowsky, Wei Tao, Betty Woolf, Lei Shen, William F. Donahue, Nadeem Tusneem, Michael P. Stromberg, Donald A. Stewart, Lu Zhang, Swati S. Ranade, Jason B. Warner, Clarence C. Lee, Brittney E. Coleman, Zheng Zhang, Stephen F. McLaughlin, Joel Malek, Jon M. SorensonAlan P. Blanchard, Jarrod Chapman, David Hillman, Feng Chen, Daniel S. Rokhsar, Kevin J. McKernan, Thomas W. Jeffries, Gabor T. Marth, Paul M. Richardson

Research output: Contribution to journalArticle

194 Citations (Scopus)

Abstract

Forward genetic mutational studies, adaptive evolution, and phenotypic screening are powerful tools for creating new variant organisms with desirable traits. However, mutations generated in the process cannot be easily identified with traditional genetic tools. We show that new high-throughput, massively parallel sequencing technologies can completely and accurately characterize a mutant genome relative to a previously sequenced parental (reference) strain. We studied a mutant strain of Pichia stipitis, a yeast capable of converting xylose to ethanol. This unusually efficient mutant strain was developed through repeated rounds of chemical mutagenesis, strain selection, transformation, and genetic manipulation over a period of seven years. We resequenced this strain on three different sequencing platforms. Surprisingly, we found fewer than a dozen mutations in open reading frames. All three sequencing technologies were able to identify each single nucleotide mutation given at least 10-15-fold nominal sequence coverage. Our results show that detecting mutations in evolved and engineered organisms is rapid and cost-effective at the whole-genome level using new sequencing technologies. Identification of specific mutations in strains with altered phenotypes will add insight into specific gene functions and guide further metabolic engineering efforts.

Original languageEnglish
Pages (from-to)1638-1642
Number of pages5
JournalGenome Research
Volume18
Issue number10
DOIs
Publication statusPublished - Oct 2008
Externally publishedYes

Fingerprint

Genome
Technology
Mutation
Genetic Transformation
Metabolic Engineering
High-Throughput Nucleotide Sequencing
Pichia
Xylose
Mutagenesis
Open Reading Frames
Ethanol
Nucleotides
Yeasts
Phenotype
Costs and Cost Analysis
Genes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Smith, D. R., Quinlan, A. R., Peckham, H. E., Makowsky, K., Tao, W., Woolf, B., ... Richardson, P. M. (2008). Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research, 18(10), 1638-1642. https://doi.org/10.1101/gr.077776.108

Rapid whole-genome mutational profiling using next-generation sequencing technologies. / Smith, Douglas R.; Quinlan, Aaron R.; Peckham, Heather E.; Makowsky, Kathryn; Tao, Wei; Woolf, Betty; Shen, Lei; Donahue, William F.; Tusneem, Nadeem; Stromberg, Michael P.; Stewart, Donald A.; Zhang, Lu; Ranade, Swati S.; Warner, Jason B.; Lee, Clarence C.; Coleman, Brittney E.; Zhang, Zheng; McLaughlin, Stephen F.; Malek, Joel; Sorenson, Jon M.; Blanchard, Alan P.; Chapman, Jarrod; Hillman, David; Chen, Feng; Rokhsar, Daniel S.; McKernan, Kevin J.; Jeffries, Thomas W.; Marth, Gabor T.; Richardson, Paul M.

In: Genome Research, Vol. 18, No. 10, 10.2008, p. 1638-1642.

Research output: Contribution to journalArticle

Smith, DR, Quinlan, AR, Peckham, HE, Makowsky, K, Tao, W, Woolf, B, Shen, L, Donahue, WF, Tusneem, N, Stromberg, MP, Stewart, DA, Zhang, L, Ranade, SS, Warner, JB, Lee, CC, Coleman, BE, Zhang, Z, McLaughlin, SF, Malek, J, Sorenson, JM, Blanchard, AP, Chapman, J, Hillman, D, Chen, F, Rokhsar, DS, McKernan, KJ, Jeffries, TW, Marth, GT & Richardson, PM 2008, 'Rapid whole-genome mutational profiling using next-generation sequencing technologies', Genome Research, vol. 18, no. 10, pp. 1638-1642. https://doi.org/10.1101/gr.077776.108
Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Research. 2008 Oct;18(10):1638-1642. https://doi.org/10.1101/gr.077776.108
Smith, Douglas R. ; Quinlan, Aaron R. ; Peckham, Heather E. ; Makowsky, Kathryn ; Tao, Wei ; Woolf, Betty ; Shen, Lei ; Donahue, William F. ; Tusneem, Nadeem ; Stromberg, Michael P. ; Stewart, Donald A. ; Zhang, Lu ; Ranade, Swati S. ; Warner, Jason B. ; Lee, Clarence C. ; Coleman, Brittney E. ; Zhang, Zheng ; McLaughlin, Stephen F. ; Malek, Joel ; Sorenson, Jon M. ; Blanchard, Alan P. ; Chapman, Jarrod ; Hillman, David ; Chen, Feng ; Rokhsar, Daniel S. ; McKernan, Kevin J. ; Jeffries, Thomas W. ; Marth, Gabor T. ; Richardson, Paul M. / Rapid whole-genome mutational profiling using next-generation sequencing technologies. In: Genome Research. 2008 ; Vol. 18, No. 10. pp. 1638-1642.
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