Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

Authors

Stefano Lonardi, University of California - RiversideFollow
Denisa Duma, University of California - Riverside
Matthew Alpert, University of California - Riverside
Francesca Cordero, Universita di TorinoFollow
Marco Beccuti, Universita di TorinoFollow
Prasanna R. Bhat, University of California - Riverside
Yonghui Wu, University of California - RiversideFollow
Gianfranco Ciardo, University of California - Riverside
Burair Alsaihati, King Abdulaziz City for Science and Technology
Steve Wanamaker, University of California - Riverside
Josh Resnik, University of California - Riverside
Serdar Bozdag, Marquette UniversityFollow
Ming-Cheng Luo, University of California - DavisFollow
Timothy J. Close, University of California - RiversideFollow

Document Type

Article

Language

eng

Publication Date

4-2013

Publisher

Public Library of Science

Source Publication

PLoS Computational Biology

Source ISSN

1553-734X

Original Item ID

doi: 10.1371/journal.pcbi.1003010

Abstract

For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

Comments

Published version. PLoS Computational Biology, Vol. 9, No. 4 (April 2013). DOI. © 2013 Public Library of Science. Used with permission.

Recommended Citation

Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; and Close, Timothy J., "Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space" (2013). Mathematics, Statistics and Computer Science Faculty Research and Publications. 113.
https://epublications.marquette.edu/mscs_fac/113