APPLICATIONS OF TECHNOLOGY:
- De novo whole genome shotgun assembly
- Structural variation detection
- 5’ and 3’ end transcript sequencing
- Longer inserts >20,000 base-pairs (20 kb)
- Higher percentage of informative pairs
- Works with high throughput short read sequencing platforms
- Easier workflow
A Berkeley Lab team led by Feng Chen at the Joint Genome Institute has developed a new and more efficient way to order and orient contigs by improving the process of long insert mate-pair library construction. Specifically, the team has developed a novel method of generating mate-pair libraries easily and efficiently.
The utility of current mate-pair libraries is limited by the length of the insert, which serves as a kind of tape measure gauging the length of a gap between contigs. Genome assembly gaps are frequently caused by long stretches of repeating DNA code, but until now, insert length was limited to about 5 kilobases (kb). That is problematic for identifying missing DNA segments and resolving repeat elements, which are frequently much longer. The Berkeley Lab technology is capable of generating inserts of >20 kb, vastly improving the efficiency of the gap-alignment process.
Speedy genome assembly relies on availability of many mate-pair combinations drawn from libraries of millions of possible choices. The Berkeley Lab team engineered a new method, called Cre-LoxP Inverse PCR Paired-End (CLIP-PE), which uses specified enzymes and procedures to quickly generate massive libraries for any genome to be sequenced. With longer insert sizes, more mate-pairs, and a streamlined workflow, the Berkeley Lab method can dramatically improve the quality of genome assembly while significantly reducing the finishing costs.
DEVELOPMENT STAGE: Implemented in JGI production.
STATUS: Patent pending. Available for licensing or collaborative research.
FOR MORE INFORMATION:
Peng, Z., Zhao, Z., Nath, N., Froula, J. L., Clum, A., Zhang, T., Cheng, J-f., Copeland, A. C., Pennacchio, L. A., Chen, F. Generation of Long Insert Pairs Using a Cre-LoxP PCR Approach, PLoSOne 7 (1): e29437. 2012.
SEE THESE OTHER BERKELEY LAB TECHNOLOGIES IN THIS FIELD:j5: Automated DNA Assembly Design Software, ECRB-2836
REFERENCE NUMBER: IB-2944