JGI Clone Resource Task

Large-insert clones for sequencing are being mapped, selected, and validated at JGI member laboratories. Jan-Fang Cheng (LBNL) discussed JGI development of clone-based maps for production sequencing; other team leaders are Norman Doggett (LANL) and Anne Olsen (LLNL). Among the major goals are the complete closure and validation of existing maps of chromosomes 5, 16, and 19; selection of new mapping targets; and creation of pools and high-density filters of newly approved BAC libraries for STS screening.

Cheng observed that this years challenge is to build templates for the FY 1999 ramp-up and beyond. Optimistic goals are to generate 70 Mb of contigs longer than 1 Mb, with associated restriction mapping data and over tenfold genome coverage. Summarizing the current map status of chromosomes 16, 19, and 5, Cheng reported that more than 70 Mb of contigs greater than 300 kb has been generated, with over 25 contigs (40 Mb) larger than 1 Mb.

Cheng pointed out that before JGI was established, the three laboratories used different clone types as well as different mapping approaches. Currently, the mapping plan calls for three autonomous map-production teams, although ideally one major production site will generate templates for PSF; a centralized clone repository will be set up with 1-Mb contigs prioritized for sequencing.

Breakdown for the clone resource task is resource production (15%), pilot R&D projects (15%), STS-content mapping (35%), and restriction mapping (35%). Cheng observed that, unlike sequencing strategies, mapping techniques evolve quickly and scientists want to retain flexibility.

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JGI Clone Resource Task

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