Using LTC Software for Wheat Physical Mapping: Increasing Contig Lengths and MTP Quality

Recently, a new analytical system for physical contig assembly was developed as a part of TriticeaeGenome initiative and implemented in LTC software as an alternative or complementary tool to FPC. LTC provides more effective detection of problematic clones and clone overlaps and better ordering of clones within contigs. These features reduce the risks associated with chimerical contigs classically encountered with FPC. The effectiveness of LTC was checked on simulated data (based on sequenced genomes of maize and rice) and on real data of different species including wheat and barley. Systematic comparison of LTC and FPC physical maps demonstrates that LTC produces longer and more reliable contigs. In addition to de novo contig assembly and minimal tilling path (MTP) selection, LTC enables curing gaps, reviewing, reordering, and elongating of contigs and MTPs obtained by standard FPC package; it includes tools for simplification of positive clone identification (during the anchoring procedure) based on the list of positive pools. LTC can utilize available marker and sequence information in manual editing, verifying, and merging of contigs and MTPs. LTC also can be used for testing the quality of clone sequencing, checking overlaps of MTP clones at the sequence level and suggesting solutions for repairing the observed gaps.