Sequencing & Assembly

Whole Genome Shotgun Overview

The Pyrenophora tritici-repentis genome was sequenced using the Whole Genome Shotgun methodology, whereby:

  1. Pyrenophora tritici-repentis DNA is shattered into small fragments (~4 kb or ~40 kb)
  2. Each fragment is inserted into a vector and cloned
  3. The two ends of the fragment are sequenced, creating paired reads

Arachne Assembly

  1. The assembly process uses the paired reads to identify contiguous stretches of sequence (contigs)
  2. Contigs are ordered and linked together into larger supercontigs by using paired reads lying in different contigs

Supercontig/Contig Numbering

  • Supercontig and contig numbers are preceded by the version of the assembly. For example:
    • Contig 1.25 - refers to contig number 25 within assembly 1.
    • Supercontig 1.2 - refers to supercontig number 2 within assembly 1.

  • Supercontigs are numbered in order of decreasing length. For example, supercontig 1.1 is the largest, and supercontig 1.2 is the next largest.

  • Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3... (in that order).

    There is no correspondence between contig or supercontigs numbers in different assemblies.