Login

Sequencing & Assembly

Methodology Overview

The Puccinia graminis f. sp. tritici genome was sequenced using the Whole Genome Shotgun methodology, whereby:

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

Assembly Data

Assembly 1, December 21, 2006

Sequencing Facts

  • Total length of assembly: 81.521 Mb
  • 7.88 (6.75 q>20)X sequencing coverage of the genome
  • 4557 contigs in 392 scaffolds (supercontigs)
  • 81.521 Mb total length of combined contigs (81,521,292 bp)
  • Average base lies in a contig with length at least 39.496 Kb (contig N50)
  • Average base lies within a supercontig with length at least 961.537 Kb (supercontig N50)

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 with 3.075 Mb, and supercontig 1.392 is the smallest with 2.878 Kb.

    See the Assembly Structure for a list of all supercontigs with their lengths and contained contigs.

  • Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3...392 (in that order).

    See the Assembly Structure to explore the contigs of each supercontig or download a comma-separated file.

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