Sequencing & Assembly

Methodology Overview

The Ustilago maydis genome was sequenced using the Whole Genome Shotgun methodology, whereby:

  1. Ustilago maydis 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, May 28, 2003

Sequencing Facts

  • Total length of assembly: 19.683 Mb
  • >10X sequencing coverage of the genome
  • 274 contigs in 48 scaffolds (supercontigs)
  • 19.683 Mb total length of combined contigs (19,683,350 bp)
  • Average base lies in a contig with length at least 127 Kb (contig N50)
  • Average base lies within a supercontig with length at least 818 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 2.465 Mb, and supercontig 1.48 is the smallest with 3.049 Kb.

  • Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3...26 (in that order).

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

Library Clones

We end-sequenced the following types of libraries: Plasmid and Fosmid

 

Library Name

# Clone ends mapped to Assembly 1

Plasmid

255,921

Fosmid

31,807

total

287,728