Aspergillus nidulans Assembly

Methodology Overview

The Aspergillus nidulans genome was sequenced using the Whole Genome Shotgun methodology, whereby:
  1. Genomic DNA is shattered into small fragments (~4 kb, ~10 kb or ~40 kb)
  2. These fragments are inserted into vectors to create 4 kb & 10 kb plasmids and 40 kb Fosmids respectively
  3. The 110 kb BAC library is provided by Dr Ralph Dean at North Carolina State University
  4. The two ends of the fragment are sequenced, creating paired reads
  5. The assembly process uses the paired reads to identify contiguous stretches of sequence (contigs)
  6. Contigs are ordered and linked together into larger supercontigs by using paired reads lying in different contigs

Assembly Data

Assembly 1, 2/18/2003

Sequencing Facts

  • 13X genomic coverage
  • 30 Mb total length of combined contigs (30,068,514 bp)
  • 248 contigs longer than 2 kb
  • 89 supercontigs (scaffolds)
  • 121 kb average contig length (range 2-1114 kb)
  • 338 kb average supercontig length (range 2-4290 kb)
  • 282 kb contig N50 (average base lies in a contig of length >= 282 kb)
  • 2.44 Mb supercontig N50 (average base lies in a supercontig of length >= 2.44 Mb)

This assembly is created from 10X reads sequenced at the Broad Institute combined with 3X reads provided by Monsanto.

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. Supercontig 1.2 contains contigs 1.22,1.23,..., 1.43.

  • Supercontigs are numbered in order of decreasing length. For example, supercontig 1.1 is the largest with 4.3 Mb, and supercontig 1.89 is the smallest with 2 kb.

    See Supercontig Table for a list of all supercontigs with their lengths and contained contigs, or download a comma-separated file supercontigs.csv.

  • Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3...20,21 (in that order).

    See Contig Table for a list of all contigs with their lengths and supercontigs, or download a comma-separated file contigs.csv.

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

Library Clones

We end sequenced plasmid, fosmid, and BAC libraries.

Library Name # Clone ends mapped to Assembly 1
Monsanto300,327
Broad Fosmid75,624
Broad 10 kb Plasmid80,757
Broad 4 kb Plasmid254,603
Dean lab BAC (AN_FBa)19,123
total730,434