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Magnaporthe Assembly

• Methodology Overview
• Assembly Data
  • Supercontig/Contig Numbering
  • Library Clones

Methodology Overview

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

1. Magnaporthe 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 2, July 18, 2002

Sequencing Facts

• Greater than 7X sequencing coverage of the genome
• 2273 contigs longer than 2 kb
• 159 supercontigs
• 17 kb average contig length (range 2-173 kb)
• 243 kb average supercontig length (range 2-4082 kb)
• 39 Mb total length of combined contigs (38,760,322 bp)
• Average base lies in a contig of length 30 kb
• Average base lies within a supercontig of length 1.6 Mb

Supercontig/Contig Numbering

• Supercontig and contig numbers are preceded by the version of the assembly. For example:
  • Contig 2.25 - refers to contig number 25 within assembly 2.
  • Supercontig 2.2 - refers to supercontig number 2 within assembly 2. Supercontig 2.2 contains contigs 1.203,1.204,..., 1.359.

• Supercontigs are numbered in order of decreasing length. For example, supercontig 2.1 is the largest with 4 Mb, and supercontig 1.159 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 2.1 contains contigs 1,2,3...201,202 (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 2	Sequenced by
Plasmid	436,993	Broad
Fosmid	50,495	Broad
BAC	15,610	FGL/NCSU
total	503,098

The BAC ends used in this assembly were sequenced by Ralph Dean and his team at the Fungal Genomics Laboratory of North Carolina State University, funded by Novartis Foundation.

You can download a comma-separated file listing all clones: BACends.csv (see Download for data details).