Sequencing & Assembly

Methodology Overview

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

Botrytis cinerea DNA is shattered into small fragments (~4 kb or ~40 kb)
Each fragment is inserted into a vector and cloned
The two ends of the fragment are sequenced, creating paired reads
The assembly process uses the paired reads to identify contiguous stretches of sequence (contigs)
Contigs are ordered and linked together into larger supercontigs by using paired reads lying in different contigs

Assembly 1, 6/15/2005

Total length of assembly: 42.663 Mb
5.41X sequencing coverage of the genome
4534 contigs in 588 scaffolds (supercontigs)
38.787 Mb total length of combined contigs (38,786,820 bp)
Average base lies in a contig with length at least 16.4 Kb (contig N50)
Average base lies within a supercontig with length at least 256.7 Kb (supercontig N50)

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 1.306 Mb, and supercontig 1.588 is the smallest with 498 bp.
Contigs within supercontigs are ordered positionally. For example, supercontig 1.1 contains contigs 1,2,3...87 (in that order).

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

We end-sequenced the following types of libraries: Plasmid

Library Name	# Clone ends mapped to Assembly 1
Plasmid	291,603
total	291,603