The tomato genome is comprised
of approximately 950 Mb of DNA - more than 75% of which
is heterochromatin and largely devoid of genes. The
majority of genes are found in long contiguous stretches
of gene-dense euchromatin located on the distal portions
of each chromosome arm. A minimal tiling path of BAC
clones will be identified through this approximately 220
Mb euchromatin. The starting point for sequencing the
genome will be approximately 1500 "seed" BAC clones
individually anchored to the tomato high density genetic
map based on a single, common L. esculentum x L.
pennellii F2 population (referred to as the F2.2000; view
map on SGN). Sequencing will proceed on a BAC-by-BAC
basis. Each sequenced anchor BAC will serve as a seed
from which to radiate out into the minimum tiling path.
Identification of the correct next BACs in the
euchromatin minimum tiling path for sequencing will be
based on the use of a BAC end sequence database that will
be created as part of this project, as well as a
fingerprint contig physical map that is currently being
constructed. A subset of the sequenced BACs will be
localized on pachytene chromosomes via FISH (fluorescence
in situ hybridization) to help guide the extension of the
tiling path through the euchromatic arms of each
chromosome and to determine when the heterochromatin and
telomeric regions have been reached on each arm. A
bioinformatics portal will be created for this project
that will be mirrored at several locations around the
world and provide a mechanism by which researchers in
different locations can develop and contribute
bioinformatics tools and information to the project. A
common set of standards for BAC sequencing and finishing,
and for gene nomenclature, and structural and functional
gene annotation (please refer to the Solanaceae Project page).
The objectives of the tomato sequencing project are to:
- produce a contiguous sequence of the gene rich,
euchromatic arms of each of the 12 tomato
chromosomes
- process and annotate this sequence in a manner
consistent and compatible with similar data from
Arabidopsis, rice and other plant species.
- create an international bioinformatics portal for
comparative Solanaceae genomics which can store,
process, and make available to the public the sequence
data and derived information from this project and
associated genomics activities in other solanaceous
plants
