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Chromosome 8 Chromosome 8 Sequencing: Current Sequencing: Current
Status and Future Status and Future Prospects toward Prospects toward
Second Tomato Finishing Workshop, Apr. 24-25, 2008
921651.8
791431.8
671712.6
621372.2
401193.0
631011.6
511122.2
33872.6
401162.9
41872.1
431032.4
391203.1
# anchorscM chr lengthcM per anchor
Distribution of Anchor Markers on Chromosomes
Initial seeds on Chr.8
Sequence strategyWe have been taking the same strategy
applied in the Lotus japonicus genome project.
<Shotgun sequencing of BAC clones>
•vector for the shotgun clone: pUC118•insert size of the shotgun clone: ca. 3 kb•template DNA preparation: TempliPhi•sequencing chemistry: AB Big Dye Terminator
•sequencer: AB 3730•gap closing in finishing phase: primer walking
shotgun clone or BAC direct
<Walking from seed clones>
• BAC end sequence database
Problem
• It is impossible to continue walking from the small number of seed points
– Extension terminated at 18/33 seed points
Complementary Efforts in Japan
1. Development of EST-derived new microsatellite markers to obtain more seed points for sequencing
2. Gap filling by an alternative sequencing strategy