Cytogenetics of the Tomato Genome Sequence

The sequenced tomato genome [Solanum lycopersicum, 2n = 2x = 24) was recently reported in Nature (485:635).  The twelve DNA pseudomolecules corresponding to tomato chromosomes consist of scaffolds separated by unsequenced gaps.  Scaffolds were ordered and oriented using the tomato molecular linkage map and fluorescence in situ hybridization (FISH).  Although results using the two methods generally agree for scaffolds in euchromatin where crossing over is frequent, they often did not agree for scaffolds in heterochromation or in small scaffolds where crossing over is infrequent.  Disagreements were resolved in favor of the linkage map in the published tomato sequence, but we believe FISH should have been given precedence for the following reasons:  1) FISH is a more direct method of ordering and orienting scaffolds.  2) FISH is equally accurate in eu- and heterochromatin. This is particularly important because 75% of the tomato genome occurs in heterochromatin where most of the disagreements occur.  3) Optical sequencing has been performed at some sites of disagreement, and the results invariably support interpretations from FISH.  4) Unlike linkage maps, FISH permits estimates of gap sizes.  And 5)  FISH can be used to localize chromosome 0 BACs (BACs with DNA sequences that are not complementary to any ordered scaffold) which are important because most chromosome 0 BACs localize to gaps where they can be used as seed BACs for sequencing gaps.  Therefore, we recommend FISH for ordering and orienting scaffolds, determining gap sizes and locating chromosome 0 BACs in all organisms with suitable chromosome cytology.