Sequence and analysis of the tomato JOINTLESS locus

Abstract

A 119-kb bacterial artificial chromosome from the JOINTLESS locus on the tomato (Lycopersicon esculentum) chromosome 11 contained 15 putative genes. Repetitive sequences in this region include one copia-like LTR retrotransposon, 13 simple sequence repeats, three copies of a novel type III foldback transposon, and four putative short DNA repeats. Database searches showed that the foldback transposon and the short DNA repeats seemed to be associated preferably with genes. The predicted tomato genes were compared with the complete Arabidopsis genome. Eleven out of 15 tomato open reading frames were found to be colinear with segments on five Arabidopsis bacterial artificial chromosome/P1-derived artificial chromosome clones. The synteny patterns, however, did not reveal duplicated segments in Arabidopsis, where over half of the genome is duplicated. Our analysis indicated that the microsynteny between the tomato and Arabidopsis genomes was still conserved at a very small scale but was complicated by the large number of gene families in the Arabidopsis genome.

Figure 1

A graphical display of the predicted ORFs and the DNA elements on BAC 240K04. Arrows for each ORF indicate the coding orientation. The pointed arrows on 240K04.1 and 240K04.15 indicate that these two ORFs are 3′ incomplete and the blunt arrows flanking the retrotransposon represent the two LTRs.

Figure 2

Characterization of foldback transposon TAPIR. a, Strong secondary structure of the TAPIR element. b, A PCR survey of the three TAPIR loci in various tomato lines/species. Primers used are: TAPIR1f, 5′GAT AGT TAA AGA TGC GCC TAA C3′; TAPIR1r, 5′CGT GTG GGT GTA TAT CTA TTC3′; TAPIR2f, 5′GGT AGA TAG GCA AAA GTT TC3′; TAPIR2r, 5′GAA TAG ATA TAC ACC CAC ACG3′; TAPIR3f, 5′CAC TTG TTA TAC ACT TGT GAT GG3′; and TAPIR3r, 5′CCT TGT TGG GTA TTT GCA TGT G3′. c, The sequence of the direct repeats (DRs) flanking the tomato TAPIRs. d, A phylogenetic tree developed using the middle loop sequences of 12 TAPIRs. 1BF09F, 3DC06F, and 3AB02F were three BAC ends. The lowercase r indicates the reverse strand.

Figure 3

A schematic display of the Arabidopsis syntenic segments to tomato BAC 240K04. The number of centiMorgans (cM) indicate the approximate positions of the corresponding Arabidopsis BAC/P1-derived artificial chromosome clones on the Arabidopsis genome. Black arrows indicate ORFs that do not fall in any colinear segments. Arrows on the tomato BAC indicate approximate positions of the predicted ORFs, whereas arrows on Arabidopsis BAC/P1-derived artificial chromosome clones indicate major homologous regions.