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Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper
Author(s) -
Peters Sander A.,
Bargsten Joachim W.,
Szinay Dóra,
van de Belt José,
Visser Richard G.F.,
Bai Yuling,
de Jong Hans
Publication year - 2012
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2012.05012.x
Subject(s) - synteny , biology , genetics , retrotransposon , homology (biology) , gene , solanaceae , genome , transposable element
Summary We have analysed the structural homology in euchromatin regions of tomato, potato and pepper with special attention for the long arm of chromosome 2 (2L). Molecular organization and colinear junctions were delineated using multi‐color BAC FISH analysis and comparative sequence alignment. We found large‐scale rearrangements including inversions and segmental translocations that were not reported in previous comparative studies. Some of the structural rearrangements are specific for the tomato clade, and differentiate tomato from potato, pepper and other Solanaceous species. Although local gene vicinity is largely preserved, there are many small‐scale synteny perturbations. Gene adjacency in the aligned segments was frequently disrupted for 47% of the ortholog pairs as a result of gene and LTR retrotransposon insertions, and occasionally by single gene inversions and translocations. Our data also suggests that long distance intra‐chromosomal rearrangements and local gene rearrangements have evolved frequently during speciation in the Solanum genus, and that small changes are more prevalent than large‐scale differences. The occurrence of sonata and harbinger transposable elements and other repeats near or at junction breaks is considered in the light of repeat‐mediated rearrangements and a reconstruction scenario for an ancestral 2L topology is discussed.