Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper

Abstract

SUMMARYWe 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 intrachromosomal 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.

A DArT marker-based linkage map for wild potato Solanum bulbocastanum facilitates structural comparisons between SolanumA and B genomes

“…Cytological and genomics analyses demonstrated that tomato and potato are differentiated by a series of whole arm inversions of chromosomes 2, 5, 6, 9, 10, 11 and 12 (Table 1) [26-30]. To date, no study has explicitly compared the organization of the proposed A and B Solanum genomes using DNA sequence technologies.…”

Indel Group in Genomes (IGG) Molecular Genetic Markers

“…We found that all 32 amplified in cultivated tomato and S. pennellii, 30 in S. tuberosum, and 28 in S. sitiens, with an annealing temperature of 55°C (success rate of approximately 88%-94%; Table IX). The genetic difference between potato and S. sitiens could explain this result (Pertuzé et al, 2002;Peters et al, 2012). We found that 30 (93.8%) of these 32 markers were triallelic relative to potato, displaying scoreable band differences between cultivated tomato, S. pennellii, and S. tuberosum (Table IX).…”

“…Here, we describe how we utilized the IGG pipeline to identify polymorphisms between three genomes that can be useful in cases where populations are developed between species with varying levels of self-incompatibility or where one parent's genome is unsequenced but a closely related sequenced genome exists. Prezygotic and postzygotic hybrid incompatibility between cultivated tomato and S. sitiens has made introgression line development a challenge (DeVerna et al, 1990;Pertuzé et al, 2002Pertuzé et al, , 2003Peters et al, 2012). To aid in the production of S. lycopersicum and S. sitiens hybrids, an interspecific bridging line, F1 S. lycopersicum 3 S. pennellii, was employed.…”

“…We ran IGGPIPE with three genomes (tomato, S. pennellii, and potato) to develop triallelic markers to genotype these crosses. The S. tuberosum (potato) sequence was used as a stand-in for the unsequenced S. sitiens genome, as the two species share the same chromosomal configuration (Pertuzé et al, 2002;Peters et al, 2012).…”

Introgression browser: high‐throughput whole‐genome SNP visualization

“…Such strategies, however, are not sufficient for unravelling complex rearrangements and identification of chromosome breakpoints at nucleotide accuracy. To this end we introduced the combined usage of BAC FISH, genetic markers and reference genome sequence information to elucidate the complex topology of tomato and potato chromosomes as well as detection of introgressed regions (Tang et al, 2008;Peters et al, 2009Peters et al, , 2012Aflitos et al, 2014).…”