Comparative Sequence Analysis Reveals Extensive Microcolinearity in the Lateral Suppressor Regions of the Tomato, Arabidopsis, and Capsella Genomes

Abstract

A 57-kb region of tomato chromosome 7 harboring five different genes was compared with the sequence of the Arabidopsis genome to search for microsynteny between the genomes of these two species. For all five genes, homologous sequences could be identified in a 30-kb region located on Arabidopsis chromosome 1. Only two inversion events distinguish the arrangement of the five genes in tomato from that in Arabidopsis. Inversions were not detected when the arrangement of the five Arabidopsis genes was compared with the arrangement in the orthologous region of Capsella, a plant closely related to Arabidopsis. These results provide evidence for microcolinearity between closely and distantly related dicotyledonous species. The degree of microcolinearity found can be exploited to localize orthologous genes in Arabidopsis and tomato in an unambiguous way. INTRODUCTIONArabidopsis, a small crucifer, has been adopted as a model in plant genome analysis. The small genome size of 125 Mbp and a low number of repetitive elements facilitated the assembly of comprehensive molecular marker and clone contig maps for the five Arabidopsis chromosomes (reviewed in Schmidt, 1998). Sequence analysis of the genome has been completed (The Arabidopsis Genome Initiative, 2000). The 430-Mbp rice genome is a model for monocotyledonous plants, and the rice genome project aims to decipher the entire genomic sequence for this species (Sasaki and Burr, 2000). Equally detailed studies are not feasible for many other plant genomes at present, especially given the large genome sizes of most crop plants. It needs to be established if and how information generated on the Arabidopsis and rice genomes can be used for the study of other plant genomes.Comparative genetic mapping experiments yielded evidence for the conservation of gene repertoire and colinear chromosome segments for related species. An extensive conservation of marker order was found for the 12 tomato and potato chromosomes, and five chromosomal inversions could explain differences in marker organization (Tanksley et al., 1992). For the Poaceae family, a remarkable degree of genome conservation could be established even between species that diverged as long as 60 million years ago and that differ considerably in genome size (reviewed in Gale and Devos, 1998). Comparing the genetic maps of Arabidopsis and different Brassica species also has revealed many colinear chromosome segments for species belonging to the Brassicaceae family (reviewed in Schmidt, 2000). The results of the first microsynteny studies using sequencelevel resolution in the Poaceae (Chen et al., 1997;Messing and Llaca, 1998;Tikhonov et al., 1999) and Brassicaceae families (Grant et al., 1998;Acarkan et al., 2000) support the view that genome colinearity can be observed at the level of genes.Few attempts to analyze genome colinearity between more distantly related species have been reported (Paterson et al., 1996;Devos et al., 1999;van Dodeweerd et al., 1999;Ku et al., 2000). The low degree of sequence homology in distantl...

Molecular analysis of theLATERAL SUPPRESSORgene inArabidopsisreveals a conserved control mechanism for axillary meristem formation

“…Microsynteny analysis between the chromosomal segments harboring the LATERAL SUPPRESSOR genes in tomato and Arabidopsis has demonstrated that both genes are orthologous (Rossberg et al 2001). However, the LATERAL SUPPRESSOR proteins of both species show only 50.5% identity.…”

“…AC005223), which both contain the most homologous LATERAL SUPPRESSOR gene (At1g55580). Microsynteny studies between the tomato Ls region and the identified BAC clones demonstrated that the gene repertoire within this region is completely conserved, but two inversions distinguish the arrangements of genes in both species (Rossberg et al 2001). These results demonstrate that the isolated DNA segment contains the Ls-orthologous gene from Arabidopsis (LAS).…”

Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy

“…Cold Spring Harbor Laboratory Press on May 9, 2018 -Published by genome.cshlp.org Downloaded from 2001a) even for species that are thought to have diverged from Arabidopsis as much as 100 Mya or more (Paterson et al 1996;Ku et al 2000;Mayer et al 2001;Rossberg et al 2001;Salse et al 2002) based largely on sequenced BACs or other large DNA fragments. However, to the degree that gene loss followed polyploidization events in these lineages, these studies chronically underestimated the degree of conserved synteny that existed Kellogg 2003).…”

Simple Sequence Repeat-Based Comparative Genomics Between Brassica rapa and Arabidopsis thaliana: The Genetic Origin of Clubroot Resistance

“…A pattern of chromosomal colinearity has been identified between Arabidopsis and other flowering plants (Grant et al 2000;Rossberg et al 2001). Genomic synteny has been found to be well conserved among a broad array of species, even though genomic size in plant exhibits a wide diversity, e.g., 125 Mb for A. thaliana to 125 Gb for Fritillaria assyriaca (Bennett and Smith 1976).…”