The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella rubella genomes

Abstract

The annotated Arabidopsis genome sequence was exploited as a tool for carrying out comparative analyses of the Arabidopsis and Capsella rubella genomes. Comparison of a set of random, short C. rubella sequences with the corresponding sequences in Arabidopsis revealed that aligned protein-coding exon sequences differ from aligned intron or intergenic sequences in respect to the degree of sequence identity and the frequency of small insertions/deletions. Molecular-mapped markers and expressed sequence tags derived from Arabidopsis were used for genetic mapping in a population derived from an interspecific cross between Capsella grandiflora and C. rubella. The resulting eight Capsella linkage groups were compared to the sequence maps of the five Arabidopsis chromosomes. Fourteen colinear segments spanning approximately 85% of the Arabidopsis chromosome sequence maps and 92% of the Capsella genetic linkage map were detected. Several fusions and fissions of chromosomal segments as well as large inversions account for the observed arrangement of the 14 colinear blocks in the analyzed genomes. In addition, evidence for small-scale deviations from genome colinearity was found. Colinearity between the Arabidopsis and Capsella genomes is more pronounced than has been previously reported for comparisons between Arabidopsis and different Brassica species.

Figure 1.

Genetic linkage map of Capsella. Linkage data for the Capsella mapping population derived from an interspecific cross were calculated with Map Manager QTX (Manly et al., 2001). Using a logarithm of odds ratio score of 5.0, 8 linkage groups labeled A to H resulted. Map distances are given in cM. PCR-based markers are shown in italics, and the remainder of the loci was mapped using RFLP. Nuclear codominant loci for which the observed ratios of plants homozygous for the C. grandiflora allele, heterozygous plants, and plants homozygous for the C. rubella allele that deviated significantly (P = 0.05) from the expected 1:2:1 ratio are marked by asterisks. Two loci corresponding to rDNA sequences were mapped: a codominant locus (rDNAa) was located on linkage group B and a dominant locus (rDNAb) was found linked to markers of linkage group G. An interrupted line indicates that the genetic distance separating rDNAb and CL5.1 has not been established.

Figure 2.

Comparative map between Arabidopsis and Capsella. The sequence maps of the five Arabidopsis chromosomes are shown. Horizontal bars mark the positions of the centromeres. The designations of the chromosomes (I to V) indicate the telomeric ends of the short arms. The eight Capsella linkage groups are labeled A to H. Linkage group G is shown in two parts, G1 and G2. Linkage groups B, D, G2, and H are shown at a smaller scale than the remainder of the genetic chromosome maps. Map positions of marker sequences are indicated as vertical lines on the chromosome maps. Two different loci in close physical proximity to each other (Supplemental Table S1) are shown for markers mi54 and m249. Lines connect all loci residing in colinear positions. A solid line indicates that the map position of the Capsella locus corresponds to the map position of the Arabidopsis marker sequence itself or the closest Arabidopsis homolog of a Capsella PCR-based marker. Colinearity between a Capsella locus and a homolog of a marker sequence is indicated by a dashed line. Capsella loci shown in bold do not have a corresponding Arabidopsis sequence in a colinear arrangement.

Figure 3.

Comparative mapping of segmental duplications. Arabidopsis markers mapping to duplicated regions of the Arabidopsis genome have been used for genetic mapping in Capsella. Selected parts of a segmental duplication harboring duplicated sequences of markers E92 and mi330 are shown in A. Genes mapping to a duplicated region between Arabidopsis chromosomes II and IV and their Capsella counterparts C and G are represented in B. In both sections, only selected parts of the Capsella genetic maps and Arabidopsis chromosome sequence maps are given schematically. The Capsella linkage groups are boxed. The representation of Arabidopsis gene codes mapping to the duplicated regions has been restricted to genes corresponding to genetically mapped markers in Capsella and those duplicated genes that are found immediately adjacent to the duplicated marker loci (shown at a smaller font size). Horizontal lines indicate colinear relationships between an Arabidopsis gene and a genetically mapped locus in Capsella. Dashed lines connect homologous Arabidopsis genes that are located in duplicated regions of the genome.