Dynamic evolution at pericentromeres

Abstract

Pericentromeres are exceptional genomic regions: in animals they contain extensive segmental duplications implicated in gene creation, and in plants they sustain rearrangements and insertions uncommon in euchromatin. To examine the mechanisms and patterns of plant pericentromere evolution, we compared pericentromere sequence from four Brassicaceae species separated by <15 million years (Myr). This flowering plant family is ideal for studying relationships between genome reorganization and pericentromere evolution-its members have undergone recent polyploidization and hybridization, with close relatives changing in genome size and chromosome number. Through sequence and hybridization analyses, we examined regions from Arabidopsis arenosa, Capsella rubella, and Olimarabidopsis pumila that are homologous to Arabidopsis thaliana pericentromeres (peri-CENs) III and V, and used FISH to demonstrate they have been maintained near centromere satellite arrays in each species. Sequence analysis revealed a set of highly conserved genes, yet we discovered substantial differences in intergenic length and species-specific changes in sequence content and gene density. We discovered that A. thaliana has undergone recent, significant expansions within its pericentromeres, in some cases measuring hundreds of kilobases; these findings are in marked contrast to euchromatic segments in these species that exhibit only minor length changes. While plant pericentromeres do contain some duplications, we did not find evidence of extensive segmental duplications, as has been documented in primates. Our data support a model in which plant pericentromeres may experience selective pressures distinct from euchromatin, tolerating rapid, dynamic changes in structure and sequence content, including large insertions of mobile elements, 5S rDNA arrays and pseudogenes.

Figure 1.

Multispecies comparisons of regions homologous to A. thaliana pericentromeres. Scale drawings of (A) A. thaliana peri-CEN3 (chromosome III bases 14,096,340–14,967,565), and sequenced BACs from A. arenosa, C. rubella, and O. pumila. (B) A. thaliana peri-CEN5 (chromosome V bases 12,566,510–13,252,797), and homologous BACs identified by hybridization, from A. arenosa, C. rubella, and O. pumila (complete list, Supplemental Table 2). Estimated times of divergence (millions of years, Myr) are shown (Koch et al. 2001). Dotted lines, estimated distance (not to scale) to the centromere satellite array (yellow boxes); (solid arrows) centromere boundary as defined by recombination (Copenhaver and Preuss 1999); (green boxes) 5S rDNA array; (red bars and ovals) expressed A. thaliana genes present in multiple species; (gray ovals) intact A. thaliana-specific genes; (left to right) At3g42050, At3g42150, and At3g42786). (*) Gene homologous to A. thaliana chromosome I expressed gene (At1g63270); (dashed arrows) all genes in the interval are present; (parentheses in B) undetermined gene order.

Figure 2.

Chromosomal localization of sequenced BACs. FISH analysis of pachytene stage C. rubella (A,B,C) and O. pumila (D–L) chromosomes; each consists of synapsed homologs. Chromosomes (DAPI-stained, blue) were probed with centromere satellites (green) and BAC DNA (red). BAC probes include (A,B,C) Cr8F1; (D,E,F) Op44L14; (G,H,I) Op14G23; and (J,K,L) Op37I22. Merged images (center and right columns) show BAC locations (arrows) relative to DAPI-stained heterochromatin and centromere satellite arrays; similar staining patterns were observed on 10–50 pachytene chromosomes/probe.

Figure 3.

Fine structure of BACs homologous to A. thaliana peri-CEN3. Scale drawing showing annotated features >100 bp (BLASTN score > 60 bits; e-values < 1e – 8); (red boxes) predicted genes shared among Brassicaceae species (1–15, Table 1); (gray bars) major stretches of sequence similarity (BLASTN score > 100 bits); (arrows) predicted direction of transcription; (blue boxes) sequence similarity to A. thaliana transposons; (green boxes) sequence similarity to A. thaliana retroelements; (orange boxes) gene fragments; (yellow boxes) centromere satellites; (turquoise boxes) 5S rDNA. For BAC Op44L14, gene 3 has been duplicated and gene CI is similar to an A. thaliana chromosome I gene. Annotations for genes within the corresponding A. thaliana peri-CEN3 region are listed in Supplemental Table 1, and a complete view of all feature annotations within this A. thaliana region can be viewed in the GenBank genome browser (http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=3702) between coordinates 14,096,340 and 14,967,565.