Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement

Abstract

Background: Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes.

Results: We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps.

Conclusions: These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

Keywords: Chromosome rearrangement; Corymbia citriodora; DArTseq; Eucalyptus grandis; Genome structure; Linkage mapping.

Fig. 1

Design of the Corymbia pedigrees used to create the linkage maps. CT refers to Corymbia torelliana, while CCV refers to Corymbia citriodora subsp. variegata

Fig. 2

Summary of methods followed to create Corymbia citriodora subsp. variegata and Corymbia torelliana linkage maps

Fig. 3

Marker positions in the Corymbia citriodora subsp. variegata comprehensive linkage map relative to the Eucalyptus grandis genome. Numbers along the x and y axis indicate the chromosome boundaries. Terminal inversions were detected in C. citriodora subsp. variegata relative to E. grandis on chromosomes 4, 9, 10 and 11; an intra-chromosomal translocation on chromosome 2; and more complex rearrangements on chromosome 6 and 8. The position of the above rearrangements are indicated by arrows, and named following Table 4. This figure was created using the package ‘ggplot2’ [103] in R [104]