Structural features of the rice chromosome 4 centromere

Abstract

A complete sequence of a chromosome centromere is necessary for fully understanding centromere function. We reported the sequence structures of the first complete rice chromosome centromere through sequencing a large insert bacterial artificial chromosome clone-based contig, which covered the rice chromosome 4 centromere. Complete sequencing of the 124-kb rice chromosome 4 centromere revealed that it consisted of 18 tracts of 379 tandemly arrayed repeats known as CentO and a total of 19 centromeric retroelements (CRs) but no unique sequences were detected. Four tracts, composed of 65 CentO repeats, were located in the opposite orientation, and 18 CentO tracts were flanked by 19 retroelements. The CRs were classified into four types, and the type I retroelements appeared to be more specific to rice centromeres. The preferential insert of the CRs among CentO repeats indicated that the centromere-specific retroelements may contribute to centromere expansion during evolution. The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism.

Figure 1

Map of the centromere region of rice chromosome 4. Four contigs, which covered the entire chromosome 4, are indicated in orange and as described. A part of tiling path of BAC clones of Contig3, which covered the whole centromeric region (yellow) was shown. It was also indicated that the genetic distance between markers S11182 (19.9 cM) and E21001S (19.9 cM) corresponds to the physical distance of 1200–1300 kb (24,29). The restriction enzyme sites of the BAC OSJNBb0062N22 of 181 kb, which contain all CentO repeats were indicated by the black vertical short-lines and described as following: B = BbvCI, F = FseI, N = NotI, H = HpaI. The CentO region was centralized on the BAC clone OSJNBb0062N22 from 19 781 to 174 142 bp, indicated by two red vertical arrows. The detailed distribution of CentO satellite repeats was shown in a square box. Each dot represented one satellite monomer.

Figure 2

The complete organization of the tandemly repeated arrays of CentO sequences and CRs in the core region of rice chromosome 4 centromere. The horizontal red arrows represented the length and orientation of the 18 CentO tracts. The detail monomer’s identity and orientation were shown by the black and red dots. The y axis showed different identity between these monomers. The CentO tracts were separated by 19 retroelements of four types. Four type retroelements were marked by four different colors, individually.

Figure 3

Sequence comparison between different rice chromosome 4 CentO monomers. From top to bottom: four typical 155-bp monomers, four typical 165-bp monomers, four monomers with several nucleotide indels, two monomers at the edge of centromere core region with the most variations. Sequence conservation between different monomers was indicated by background shading. Dark shading represented 100% conservation and light shading >80%. The preferential insertion sites of CR were indicated by the vertical arrows.

Figure 4

Detailed structural features of three types of CRs. CR4-2, CR4-16 and CR4-11 were intact retroelements. Others were fragments of retroelements. Types I, II and III retroelements were indicated in green, light blue and dark blue, respectively. It was also indicated that the previous identified rice centromeric repetitive DNA fragments (RCE1, RCS1, RCH2, RCH1) were found to correspond to type I or II retroelements.