A lineage-specific centromere retrotransposon in Oryza brachyantha.

Most eukaryotic centromeres contain large quantities of repetitive DNA, such as satellite repeats and retrotransposons. Unlike most transposons in plant genomes, the centromeric retrotransposon (CR) family is conserved over long evolutionary periods among a majority of the grass species. CR elements are highly concentrated in centromeres, and are likely to play a role in centromere function. In order to study centromere evolution in the Oryza (rice) genus, we sequenced the orthologous region to centromere 8 of Oryza sativa from a related species, Oryza brachyantha. We found that O. brachyantha does not have the canonical CRR (CR of rice) found in the centromeres of all other Oryza species. Instead, a new Ty3-gypsy (Metaviridae) retroelement (FRetro3) was found to colonize the centromeres of this species. This retroelement is found in high copy numbers in the O. brachyantha genome, but not in other Oryza genomes, and based on the dating of long terminal repeats (LTRs) of FRetro3 it was amplified in the genome in the last few million years. Interestingly, there is a high level of removal of FRetro3 based on solo-LTRs to full-length elements, and this rapid turnover may have played a role in the replacement of the canonical CRR with the new element by active deletion. Comparison with previously described ChIP cloning data revealed that FRetro3 is found in CENH3-associated chromatin sequences. Thus, within a single lineage of the Oryza genus, the canonical component of grass centromeres has been replaced with a new retrotransposon that has all the hallmarks of a centromeric retroelement.

Gao D ，Gill N ，Kim HR ，Walling JG ，Zhang W ，Fan C ，Yu Y ，Ma J ，SanMiguel P ，Jiang N ，Cheng Z ，Wing RA ，Jiang J ，Jackson SA ... -  《-》

Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice.

The centromeric retrotransposon (CR) family in the grass species is one of few Ty3-gypsy groups of retroelements that preferentially transpose into highly specialized chromosomal domains. It has been demonstrated in both rice and maize that CRR (CR of rice) and CRM (CR of maize) elements are intermingled with centromeric satellite DNA and are highly concentrated within cytologically defined centromeres. We collected all of the CRR elements from rice chromosomes 1, 4, 8, and 10 that have been sequenced to high quality. Phylogenetic analysis revealed that the CRR elements are structurally diverged into four subfamilies, including two autonomous subfamilies (CRR1 and CRR2) and two nonautonomous subfamilies (noaCRR1 and noaCRR2). The CRR1/CRR2 elements contain all characteristic protein domains required for retrotransposition. In contrast, the noaCRR elements have different structures, containing only a gag or gag-pro domain or no open reading frames. The CRR and noaCRR elements share substantial sequence similarity in regions required for DNA replication and for recognition by integrase during retrotransposition. These data, coupled with the presence of young noaCRR elements in the rice genome and similar chromosomal distribution patterns between noaCRR1 and CRR1/CRR2 elements, suggest that the noaCRR elements were likely mobilized through the retrotransposition machinery from the autonomous CRR elements. Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed.

Nagaki K ，Neumann P ，Zhang D ，Ouyang S ，Buell CR ，Cheng Z ，Jiang J ... -  《MOLECULAR BIOLOGY AND EVOLUTION》

Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure.

Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. This function is conserved across species, but the DNA components that are involved in kinetochore formation differ greatly, even between closely related species. To shed light on the nature, evolutionary timing and evolutionary dynamics of rice centromeres, we decoded a 2.25-Mb DNA sequence covering the centromeric region of chromosome 8 of an indica rice variety, 'Kasalath' (Kas-Cen8). Analysis of repetitive sequences in Kas-Cen8 led to the identification of 222 long terminal repeat (LTR)-retrotransposon elements and 584 CentO satellite monomers, which account for 59.2% of the region. A comparison of the Kas-Cen8 sequence with that of japonica rice 'Nipponbare' (Nip-Cen8) revealed that about 66.8% of the Kas-Cen8 sequence was collinear with that of Nip-Cen8. Although the 27 putative genes are conserved between the two subspecies, only 55.4% of the total LTR-retrotransposon elements in 'Kasalath' had orthologs in 'Nipponbare', thus reflecting recent proliferation of a considerable number of LTR-retrotransposons since the divergence of two rice subspecies of indica and japonica within Oryza sativa. Comparative analysis of the subfamilies, time of insertion, and organization patterns of inserted LTR-retrotransposons between the two Cen8 regions revealed variations between 'Kasalath' and 'Nipponbare' in the preferential accumulation of CRR elements, and the expansion of CentO satellite repeats within the core domain of Cen8. Together, the results provide insights into the recent proliferation of LTR-retrotransposons, and the rapid expansion of CentO satellite repeats, underlying the dynamic variation and plasticity of plant centromeres.

Wu J ，Fujisawa M ，Tian Z ，Yamagata H ，Kamiya K ，Shibata M ，Hosokawa S ，Ito Y ，Hamada M ，Katagiri S ，Kurita K ，Yamamoto M ，Kikuta A ，Machita K ，Karasawa W ，Kanamori H ，Namiki N ，Mizuno H ，Ma J ，Sasaki T ，Matsumoto T ... -  《-》

Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison.

The availability of complete or nearly complete genome sequences from several plant species permits detailed discovery and cross-species comparison of transposable elements (TEs) at the whole genome level. We initially investigated 510 long terminal repeat-retrotransposon (LTR-RT) families comprising 32370 elements in soybean (Glycine max (L.) Merr.). Approximately 87% of these elements were located in recombination-suppressed pericentromeric regions, where the ratio (1.26) of solo LTRs to intact elements (S/I) is significantly lower than that of chromosome arms (1.62). Further analysis revealed a significant positive correlation between S/I and LTR sizes, indicating that larger LTRs facilitate solo LTR formation. Phylogenetic analysis revealed seven Copia and five Gypsy evolutionary lineages that were present before the divergence of eudicot and monocot species, but the scales and timeframes within which they proliferated vary dramatically across families, lineages and species, and notably, a Copia lineage has been lost in soybean. Analysis of the physical association of LTR-RTs with centromere satellite repeats identified two putative centromere retrotransposon (CR) families of soybean, which were grouped into the CR (e.g. CRR and CRM) lineage found in grasses, indicating that the 'functional specification' of CR pre-dates the bifurcation of eudicots and monocots. However, a number of families of the CR lineage are not concentrated in centromeres, suggesting that their CR roles may now be defunct. Our data also suggest that the envelope-like genes in the putative Copia retrovirus-like family are probably derived from the Gypsy retrovirus-like lineage, and thus we propose the hypothesis of a single ancient origin of envelope-like genes in flowering plants.

Du J ，Tian Z ，Hans CS ，Laten HM ，Cannon SB ，Jackson SA ，Shoemaker RC ，Ma J ... -  《-》

Lineage-specific adaptive evolution of the centromeric protein CENH3 in diploid and allotetraploid Oryza species.

Centromeres in eukaryotic species are defined by the presence of a centromere-specific histone H3 variant, CENH3. CENH3 plays a key role in recruiting other centromeric proteins; thus, it is the central component in kinetochore formation and centromere function. The CENH3 proteins in several plant and animal species were found to be under positive selection, which was hypothesized to respond to the rapid changing of the repetitive DNA sequences associated with the centromeres. Here, we report the expression and evolution of the CenH3 genes in two allotetraploid rice species as well as their representative diploid progenitor species. Both copies of the CenH3 genes were transcribed in the two allotetraploid species and showed a nonpreferential expression pattern. Contrasting positive and stabilizing selection of the CenH3 genes was associated with different diploid Oryza species. This lineage-specific adaptive evolution of CENH3 was maintained in the two allotetraploid species. Thus, we demonstrate that the allopolyploidization events did not alter the expression or evolutionary patterns of the CenH3 genes in the Oryza species.

Hirsch CD ，Wu Y ，Yan H ，Jiang J ... -  《-》