Centromeric retrotransposon lineages predate the maize/rice divergence and differ in abundance and activity |
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Authors: | Anupma Sharma Gernot G Presting |
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Institution: | (1) Department of Molecular Biosciences and Bioengineering, University of Hawaii, 1955 East-West Road, Ag Science Bldg. Rm 218, Honolulu, HI 96822, USA |
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Abstract: | Centromeric retrotransposons (CR) are located almost exclusively at the centromeres of plant chromosomes. Analysis of the
emerging Zea mays inbred B73 genome sequence revealed two novel subfamilies of CR elements of maize (CRM), bringing the total number of known
CRM subfamilies to four. Orthologous subfamilies of each of these CRM subfamilies were discovered in the rice lineage, and
the orthologous relationships were demonstrated with extensive phylogenetic analyses. The much higher number of CRs in maize
versus Oryza sativa is due primarily to the recent expansion of the CRM1 subfamily in maize. At least one incomplete copy of a CRM1 homolog was
found in O. sativa ssp. indica and O. officinalis, but no member of this subfamily could be detected in the finished O. sativa ssp. japonica genome, implying loss of this prolific subfamily in that subspecies. CRM2 and CRM3, as well as the corresponding
rice subfamilies, have been recently active but are present in low numbers. CRM3 is a full-length element related to the non-autonomous
CentA, which is the first described CRM. The oldest subfamily (CRM4), as well as its rice counterpart, appears to contain
only inactive members that are not located in currently active centromeres. The abundance of active CR elements is correlated
with chromosome size in the three plant genomes for which high quality genomic sequence is available, and the emerging picture
of CR elements is one in which different subfamilies are active at different evolutionary times. We propose a model by which
CR elements might influence chromosome and genome size.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. |
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Keywords: | CentA Centromere Genome expansion |
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