Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice

Abstract

In Arabidopsis, tandemly arrayed genes (TAGs) comprise >10% of the genes in the genome. These duplicated genes represent a rich template for genetic innovation, but little is known of the evolutionary forces governing their generation and maintenance. Here we compare the organization and evolution of TAGs between Arabidopsis and rice, two plant genomes that diverged ~150 million years ago. TAGs from the two genomes are similar in a number of respects, including the proportion of genes that are tandemly arrayed, the number of genes within an array, the number of tandem arrays, and the dearth of TAGs relative to single copy genes in centromeric regions. Analysis of recombination rates along rice chromosomes confirms a positive correlation between the occurrence of TAGs and recombination rate, as found in Arabidopsis. TAGs are also biased functionally relative to duplicated, nontandemly arrayed genes. In both genomes, TAGs are enriched for genes that encode membrane proteins and function in “abiotic and biotic stress” but underrepresented for genes involved in transcription and DNA or RNA binding functions. We speculate that these observations reflect an evolutionary trend in which successful tandem duplication involves genes either at the end of biochemical pathways or in flexible steps in a pathway, for which fluctuation in copy number is unlikely to affect downstream genes. Despite differences in the age distribution of tandem arrays, the striking similarities between rice and Arabidopsis indicate similar mechanisms of TAG generation and maintenance.

The Contribution of Transposable Elements to Expressed Coding Sequence in Arabidopsis thaliana

“…To examine the effect of gene family definitions on our study, we repeated the phylogenetic analyses using lowerstringency gene family definitions (paralogues with C30% identity over C70% of the peptide) (Rizzon et al 2006). BLAST resampling of the originally-identified TE genes, however, often showed very low match proportions, making it difficult to interpret whether the TE-like region was unique.…”

“…The phylogenetic distribution of the TE on a gene family should allow one to distinguish TE insertion from acquisition, using parsimony arguments. For these analyses, we relied on the Arabidopsis high-stringency gene family data set of Rizzon et al (2006). These gene families were defined by a homology criterion of pairwise identities C50% over C90% of the peptide sequence; paralogues were grouped using the single-linkage criterion, resulting in 10,542 genes clustered into 3544 gene families.…”

Clustered Transcription Factor Genes Regulate Nicotine Biosynthesis in Tobacco

“…Sequenced plant genomes contain substantial numbers of tandemly arrayed gene families, varying from a few percent to 15% or more of the identified genes (Jander and Barth, 2007;Huang et al, 2009). Most tandem arrays contain only two duplicated genes, and arrays with more than three members are rare (Rizzon et al, 2006). Although transcription factor families have much higher expansion rates in plants than in animals (Shiu et al, 2005), the Arabidopsis genome contains only one region with more than five duplicated transcription factor genes in tandem, whereas several such regions are present in soybean (Glycine max; Schmutz et al, 2010).…”

Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

“…Why these genomes differ in this respect remains to be investigated (Gaut et al 2007). To date, the genome-wide estimates of GR rates have been derived for only two plant (Arabidopsis and rice) genomes by the comparison of genomic sequences and genetic maps (Zhang and Gaut 2003;Rizzon et al 2006). This study thus provides the first in-depth analysis of the structural variation of LTR-RTs and their distribution in relation to GR rates in any plant genome.…”

“…2), resulting in GR rates for nonoverlapping 1-Mb windows along the 12 chromosomes (see Methods). To minimize a potential ''centromere effect'' (Wu et al 2003;Zhang and Gaut 2003;Ma and Bennetzen 2006;Rizzon et al 2006), presumably GR-suppressed pericentromeric regions (Supplemental Table 5) were excluded from correlation analyses.…”