Investigation On Presence/absence Genes Among80Arabidopsis Accessions

Presence/absence (P/A) polymorphisms, which are commonly observed in plants, play an important role in species differentiation and genetic diversity reservation. In a given species, detecting the abundance, distribution and variation among individuals would help to understand the role played by these polymorphisms. The recently sequenced80Arabidopsis genomes provide an opportunity to settle these questions.By systematically investigating these80accessions, we identified2,407P/A genes (8.9%of total genes) absent in one or more genomes, averaging444absent genes per accession. Of all the P/A genes,50.6%belonged to multi-copy gene families, or31.0%to clustered genes, indicating that asymmetric recombination may be major mechanism to generate P/A polymorphism. Meanwhile, the regions near centromeres were found to contain the highest proportion of P/A genes, mainly consisting of singleton genes. Besides, a significant correlation was observed between the P/A gene frequency and the diversity level at P/A loci among the80accessions. Furthermore, different proportions of P/A genes were observed among functional gene categories. Finally, a P/A gene tree was built to show a diversified population structure in the worldwide Arabidopsis accessions.little geographic differentiation was found in the distribution of P/A genes among populations, implying that these genes were generated and maintained randomly at relatively high frequency. The high nucleotide diversity and high absent gene frequency suggested that balancing selection could be a mechanism maintaining P/A polymorphisms.An estimate of P/A genes and their frequency distribution in the80Arabidopsis accessions was obtained. Our results suggest that there are diverse mechanisms to generate or maintain P/A genes. And by these mechanisms, individuals and functionally different genes can selectively maintain P/A polymorphisms for a specific adaptation.