ARS | Publication request: Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 10, 2013
Publication Date: January 29, 2013
Repository URL: http://www.biomedcentral.com/1471-2164/14/60/abstract
Citation: Fellers, J.P., Soltani, B., Bruce, M.A., Linning, R., Cuomo, C.A., Szabo, L.J., Bakkeren, G. 2013. Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements. Biomed Central (BMC) Genomics. doi:10.1186/1471-2164-14-60.

Interpretive Summary: Leaf rust of wheat, caused by the fungus Puccinia triticina, results in significant yield losses each year and is found wherever wheat is grown around the world. Wheat geneticists are constantly trying to find new leaf rust resistance genes to introduce into adapted varieties because the fungus usually overcomes genetic resistance in just a few years. To develop better resistance strategies, we need to know how the fungus manipulates the plant metabolism and how it can overcome host plant resistance. The objective of this research is to better understand the genes and gene organization in the leaf rust fungus by comparing to the stem rust fungus. Three large stretches of DNA from leaf rust were sequenced and the genes were identified. The leaf rust fungus DNA sequences were then compared to an existing database of the wheat stem rust fungus genomic sequence to determine similarities and differences. Gene order was similar, but sequence identity varied from 26-99%. Numerous repetitive elements called retrotransposons were also found in the leaf rust fungus DNA sequence. Identification of genes that are highly conserved between the two pathogens may reveal vulnerable targets of future control strategies. Comparisons may also reveal important differences in how leaf rust and stem rust have adapted to cause disease in wheat.

Technical Abstract: Background: Wheat leaf rust (Puccinia triticina Eriks; Pt) and stem rust (P. graminis f.sp. tritici; Pgt) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The Pt genome, currently estimated at 135 Mb, is significantly larger than Pgt, at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of Pt conserved proteins were characterized to gain insight into gene content, genome complexity and expansion. A bacterial artificial chromosome (BAC) library was made from P. triticina race 1, BBBD and probed with Pt homologs of two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny) was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in Pgt. Conclusions: The three Pt loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes is extended to the more distant rust, Melampsora larici-populina. The loci also reveal that genome expansion in Pt is in part due to higher occurrence of repeat-elements in this species.