Abstract
Actinorhizal root nodule symbioses are very diverse, and the symbiosis of Datisca glomerata has previously been shown to have many unusual aspects. In order to gain molecular information on the infection mechanism, nodule development and nodule metabolism, we compared the transcriptomes of D. glomerata roots and nodules. Root and nodule libraries representing the 3′-ends of cDNAs were subjected to high-throughput parallel 454 sequencing. To identify the corresponding genes and to improve the assembly, Illumina sequencing of the nodule transcriptome was performed as well. The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology. Analysis of the nodule transcriptome showed that genes encoding components of the common symbiosis signaling pathway were present in nodules of D. glomerata, which in combination with the previously established function of SymRK in D. glomerata nodulation suggests that this pathway is also active in actinorhizal Cucurbitales. Furthermore, comparison of the D. glomerata nodule transcriptome with nodule transcriptomes from actinorhizal Fagales revealed a new subgroup of nodule-specific defensins that might play a role specific to actinorhizal symbioses. The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.
Highlights
Two types of nitrogen-fixing root nodule symbioses are known: legume-rhizobia symbioses and actinorhizal symbioses
The mechanism of nodule induction on roots of actinorhizal Cucurbitales has not been examined yet, but detailed cytological analyses of mature nodules of D. glomerata [12] have led to the conclusion that the mechanism by which the bacteria enter plant cells may be different from those found in actinorhizal Fagales and Rosales, respectively [3]
In order to obtain an overview of the D. glomerata root and nodule transcriptome, a high-throughput method for sequencing of serial analysis of gene expression (SAGE)-type cDNA libraries by 454 GS FLX technology (Roche) was used [26]. 39-End cDNA libraries were prepared from high quality total RNA from roots and nodules of D. glomerata, respectively (Figure S1)
Summary
Two types of nitrogen-fixing root nodule symbioses are known: legume-rhizobia symbioses and actinorhizal symbioses. Nodules of Cucurbitales are unusual in other respects as well; nodule physiology [6,7], anatomy [8,9] and metabolism [10,11,12] of the bestexamined member of actinorhizal Cucurbitales, Datisca glomerata, differ from those of actinorhizal nodules formed on Fagales or Rosales. The mechanism of nodule induction on roots of actinorhizal Cucurbitales has not been examined yet, but detailed cytological analyses of mature nodules of D. glomerata [12] have led to the conclusion that the mechanism by which the bacteria enter plant cells may be different from those found in actinorhizal Fagales (intracellular infection) and Rosales (intercellular infection), respectively [3]. Actinorhizal Cucurbitales may have a unique mechanism for transcellular infection thread growth [3]
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