Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin

Abstract

Host/symbiont compatibility is a hallmark of the symbiotic nitrogen-fixing interaction between rhizobia and legumes, mediated in part by plant-produced nodule-specific cysteine-rich (NCR) peptides and the bacterial BacA membrane protein that can act as a NCR peptide transporter. In addition, the genetic and metabolic properties supporting symbiotic nitrogen fixation often differ between compatible partners, including those sharing a common partner, highlighting the need for multiple study systems. Here, we report high-quality nodule transcriptome assemblies for Medicago sativa cv. Algonquin and Melilotus officinalis, two legumes able to form compatible symbioses with Sinorhizobium meliloti. The compressed M. sativa and M. officinalis assemblies consisted of 79,978 and 64,593 contigs, respectively, of which 33,341 and 28,278 were assigned putative annotations, respectively. As expected, the two transcriptomes showed broad similarity at a global level. We were particularly interested in the NCR peptide profiles of these plants, as these peptides drive bacterial differentiation during the symbiosis. A total of 412 and 308 NCR peptides were predicted from the M. sativa and M. officinalis transcriptomes, respectively, with approximately 9% of the transcriptome of both species consisting of NCR transcripts.Notably, transcripts encoding highly cationic NCR peptides (isoelectric point > 9.5), which are known to have antimicrobial properties, were $2-fold more abundant in M. sativa than in M. officinalis, and $27-fold more abundant when considering only NCR peptides in the six-cysteine class. We hypothesize that the difference in abundance of highly cationic NCR peptides explains our previous observation that some rhizobial bacA alleles which can support symbiosis with M. officinalis are unable to support symbiosis with M. sativa.

Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host-microbe interactions

“…Algonquin (alfalfa) and M. officinalis (yellow-blossom sweet clover) (Speare Seeds Limited; Harriston, Ontario, Canada) were surface-sterilized and germinated on water agar plates for two nights in the dark, as described previously (13). Leonard assemblies were prepared as described before (13), with a 1:1 (w/w) mixture of vermiculite and silica sand in the top pot, 250 mL Jensen’s medium (59) in the bottom pot, and a cotton wick connecting the pots, and then autoclaved. Five seedlings were sown per pot, and assemblies were incubated for two nights.…”

“…TBD is essential for SNF in these legumes and is driven by a family of small, plant-encoded proteins known as nodule-specific cysteine-rich (NCR) peptides, which target the intracellular symbiotic bacteria to promote TBD (9, 10). IRLC and Dalbergioid legumes encode between <10 and >700 NCR peptides that contain four, six, or eight conserved cysteine residues (11, 12) but otherwise share little sequence conservation and have isoelectric points (pI) that vary from 3 (anionic) to 11 (cationic) (11, 13). Cationic NCR peptides with pI values above nine display antimicrobial activity, likely due to interaction with the negatively-charged surface of bacterial plasma membranes resulting in membrane depolarization (14, 15).…”

“…However, despite the lack of complementation of symbiotic phenotypes, most bacA and bclA orthologs still complement the gentamicin and/or bleomycin phenotypes of S. meliloti bacA null mutants (20, 23, 28, 33, 35–37). These results suggest that BacA and BclA orthologs display slight variations in their peptide substrate range or rate of transport (13).…”

Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics

“…Sweet yellow clover ( Melilotus officinalis ) is a legume that is native to Europe and widely distributed in North America, temperate Europe, the Mediterranean, subtropical Asia, and North Africa [ 1 , 2 ]. It can adapt to a variety of extreme types of weather, including hot and cold climates.…”