Assembly of high‐quality genomes of the locoweed Oxytropis ochrocephala and its endophyte Alternaria oxytropis provides new evidence for their symbiotic relationship and swainsonine biosynthesis

Abstract

Locoweeds are perennial forbs poisonous to livestock and cause extreme losses to animal husbandry. Locoweed toxicity is attributed to the symbiotic endophytes in Alternaria sect. Undifilum, which produce a mycotoxin swainsonine (SW). We performed a de novo whole genome sequencing of the most common locoweed in China, Oxytropis ochrocephala (2n = 16), and assembled a high‐quality, chromosome‐level reference genome. Its genome size is 958.83 Mb with 930.94 Mb (97.09%) anchored and oriented onto eight chromosomes, and 31,700 protein‐coding genes were annotated. Phylogenetic and collinearity analysis showed it is closely related to Medicago truncatula with a pair of large interchromosomal rearrangements, and both species underwent a whole‐genome duplication event. We also derived the genome of A. oxytropis at 74.48 Mb with a contig N50 of 8.87 Mb and 10,657 protein‐coding genes, and refined the genes of SW biosynthesis. Multiple Alternaria species containing the swnK gene were grouped into a single clade, but in other genera, swnK's homologues are diverse. Resequencing of 41 A. oxytropis strains revealed one SNP in the SWN cluster causing changes in SW concentration. Comparing the transcriptomes of symbiotic and nonsymbiotic interactions identified differentially expressed genes (DEGs) linked to defence and secondary metabolism in the host. Within the endophyte DEGs were linked to cell wall degradation, fatty acids and nitrogen metabolism. Symbiosis induced the upregulation of most of the SW biosynthetic genes. These two genomes and relevant sequencing data should provide valuable genetic resources for the study of the evolution, interaction, and SW biosynthesis in the symbiont.

Community ecological succession of endophytic fungi associates with medicinal compound accumulation in Sophora alopecuroides

“…Other studies have shown that Alternaria oxytropis forms a symbiotic relationship with Oxytropis ochrocephala. Alternaria oxytropis is the key strain that produces swainsonine in Oxytropis ochrocephala , and it is also the direct producer of swainsonine ( 58 , 59 ). Alternaria fungi are themselves a huge reservoir of secondary metabolites, producing numerous bioactive substances, such as vincaleukoblastinum ( 60 ), resveratrol ( 61 ), and some alcohols ( 59 ).…”

Impaired Indole Acetic Acid and Reduced Indole-Producing Bacteria Contribute to Swainsonine-Induced Liver Inflammation

“…Swainsonine is a cytotoxic fungal alkaloid found in some locoweeds with significant toxicity, causing lysosomal storage disease, nerve damage, and hepatic inflammation, which is poisonous to livestock and wildlife. 22 However, the underlying mechanism of hepatic inflammation caused by swainsonine is unclear. Herein, we used a combination of microbiome and targeted metabolomics to study the specific mechanisms of hepatic inflammation in mice caused by swainsonine and focused on indole metabolites and indole-producing bacteria.…”

The complete chloroplast genome of Oxytropis ochrocephala Bunge 1874 (Fabaceae) and its phylogenetic analysis

“…2019 ; Zhang et al. 2022 ). However, there is a noticeable gap in the literature regarding the structural characteristics and phylogeny of its complete chloroplast (cp) genome.…”