Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants

Lingfeng Mao, Hiroshi Kawaide, Toshiya Higuchi, Meihong Chen, Koji Miyamoto, Yoshiki Hirata, Honoka Kimura, Sho Miyazaki, Miyu Teruya,  Kaoru Fujiwara,  Keisuke Tomita, Hisakazu Yamane, Ken-ichiro Hayashi, Hideaki Nojiri, Lei Jia,  Jie Qiu, Chuyu Ye,  Michael P. Timko, Longjiang Fan, and Kazunori Okada

PNAS June 2, 2020 117 (22) 12472-12480

Significance

The biosynthetic genes of some specialized plant metabolites appear to be clustered in the genomes of higher plants. Momilactones are defense compounds produced in rice and barnyard grass by family-conserved biosynthetic gene clusters (BGCs). We sequenced the genome of Calohypnum plumiforme, a momilactone-producing nonvascular bryophyte, and showed that it also contains a functionally similar momilactone BGC distinguished by its lack of synteny with the clusters found in vascular plants. The expression of the Calohypnum biosynthetic genes in tobacco demonstrated their role in momilactone A production. This is the first report of a BGC for a specialized metabolite in bryophytes. Our findings indicate that the momilactone clusters present in three different plant species may have evolved independently via convergent evolution.

Abstract

Momilactones are bioactive diterpenoids that contribute to plant defense against pathogens and allelopathic interactions between plants. Both cultivated and wild grass species of Oryza and Echinochloa crus-galli (barnyard grass) produce momilactones using a biosynthetic gene cluster (BGC) in their genomes. The bryophyte Calohypnum plumiforme (formerly Hypnum plumaeforme) also produces momilactones, and the bifunctional diterpene cyclase gene CpDTC1/HpDTC1, which is responsible for the production of the diterpene framework, has been characterized. To understand the molecular architecture of the momilactone biosynthetic genes in the moss genome and their evolutionary relationships with other momilactone-producing plants, we sequenced and annotated the C. plumiforme genome. The data revealed a 150-kb genomic region that contains two cytochrome P450 genes, the CpDTC1/HpDTC1 gene and the “dehydrogenase momilactone A synthase” gene tandemly arranged and inductively transcribed following stress exposure. The predicted enzymatic functions in yeast and recombinant assay and the successful pathway reconstitution in Nicotiana benthamiana suggest that it is a functional BGC responsible for momilactone production. Furthermore, in a survey of genomic sequences of a broad range of plant species, we found that momilactone BGC is limited to the two grasses (Oryza and Echinochloa) and C. plumiforme, with no synteny among these genomes. These results indicate that while the gene cluster in C. plumiforme is functionally similar to that in rice and barnyard grass, it is likely a product of convergent evolution. To the best of our knowledge, this report of a BGC for a specialized plant defense metabolite in bryophytes is unique.

See https://www.pnas.org/content/117/22/12472

Figure 1:

Evolution of the Calohypnum genome. (A) Graph showing the Ks (rate of synonymous substitution) distribution of paralogous gene pairs of C. plumiforme and orthologous gene pairs between C. plumiforme and P. patens. The Inset in the panel is a photograph of the two moss species under analysis in this study. (B) Phylogenetic trees of showing the relation between of bryophytes and seed plants based on single-copy genes of their chloroplast genomes. The alga Chara (a nonland plant) was used as outgroup. The divergence time periods (Mya) at branches and time scales are shown.