Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway

PLoS One. 2022 Jul 14;17(7):e0266892. doi: 10.1371/journal.pone.0266892. eCollection 2022.

Abstract

The discovery of lignins in the coralline red alga Calliarthron tuberculosum raised new questions about the deep evolution of lignin biosynthesis. Here we present the transcriptome of C. tuberculosum supported with newly generated genomic data to identify gene candidates from the monolignol biosynthetic pathway using a combination of sequence similarity-based methods. We identified candidates in the monolignol biosynthesis pathway for the genes 4CL, CCR, CAD, CCoAOMT, and CSE but did not identify candidates for PAL, CYP450 (F5H, C3H, C4H), HCT, and COMT. In gene tree analysis, we present evidence that these gene candidates evolved independently from their land plant counterparts, suggesting convergent evolution of a complex multistep lignin biosynthetic pathway in this red algal lineage. Additionally, we provide tools to extract metabolic pathways and genes from the newly generated transcriptomic and genomic datasets. Using these methods, we extracted genes related to sucrose metabolism and calcification. Ultimately, this transcriptome will provide a foundation for further genetic and experimental studies of calcifying red algae.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biosynthetic Pathways / genetics
  • Gene Expression Regulation, Plant
  • Lignin* / metabolism
  • Rhodophyta* / genetics
  • Rhodophyta* / metabolism
  • Transcriptome

Substances

  • Lignin

Grant support

C.X.C. was supported by Australian Research Council grants (DP150101875 and DP190102474). P.M. was supported by Natural Sciences and Engineering Research Council (NSERC) Discovery Grants (RGPIN 356403-09; 2014-06288; 2019-06240). K.H. and M.L. were supported by the Hakai Institute. J.X. was supported by the UBC Summer Undergraduate Research award, NSERC Graduate Student fellowship and Patrick David Campbell Graduate Student fellowship. K.H. was supported by a postdoctoral scholarship from the Tula Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.