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

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.

Announcement of the First Draft Genome of Crustose Coralline Algae

“…Calliarthron tuberculosum, is a non-encrusting (branching) coralline red algae, which was sequenced for gene sharing studies and was assembled to the contig level 40 . Recently, C. tuberculosum genome and transcriptome study, for the evolution of partial lignin biosynthetic pathway generating a highly fragmented genome 41 , was the highest level in the genomic research till date from closely related non-encrusting coralline algae. In addition, very few transcriptomic studies have been carried out on coralline algae 39,41,42,43 .…”

“…Recently, C. tuberculosum genome and transcriptome study, for the evolution of partial lignin biosynthetic pathway generating a highly fragmented genome 41 , was the highest level in the genomic research till date from closely related non-encrusting coralline algae. In addition, very few transcriptomic studies have been carried out on coralline algae 39,41,42,43 . Additionally, for some species, mitochondrial 44,45,46,47,48 and plastidial genomes 47,48 have been sequenced.…”