Phylogenomic and synteny analysis of BAHD and SCP/SCPL gene families reveal their evolutionary histories in plant specialized metabolism.

Publisher: Royal Society Country of Publication: England NLM ID: 7503623 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1471-2970 (Electronic) Linking ISSN: 09628436 NLM ISO Abbreviation: Philos Trans R Soc Lond B Biol Sci Subsets: MEDLINE

Original Publication: London : Royal Society, 1934-

Phylogeny* ; Synteny* ; Evolution, Molecular* ; Carboxypeptidases*/genetics ; Carboxypeptidases*/metabolism ; Multigene Family*; Plant Proteins/genetics ; Plant Proteins/metabolism ; Zea mays/genetics ; Solanum lycopersicum/genetics ; Arabidopsis/genetics ; Acyltransferases/genetics ; Acyltransferases/metabolism ; Genome, Plant

Plant chemical diversity is largely owing to a number of enzymes which catalyse reactions involved in the assembly, and in the subsequent chemical modifications, of the core structures of major classes of plant specialized metabolites. One such reaction is acylation. With this in mind, to study the deep evolutionary history of BAHD and the serine-carboxypeptidase-like (SCPL) acyltransferase genes, we assembled phylogenomic synteny networks based on a large-scale inference analysis of orthologues across whole-genome sequences of 126 species spanning Stramenopiles and Archaeplastida, including Arabidopsis thaliana , tomato ( Solanum lycopersicum ) and maize ( Zea mays ). As such, this study combined the study of genomic location with changes in gene sequences. Our analyses revealed that serine-carboxypeptidase (SCP)/serine-carboxypeptidase-like (SCPL) genes had a deeper evolutionary origin than BAHD genes, which expanded massively on the transition to land and with the development of the vascular system. The two gene families additionally display quite distinct patterns of copy number variation across phylogenies as well as differences in cross-phylogenetic syntenic network components. In unlocking the above observations, our analyses demonstrate the possibilities afforded by modern phylogenomic (syntenic) networks, but also highlight their current limitations, as demonstrated by the inability of phylogenetic methods to separate authentic SCPL acyltransferases from standard SCP peptide hydrolases.This article is part of the theme issue 'The evolution of plant metabolism'.

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Keywords: BAHD; SCPL; acyltransferase; phylogenomics; secondary metabolism; synteny

EC 3.4.- (Carboxypeptidases)
EC 3.4.16.5 (serine carboxypeptidase)
0 (Plant Proteins)
EC 2.3.- (Acyltransferases)

Date Created: 20240929 Date Completed: 20240929 Latest Revision: 20241005

20241005

PMC11449225

10.1098/rstb.2023.0349

39343028