Plastid-encoded gene comparison reveals usefulness of atpB, psaA, and rbcL for identification and phylogeny of plastid-containing cryptophyte clades

Abstract

Cryptophytes are a ubiquitous algal group and are important primary producers in aquatic ecosystems. Identification of lineages within the group is difficult because of their simple morphology and they are often enumerated at the class level in ecological research. Despite the increasing number of molecular probes used for identification of microorganisms, rRNA genes (i.e. nuclear 18S, ITS, and 28S, and nucleomorph 18S) are the markers most commonly used to identify cryptophytes. To provide a broader choice of markers, we compared and characterised the utility of 13 plastid genes in 23 culture strains, which cover the spectrum cryptophycean lineages (Clades 1-5). The genes include 11 protein-coding (atpA, atpB, chlI, clpC, dnaK, psaA, psbA, rbcL, rpoC1, secA, and tufA) and two ribosomal RNA (plastid 16S and 23S) genes. Most of the genes were successfully amplified and sequenced using newly designed primers, and the sequences aligned with minimal indels. The protein-coding genes showed higher levels of divergence (P-distance, and synonymous and nonsynonymous substitution rates) and higher identification index than those of rRNAs. Considering divergence and phylogenetic usefulness, we selected atpB, psaA, and rbcL as the best candidates for cryptophycean clade identification and further field research.