Development of taxonomical biomarkers for Ulva genus
Abstract
Ulva species play important roles in coastal ecosystems and the global mariculture industry, both for direct human consumption and their potential role as efficient biofilter. However, the identification of Ulva species remains challenging due to their simple morphologies and intraspecific and interspecific overlaps between those morphological characters that are classically used for species delimitation. In addition, currently used molecular markers (ITS, rbcL, tufA) fail to reliably separate Ulva species. Phylogenies reconstructed from either the chloroplast or the mitochondrial genomes yield contrasting results. Various academic, ecological and industrial communities could benefit from a reliable, quick and cheap way to delimit Ulva species, which is currently lacking. In this study, we present a resolved Ulva species tree based on the combined information gathered from 70 chloroplast and 29 mitochondrial protein-coding genes from 49 Ulva isolates belonging to more than 15 Ulva species. We also performed a rigorous genomic comparison of all high quality Ulva organelles sequences available to confirm that genomic signatures segregate according to the species tree we reconstructed. Then, we developed a novel combinatorial approach that tested 945 unique combinations of chloroplast and mitochondrial genes (up to 10 distinct organellar genes) to identify a minimum set of organellar molecular markers necessary to resolve Ulva phylogeny at the species level (universal Ulva species markers). We suggest the combination of the following chloroplast and mitochondrial genes as the minimum set of organellar molecular markers sufficient to discriminate Ulva at the species level: psaA, psbD, cox1 and cox2. Interestingly, chloroplast markers commonly used for Ulva species delimitation (i.e.: rbcL and tufA) showed a reduced resolution power compared to psaA and psbD and resulted in a phylogenetic tree more distant to the Ulva species tree we reconstructed. In addition to describing a rigorous approach for species resolution in green seaweeds based on organellar markers, we provide a useful resource for researchers and conservation ecologists and promote the selection of Ulva species for mariculture applications worldwide.