Reappraising plastid markers of the red algae for phylogenetic community ecology in the genomic era

Abstract

Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of phycologists has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). In this proof‐of‐concept study, we leveraged this resource by developing and applying a phylogenomic strategy to seek candidate plastid markers suitable for phylogenetic community analysis. We ranked the core genes of 107 published plastid genomes based on various sequence‐derived properties and their tree distance to plastid genome phylogenies. The resulting ranking revealed that the most widely used marker, rbcL, is not necessarily the optimal marker, while other promising markers might have been overlooked. We designed and tested PCR primers for several candidate marker genes, and successfully amplified one of them, rpoC1, in a taxonomically broad set of red algal specimens. We suggest that our general marker identification methodology and the rpoC1 primers will be useful to the phycological community for investigating the biodiversity and community ecology of the red algae.

Hidden introductions of freshwater red algae via the aquarium trade exposed by DNA barcodes

“…The rbc L sequences of the specimens sampled worldwide enabled us to identify tentative cases of freshwater red algae introduced to Taiwan from distant regions. In future investigations, it may be fruitful to explore the utility of alternative marker genes (e.g., rpoC1 ; Zhan et al., 2020) and population‐level markers (e.g., microsatellite loci; Kinziger et al., 2011) to unveil candidate algal introductions alongside rbc L. Population‐level markers would help to better evaluate differences in genetic diversity between an introduced population and its potential source population(s) (e.g., Muirhead et al., 2008), thereby refining our criteria of potential introduced algae. Presently, a disadvantage of using these marker loci is their geographically restricted sampling, which limits our capacity to detect long‐distance introductions (e.g., between Taiwan and South America).…”

Genomic Rearrangements and Sequence Evolution across Brown Algal Organelles

“…To aid with the future selection of organellar genes for phylogenetic analysis and DNA barcoding or metabarcoding, as has recently been done for red algae ( Janouškovec et al 2013 ; Graf et al 2017 ; Zhan et al 2020 ), we provide a supplementary table S1 , Supplementary Material online with median and interquartile range (IQR) of both synonymous and nonsynonymous divergence ( supplementary table S1 , Supplementary Material online). While the median gives a general measure of sequence evolution rate, IQR gives a measure of differential rate across taxa.…”

Marine Natural Products: The Important Resource of Biological Insecticide

“…The Photosynthesis of marine plants is the energy source of all living activities in the ocean and provides a material basis for the composition and operation of marine ecological environment [30–33] . Wide variety of algae are the main components of marine plants, unique marine habitats cause differences in algae form and metabolism, making it an important source of marine natural products [34–37] . Marine natural products research on insecticides has gradually increased in recent years, and the number of compounds identified from marine plants have been increasing [38] …”