Details

Autor(en) / Beteiligte

• Zhan, Shing Hei
• Shih, Chun‐Chi
• Liu, Shao‐Lun

Titel

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

Ist Teil von

• Ecology and evolution, 2020-02, Vol.10 (3), p.1299-1310

Ort / Verlag

England: John Wiley & Sons, Inc

Erscheinungsjahr

2020

Link zum Volltext

Quelle

Wiley Online Library

Beschreibungen/Notizen

• 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. Environmental DNA metabarcoding utilizes a single genetic marker to determine the species composition of communities and to measure the phylogenetic diversity within and among communities. In a re‐analysis of 107 plastid genomes of the red algae (Rhodophyta), we found that traditional phylogenetic markers, such as rbcL and psbA, may not necessarily be optimal for those purposes in those organisms. Instead, we uncovered potentially superior candidate markers and proposed and successfully tested a novel marker, rpoC1, for future community ecology studies of the red algae