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

Selection of appropriate genetic markers to quantify phylogenetic diversity is crucial for phylogenetic community ecology studies. Yet, systematic evaluation of marker genes for this purpose is scarcely done. Recently, the combined effort of the phycological community has produced a rich plastid genome resource with taxonomic representation spanning all of the major lineages of the red algae (Rhodophyta). As a proof-of-concept study, we leverage this resource to develop and apply a phylogenomic strategy to seek candidate plastid markers that best capture the identity of component species in an eDNA metabarcoding study. We ranked the core plastid genes of 107 published plastid genomes based on various sequence-derived properties and their tree distance to plastid genome phylogenies and found that the most widely used marker, rbcL, is not necessarily the optimal marker, while more informative markers might have been overlooked. We designed and tested PCR primers for several candidate mark...

筛选适用于量化系统发育多样性的遗传标记，是系统发育群落生态学研究的核心需求。然而，针对该研究用途的标记基因系统性评估工作却长期缺位。近期，藻类学界的协同攻关已产出一套丰富的质体基因组（plastid genome）资源，其分类学覆盖范围囊括红藻门（Rhodophyta）所有主要演化支系。本研究作为一项概念验证（proof-of-concept）研究，依托该资源开发并应用了一套系统发育基因组学策略，旨在筛选可在环境DNA（eDNA）元条形码（metabarcoding）研究中最优区分组分物种的候选质体标记。我们基于多项序列衍生特征，以及各基因与质体基因组系统发育树的树距，对107个已发表质体基因组的核心质体基因进行了排序，结果发现，当前最常用的标记基因rbcL未必是最优标记，而更具信息价值的标记或已被学界忽视。我们为若干候选标记设计并测试了聚合酶链式反应（PCR）引物……