Data from: Utilizing next-generation sequencing to resolve the backbone of the Core Goodeniaceae and inform future taxonomic and floral form studies

Though considerable progress has been made in inferring phylogenetic relationships of many plant lineages, deep unresolved nodes remain a common problem that can impact downstream efforts, including taxonomic decision-making and character reconstruction. The Core Goodeniaceae is a group affected by this issue: data from the plastid regions trnL-trnF and matK have been insufficient to generate adequate support at key nodes along the backbone of the phylogeny. We performed genome skimming for 24 taxa representing major clades within Core Goodeniaceae. The plastome coding regions (CDS) and nuclear ribosomal repeats (NRR) were assembled and complemented with additional accessions sequenced for nuclear G3PDH and plastid trnL-trnF and matk. The CDS, NRR, and G3PDH alignments were analyzed independently and topology tests were used to detect the alignments’ ability to reject alternative topologies. The CDS, NRR, and G3PDH alignments independently supported a Brunonia (Scaevola s.l. (Coopernookia (Goodenia s.l.))) backbone topology, but within Goodenia s.l., the strongly-supported plastome topology (Goodenia A (Goodenia B (Velleia + Goodenia C))) contrasts with the poorly supported nuclear topology ((Goodenia A + Goodenia B) (Velleia + Goodenia C)). A fully resolved and maximally supported topology for Core Goodeniaceae was recovered from the plastome CDS, and there is excellent support for most of the major clades and relationships among them in all alignments. The composition of these seven major clades renders many of the current taxonomic divisions non-monophyletic, prompting us to suggest that Goodenia may be split into several segregate genera.

尽管在推断众多植物支系的系统发育关系方面已取得显著进展，但深层未分辨节点仍是一类普遍存在的问题，这类问题会对后续研究工作产生影响，其中包括分类学决策与性状重建。核心草海桐类群（Core Goodeniaceae）正是受该问题影响的类群：此前基于质体区域trnL-trnF与matK的测序数据，无法为该类群系统发育主干上的关键节点提供足够的支持度。我们针对代表核心草海桐类群内主要演化支的24个类群开展了基因组浅层测序（genome skimming）。我们组装得到了质体基因组（plastome）编码区（CDS，Coding Sequence）与核核糖体重复序列（NRR，nuclear ribosomal repeats），并补充了利用核基因G3PDH与质体区域trnL-trnF、matK测序获得的额外样品数据。我们分别对CDS、NRR与G3PDH的序列比对（alignments）进行分析，并借助拓扑结构检验（topology tests）评估各序列比对能否拒绝备选系统发育拓扑结构。上述三类序列比对的单独分析结果均支持如下核心草海桐类群系统发育主干拓扑结构：布伦尼亚属（Brunonia）+（广义草海桐属（Scaevola s.l.）+（库珀诺基阿属（Coopernookia）+广义好望草属（Goodenia s.l.）））；但在广义好望草属内部，支持度极高的质体基因组拓扑结构（好望草支系A（Goodenia A）+（好望草支系B（Goodenia B）+（韦利亚属（Velleia）+好望草支系C（Goodenia C）））），与支持度较低的核基因拓扑结构（（好望草支系A + 好望草支系B）+（韦利亚属 + 好望草支系C））存在显著差异。基于质体基因组编码区数据，我们得到了完全解析且支持度最大化的核心草海桐类群系统发育拓扑结构；且在所有序列比对结果中，多数主要演化支及其间的亲缘关系均获得了极佳的支持度。上述七个主要演化支的组成结构，使得当前多数分类学划分不再符合单系性要求，因此我们建议将广义好望草属拆分为若干分离属。