CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, Yunnan, China.
Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, 650201, Kunming, China.
BMC Plant Biol. 2022 Mar 15;22(1):116. doi: 10.1186/s12870-022-03491-2.
Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic discordance, in resolving the phylogeny within a lineage. Here we examine plastome characteristics of Cycas L., the most diverse genus among extant cycads, and investigate the deep phylogenetic relationships within Cycas by sampling 47 plastomes representing all major clades from six sections.
All Cycas plastomes shared consistent gene content and structure with only one gene loss detected in Philippine species C. wadei. Three novel plastome regions (psbA-matK, trnN-ndhF, chlL-trnN) were identified as containing the highest nucleotide variability. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection except ndhB. Phylogenomic analyses that alternatively included concatenated and coalescent methods, both identified four clades but with conflicting topologies at shallow nodes. Specifically, we found three species-rich Cycas sections, namely Stangerioides, Indosinenses and Cycas, were not or only weakly supported as monophyly based on plastomic phylogeny. Tree space analyses based on different tree-inference methods both revealed three gene clusters, of which the cluster with moderate genetic properties showed the best congruence with the favored phylogeny.
Our exploration in plastomic data for Cycas supports the idea that plastid protein-coding genes may exhibit discordance in phylogenetic signals. The incongruence between molecular phylogeny and morphological classification reported here may largely be attributed to the uniparental attribute of plastid, which cannot offer sufficient information to resolve the phylogeny. Contrasting to a previous consensus that genes with longer sequences and a higher proportion of variances are superior for phylogeny reconstruction, our result implies that the most effective phylogenetic signals could come from loci that own moderate variation, GC content, sequence length, and underwent modest selection.
质体基因组（质体基因组）在解决多尺度系统发育关系方面具有巨大潜力，但很少有研究关注质体基因的遗传特征，如遗传变异和系统发育分歧，在解决谱系内的系统发育关系。在这里，我们检查了苏铁科中最具多样性的苏铁属的质体特征，并通过采样来自六个节的代表所有主要分支的 47 个质体，调查了苏铁属内的深系统发育关系。
所有苏铁质体基因组都具有一致的基因内容和结构，仅在菲律宾物种 C. wadei 中检测到一个基因丢失。鉴定出三个新的质体区域（psbA-matK、trnN-ndhF、chlL-trnN），这些区域的核苷酸变异率最高。分子进化分析表明，除了 ndhB 外，大多数质体蛋白编码基因都受到了纯化选择的作用。替代地包括串联和合并方法的基因组分析都确定了四个分支，但在浅节点处的拓扑结构存在冲突。具体来说，我们发现三个苏铁科物种丰富的节，即 Stangerioides、Indosinenses 和 Cycas，根据质体系统发育学，它们要么没有被支持为单系群，要么只有微弱的支持。基于不同树推断方法的树空间分析都揭示了三个基因簇，其中具有中等遗传特性的簇与首选系统发育的一致性最好。
我们对苏铁质体数据的探索支持了这样一种观点，即质体蛋白编码基因在系统发育信号中可能表现出不一致性。这里报道的分子系统发育与形态分类之间的不一致性主要归因于质体的单亲属性，它不能提供足够的信息来解决系统发育问题。与先前认为具有较长序列和更高变异比例的基因更适合系统发育重建的共识相反，我们的结果表明，最有效的系统发育信号可能来自拥有适度变异、GC 含量、序列长度和经历适度选择的基因。
