Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis.
Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis.
复制标题
苏铁科 (Cycadaceae) 的质体进化和系统发育：分子形态不一致和基因树空间分析
DOI：
10.1186/s12870-022-03491-2
复制
发表时间：
2022-03-15
影响因子：
5.3
通讯作者：
Gong X
中科院分区：
文献类型：
--
作者：
Liu J;Lindstrom AJ;Gong X
背景
质体基因组（plastomes）在解决多尺度系统发育关系方面具有巨大的潜力，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不一致性对解决一个谱系内系统发育的影响。在这里，我们研究了苏铁属植物的质体特征，现存苏铁中最具多样性的属，并通过对来自6个组的47个代表所有主要分支的质体进行取样，研究苏铁内的深层系统发育关系。
结果
所有苏铁属植物的质体都具有一致的基因含量和结构，只有一个基因在菲律宾苏铁中丢失。瓦代。三个新的质体区域（psbA-matK，trnN-ndhF，chlL-trnN）被确定为含有最高的核苷酸变异性。分子进化分析表明，除ndhB外，大部分质体蛋白编码基因都经历了纯化选择。系统基因组分析，或者包括连接和合并的方法，都确定了四个分支，但在浅节点的拓扑结构冲突。具体来说，我们发现三个物种丰富的苏铁部分，即Stangerioides，Indosinenses和苏铁，没有或只有微弱的支持，作为单系的基础上的质体共生。树空间分析的基础上不同的树推理方法都揭示了三个基因簇，其中具有中等遗传特性的集群表现出最好的一致性与有利的同源性。
结论
我们的探索苏铁的质体数据支持的想法，质体蛋白编码基因可能表现出不一致的系统发育信号。本文所报道的分子系统发育与形态分类之间的不一致性可能主要归因于质体的单亲属性，这不能提供足够的信息来解决系统发育问题。与先前的共识相比，具有较长序列和较高变异比例的基因在系统发育重建中具有上级优势，我们的结果表明，最有效的系统发育信号可能来自具有中等变异、GC含量、序列长度和经历适度选择的基因座。
Background
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.
Results
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.
Conclusions
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.
DOI：
10.1080/23802359.2019.1679683
发表时间：
2019-10-23
期刊：
Mitochondrial DNA. Part B, Resources
影响因子：
--
作者：
Liu J;Lindstrom AJ;Gong X
通讯作者：
Gong X