Witharana Eranga Pawani, Iwasaki Takaya, San Myat Htoo, Jayawardana Nadeeka U, Kotoda Nobuhiro, Yamamoto Masashi, Nagano Yukio
Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka.
Analytical Research Center for Experimental Sciences, Saga University, Saga, Japan.
Sci Rep. 2025 Jan 3;15(1):687. doi: 10.1038/s41598-024-83292-9.
The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp genome data with nuclear DNA information offers a more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives. The resulting nuclear DNA trees were consistent with existing nuclear evolutionary relationships derived from high-throughput sequencing, but diverged from cp genome-based trees. To elucidate the underlying complex evolutionary processes causing these discordances, we implemented an integrative workflow that utilized multiple alignments of each gene generated by Read2Tree, in conjunction with other phylogenomic methods. Our analysis revealed that incomplete lineage sorting predominantly drives these discordances, while introgression and ancient introgression also contribute to topological discrepancies within certain clades. This study underscores the cost-effectiveness of using the same raw sequencing data for both cp and nuclear DNA analyses in understanding plant evolutionary relationships.
叶绿体（cp）基因组是探索植物进化关系的一种广泛使用的工具，但其在完全解析这些关系方面的有效性仍不确定。将cp基因组数据与核DNA信息相结合可以提供更全面的视角，但通常需要单独的数据集。为此，我们使用相同的原始读取测序数据，通过Read2Tree构建基于cp基因组的树和核DNA系统发育树，Read2Tree是一种从原始读取数据中提取保守核基因序列的经济高效的方法，重点关注包括柑橘及其近缘种在内的金橘亚科。由此产生的核DNA树与从高通量测序得出的现有核进化关系一致，但与基于cp基因组的树不同。为了阐明导致这些不一致的潜在复杂进化过程，我们实施了一种综合工作流程，该流程利用Read2Tree生成的每个基因的多序列比对，并结合其他系统发育基因组学方法。我们的分析表明，不完全谱系分选是导致这些不一致的主要原因，而基因渗入和古老基因渗入也导致了某些分支内的拓扑差异。这项研究强调了在理解植物进化关系时，使用相同的原始测序数据进行cp和核DNA分析的成本效益。
