OHDLF: A Method for Selecting Orthologous Genes for Phylogenetic Construction and Its Application in the Genus Camellia

文献类型： 外文期刊

第一作者： Cai, Junhao

作者： Cai, Junhao;Cui, Yuwei;Wang, Zhentao;Zhang, Qunjie;Lu, Cui

作者机构：

关键词： phylogenetic tree construction; orthologous genes selection; Camellia genus; heterozygosity

期刊名称：GENES （ 影响因子：2.8； 五年影响因子：3.2 ）

ISSN：

年卷期： 2024 年 15 卷 11 期

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收录情况： SCI

摘要： Accurate phylogenetic tree construction for species without reference genomes often relies on de novo transcriptome assembly to identify single-copy orthologous genes. However, challenges such as whole-genome duplication (WGD), heterozygosity, gene duplication, and loss can hinder the selection of these genes, leading to limited data for constructing reliable species trees. To address these issues, we developed a new analytical pipeline, OHDLF (Orthologous Haploid Duplication and Loss Filter), which filters orthologous genes from transcript data and adapts parameter settings based on genomic characteristics for further phylogenetic tree construction. In this study, we applied OHDLF to the genus Camellia and evaluated its effectiveness in constructing phylogenetic trees. The results highlighted the pipeline's ability to handle challenges like high heterozygosity and recent gene duplications by selectively retaining genes with a missing rate and merging duplicates with high similarity. This approach ensured the preservation of informative sites and produced a highly supported consensus tree for Camellia. Additionally, we evaluate the accuracy of the OHDLF phylogenetic trees for different species, demonstrating that the OHDLF pipeline provides a flexible and effective method for selecting orthologous genes and constructing accurate phylogenetic trees, adapting to the genomic characteristics of various plant groups.

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