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

Junhao Cai, Cui Lu, Yuwei Cui, Zhentao Wang, Qunjie Zhang

Abstract read

In one paragraph

Article in Genes, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

5 authors.

Junhao CaiCenter of Genomics and Bioinformatics, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

Cui LuInstitute of Horticulture, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.ORCID 0000-0003-1955-4321

Yuwei CuiCenter of Genomics and Bioinformatics, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

Zhentao WangCenter of Genomics and Bioinformatics, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

Qunjie ZhangCenter of Genomics and Bioinformatics, Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.

Funding

Double First-Class Discipline Promotion Project 2021B10564001Natural Science Foundation of China 32170625

6 · The paper itself

Abstract

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

Indexed as

CamelliaPhylogenyGene DuplicationGenes, PlantGenome, PlantGenomicsCamellia genusheterozygosityorthologous genes selectionphylogenetic tree construction

Identifiers

PMID39596605

DOI10.3390/genes15111404

PMCPMC11593501

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.