Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution

Abstract The family Daphniphyllaceae has a single genus, and no relevant comparative phylogenetic study has been reported on it. To explore the phylogenetic relationships and organelle evolution mechanisms of Daphniphyllaceae species, we sequenced and assembled the chloroplast and mitochondrial geno...

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Main Authors: Rongxiang Zhang, Ying Liu, Shuwen Liu, Yuemei Zhao, Niyan Xiang, Xiaoman Gao, Tao Yuan
Format: Article
Language:English
Published: BMC 2025-01-01
Series:BMC Genomics
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Online Access:https://doi.org/10.1186/s12864-025-11213-9
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author Rongxiang Zhang
Ying Liu
Shuwen Liu
Yuemei Zhao
Niyan Xiang
Xiaoman Gao
Tao Yuan
author_facet Rongxiang Zhang
Ying Liu
Shuwen Liu
Yuemei Zhao
Niyan Xiang
Xiaoman Gao
Tao Yuan
author_sort Rongxiang Zhang
collection DOAJ
description Abstract The family Daphniphyllaceae has a single genus, and no relevant comparative phylogenetic study has been reported on it. To explore the phylogenetic relationships and organelle evolution mechanisms of Daphniphyllaceae species, we sequenced and assembled the chloroplast and mitochondrial genomes of Daphniphyllum macropodum. We also conducted comparative analyses of organelles in Daphniphyllaceae species in terms of genome structure, phylogenetic relationships, divergence times, RNA editing events, and evolutionary rates, etc. Results indicated differences in the evolutionary patterns of the plastome and mitogenome in D. macropodum. The plastome had a more conserved structure but a faster nucleotide substitution rate, and the mitogenome showed a more complex structure while the mitotic genome shows a more complex structure but a slower nucleotide substitution rate. We identified several unidirectional protein-coding gene transfer events from the plastome to the mitogenome based on homology analysis, but no transfer events occurred from the mitogenome to the plastome. Multiple TE fragments existed in organelle genomes, and two organelles showed different preferences for nuclear TE insertion types. The estimation of divergence time indicated that the differentiation of Daphniphyllaceae and Altingiaceae at around 29.86 Mya might be due to the dramatic uplift of Tibetan Plateau during the Oligocene. About 75% of codon changes in organelles were found to be hydrophilic to hydrophobic amino acids. The RNA editing in protein-coding transcripts is the result of amino acid changes to increase their hydrophobicity and conservation in alleles, which may contribute to the formation of functional 3D structures in proteins. This study would enrich genomic resources and provide valuable insights into the structural dynamics and molecular biology of Daphniphyllaceae species.
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spelling doaj-art-586ad7872b834818a37c7c46442093962025-02-02T12:10:04ZengBMCBMC Genomics1471-21642025-01-0126111610.1186/s12864-025-11213-9Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolutionRongxiang Zhang0Ying Liu1Shuwen Liu2Yuemei Zhao3Niyan Xiang4Xiaoman Gao5Tao Yuan6School of Biological Science, Guizhou Education UniversityState Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan UniversitySchool of Biological Science, Guizhou Education UniversitySchool of Biological Science, Guizhou Education UniversitySchool of Ecology and Environment, Tibet UniversityState Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan UniversityState Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan UniversityAbstract The family Daphniphyllaceae has a single genus, and no relevant comparative phylogenetic study has been reported on it. To explore the phylogenetic relationships and organelle evolution mechanisms of Daphniphyllaceae species, we sequenced and assembled the chloroplast and mitochondrial genomes of Daphniphyllum macropodum. We also conducted comparative analyses of organelles in Daphniphyllaceae species in terms of genome structure, phylogenetic relationships, divergence times, RNA editing events, and evolutionary rates, etc. Results indicated differences in the evolutionary patterns of the plastome and mitogenome in D. macropodum. The plastome had a more conserved structure but a faster nucleotide substitution rate, and the mitogenome showed a more complex structure while the mitotic genome shows a more complex structure but a slower nucleotide substitution rate. We identified several unidirectional protein-coding gene transfer events from the plastome to the mitogenome based on homology analysis, but no transfer events occurred from the mitogenome to the plastome. Multiple TE fragments existed in organelle genomes, and two organelles showed different preferences for nuclear TE insertion types. The estimation of divergence time indicated that the differentiation of Daphniphyllaceae and Altingiaceae at around 29.86 Mya might be due to the dramatic uplift of Tibetan Plateau during the Oligocene. About 75% of codon changes in organelles were found to be hydrophilic to hydrophobic amino acids. The RNA editing in protein-coding transcripts is the result of amino acid changes to increase their hydrophobicity and conservation in alleles, which may contribute to the formation of functional 3D structures in proteins. This study would enrich genomic resources and provide valuable insights into the structural dynamics and molecular biology of Daphniphyllaceae species.https://doi.org/10.1186/s12864-025-11213-9DaphniphyllaceaeOrganelle genomesStructure dynamicPhylogenetic relationshipsDivergence time
spellingShingle Rongxiang Zhang
Ying Liu
Shuwen Liu
Yuemei Zhao
Niyan Xiang
Xiaoman Gao
Tao Yuan
Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution
BMC Genomics
Daphniphyllaceae
Organelle genomes
Structure dynamic
Phylogenetic relationships
Divergence time
title Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution
title_full Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution
title_fullStr Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution
title_full_unstemmed Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution
title_short Comparative organelle genomics in Daphniphyllaceae reveal phylogenetic position and organelle structure evolution
title_sort comparative organelle genomics in daphniphyllaceae reveal phylogenetic position and organelle structure evolution
topic Daphniphyllaceae
Organelle genomes
Structure dynamic
Phylogenetic relationships
Divergence time
url https://doi.org/10.1186/s12864-025-11213-9
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