Subfamily evolution analysis using nuclear and chloroplast data from the same reads
Abstract 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 separ...
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Nature Portfolio
2025-01-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-83292-9 |
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| author | Eranga Pawani Witharana Takaya Iwasaki Myat Htoo San Nadeeka U. Jayawardana Nobuhiro Kotoda Masashi Yamamoto Yukio Nagano |
| author_facet | Eranga Pawani Witharana Takaya Iwasaki Myat Htoo San Nadeeka U. Jayawardana Nobuhiro Kotoda Masashi Yamamoto Yukio Nagano |
| author_sort | Eranga Pawani Witharana |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-daabab566c724d75b98de11a28f8498b |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-daabab566c724d75b98de11a28f8498b2025-01-05T12:22:53ZengNature PortfolioScientific Reports2045-23222025-01-0115111510.1038/s41598-024-83292-9Subfamily evolution analysis using nuclear and chloroplast data from the same readsEranga Pawani Witharana0Takaya Iwasaki1Myat Htoo San2Nadeeka U. Jayawardana3Nobuhiro Kotoda4Masashi Yamamoto5Yukio Nagano6Faculty of Agriculture, University of PeradeniyaFaculty of Science, Ochanomizu UniversityAnalytical Research Center for Experimental Sciences, Saga UniversityFaculty of Agriculture, University of PeradeniyaGraduate School of Advanced Health Science, Saga UniversityThe United Graduate School of Agricultural Sciences, Kagoshima UniversityAnalytical Research Center for Experimental Sciences, Saga UniversityAbstract 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.https://doi.org/10.1038/s41598-024-83292-9Chloroplast genome sequencesRead2TreeAurantioideae subfamilyPhylogenetic discordanceIncomplete lineage sortingIntrogression |
| spellingShingle | Eranga Pawani Witharana Takaya Iwasaki Myat Htoo San Nadeeka U. Jayawardana Nobuhiro Kotoda Masashi Yamamoto Yukio Nagano Subfamily evolution analysis using nuclear and chloroplast data from the same reads Scientific Reports Chloroplast genome sequences Read2Tree Aurantioideae subfamily Phylogenetic discordance Incomplete lineage sorting Introgression |
| title | Subfamily evolution analysis using nuclear and chloroplast data from the same reads |
| title_full | Subfamily evolution analysis using nuclear and chloroplast data from the same reads |
| title_fullStr | Subfamily evolution analysis using nuclear and chloroplast data from the same reads |
| title_full_unstemmed | Subfamily evolution analysis using nuclear and chloroplast data from the same reads |
| title_short | Subfamily evolution analysis using nuclear and chloroplast data from the same reads |
| title_sort | subfamily evolution analysis using nuclear and chloroplast data from the same reads |
| topic | Chloroplast genome sequences Read2Tree Aurantioideae subfamily Phylogenetic discordance Incomplete lineage sorting Introgression |
| url | https://doi.org/10.1038/s41598-024-83292-9 |
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