Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences
Lagerstroemia L. (Lythraceae) is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia, with numerous species highly valued as ornamentals. Although the plastomes of many species in this genus have been sequenced, the rates of...
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KeAi Communications Co., Ltd.
2023-04-01
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| Series: | Horticultural Plant Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468014122000589 |
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| author | Jie Wang Wenchuang He Xuezhu Liao Jin Ma Wei Gao Haoqi Wang Dili Wu Luke R. Tembrock Zhiqiang Wu Cuihua Gu |
| author_facet | Jie Wang Wenchuang He Xuezhu Liao Jin Ma Wei Gao Haoqi Wang Dili Wu Luke R. Tembrock Zhiqiang Wu Cuihua Gu |
| author_sort | Jie Wang |
| collection | DOAJ |
| description | Lagerstroemia L. (Lythraceae) is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia, with numerous species highly valued as ornamentals. Although the plastomes of many species in this genus have been sequenced, the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined. We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses. Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods. Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility. These results as well as analyses of non-synonymous and synonymous mutations, indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution. In addition, divergence events within the Lagerstroemia were dated for the first time. Several of the divergence estimates corresponded to well-known Earth history events, such as the reduction in global temperatures at the Eocene/Oligocene boundary. Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders, as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species. |
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| id | doaj.art-2d7cd788b1174bc580bfa9e41946263f |
| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-04-24T08:32:05Z |
| publishDate | 2023-04-01 |
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| series | Horticultural Plant Journal |
| spelling | doaj.art-2d7cd788b1174bc580bfa9e41946263f2024-04-16T19:16:32ZengKeAi Communications Co., Ltd.Horticultural Plant Journal2468-01412023-04-0192345355Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequencesJie Wang0Wenchuang He1Xuezhu Liao2Jin Ma3Wei Gao4Haoqi Wang5Dili Wu6Luke R. Tembrock7Zhiqiang Wu8Cuihua Gu9Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen, Guangdong 518120, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen, Guangdong 518120, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen, Guangdong 518120, ChinaZhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, Zhejiang 311300, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen, Guangdong 518120, ChinaShenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen, Guangdong 518120, ChinaShenzhen Middle School, Shenzhen, Guangdong 518000, ChinaDepartment of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA; Corresponding author.Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Shenzhen, Guangdong 518120, China; Kunpeng Institute of Modern Agriculture at Foshan, Foshan, Guangdong 528200, China; Corresponding author.Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, College of Landscape and Architecture, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China; Corresponding author.Lagerstroemia L. (Lythraceae) is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia, with numerous species highly valued as ornamentals. Although the plastomes of many species in this genus have been sequenced, the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly examined. We compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic analyses. Robust phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic methods. Identification of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear incompatibility. These results as well as analyses of non-synonymous and synonymous mutations, indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular evolution. In addition, divergence events within the Lagerstroemia were dated for the first time. Several of the divergence estimates corresponded to well-known Earth history events, such as the reduction in global temperatures at the Eocene/Oligocene boundary. Our analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders, as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.http://www.sciencedirect.com/science/article/pii/S2468014122000589Lagerstroemia L.Evolutionary rateSingle-nucleotide variantsMolecular datingChloroplastCodon |
| spellingShingle | Jie Wang Wenchuang He Xuezhu Liao Jin Ma Wei Gao Haoqi Wang Dili Wu Luke R. Tembrock Zhiqiang Wu Cuihua Gu Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences Horticultural Plant Journal Lagerstroemia L. Evolutionary rate Single-nucleotide variants Molecular dating Chloroplast Codon |
| title | Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences |
| title_full | Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences |
| title_fullStr | Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences |
| title_full_unstemmed | Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences |
| title_short | Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences |
| title_sort | phylogeny molecular evolution and dating of divergences in lagerstroemia using plastome sequences |
| topic | Lagerstroemia L. Evolutionary rate Single-nucleotide variants Molecular dating Chloroplast Codon |
| url | http://www.sciencedirect.com/science/article/pii/S2468014122000589 |
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