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Article

Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses

by
Hao-Zhi Zheng
1,2,
Wei Dai
1,2,
Meng-Han Xu
1,2,
Yu-Ye Lin
1,2,
Xing-Li Zhu
1,2,
Hui Long
1,2,
Li-Li Tong
3 and
Xiao-Gang Xu
1,2,*
1
Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China
2
State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains, Nanjing 210037, China
3
School of Horticulture & Landscape Architecture, Jinling Institute of Technology, Nanjing 210038, China
*
Author to whom correspondence should be addressed.
Genes 2024, 15(7), 940; https://doi.org/10.3390/genes15070940
Submission received: 6 June 2024 / Revised: 15 July 2024 / Accepted: 16 July 2024 / Published: 18 July 2024
(This article belongs to the Special Issue 5Gs in Crop Genetic and Genomic Improvement: 2nd Edition)
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Abstract

Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914–157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.
Keywords: Styrax japonicus; chloroplast; adaptive evolution; morphological variation; selection pressure Styrax japonicus; chloroplast; adaptive evolution; morphological variation; selection pressure

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MDPI and ACS Style

Zheng, H.-Z.; Dai, W.; Xu, M.-H.; Lin, Y.-Y.; Zhu, X.-L.; Long, H.; Tong, L.-L.; Xu, X.-G. Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses. Genes 2024, 15, 940. https://doi.org/10.3390/genes15070940

AMA Style

Zheng H-Z, Dai W, Xu M-H, Lin Y-Y, Zhu X-L, Long H, Tong L-L, Xu X-G. Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses. Genes. 2024; 15(7):940. https://doi.org/10.3390/genes15070940

Chicago/Turabian Style

Zheng, Hao-Zhi, Wei Dai, Meng-Han Xu, Yu-Ye Lin, Xing-Li Zhu, Hui Long, Li-Li Tong, and Xiao-Gang Xu. 2024. "Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses" Genes 15, no. 7: 940. https://doi.org/10.3390/genes15070940

APA Style

Zheng, H.-Z., Dai, W., Xu, M.-H., Lin, Y.-Y., Zhu, X.-L., Long, H., Tong, L.-L., & Xu, X.-G. (2024). Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses. Genes, 15(7), 940. https://doi.org/10.3390/genes15070940

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