Previous Article in Journal
Transcriptomic Analysis Reveals the Impact of Interstock on Vesicle Granulation in ‘Hainan Qingyou’ Pomelo (Citrus maxima) Fruit
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Horticulturae
Volume 11
Issue 10
10.3390/horticulturae11101231
horticulturae-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Mitochondrial Genome Assembly and Comparative Analysis of Three Closely Related Oaks

by
Zhi-Tong Xiao
1,†,
Ying Song
1,†,
Lu-Ting Liu
2,†,
Bo Chen
1,
Yue Xu
1,
Li-Jun Huang
1,
He Li
1,
Xiao-Long Jiang
1,*,
Xiong-Sheng Liu
3,* and
Min Deng
2
1
School of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
2
School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
3
Guangxi Forestry Research Institute, Nanning 530002, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Horticulturae 2025, 11(10), 1231; https://doi.org/10.3390/horticulturae11101231 (registering DOI)
Submission received: 11 August 2025 / Revised: 29 September 2025 / Accepted: 9 October 2025 / Published: 12 October 2025
(This article belongs to the Topic Plant Breeding, Genetics and Genomics, 2nd Edition)
Versions Notes

Abstract

The genus Quercus is an ecological keystone and economically vital component of Northern Hemisphere forests. While genomic studies have advanced our understanding of its nuclear and chloroplast genomes, the mitochondrial genomes of oaks remain less explored due to their complex evolutionary dynamics, which include extreme size variation, frequent rearrangements, and recurrent horizontal gene transfer. This study presents the assembly, annotation, and comparative analysis of mitogenomes from three closely related Asian oaks—Q. engleriana, Q. kongshanensis, and Q. tungmaiensis—using PacBio HiFi sequencing. The assemblies revealed distinct structural organizations: the Q. engleriana and Q. kongshanensis mitogenomes each comprised one circular contig and one linear contig, whereas the Q. tungmaiensis mitogenome comprised one circular contig and two linear contigs. Comparative analyses revealed variations in codon usage bias, simple sequence repeats, and predicted RNA editing sites. Notably, RNA editing in rps12 was uniquely observed in Q. kongshanensis. Mitochondrial targeting of plastid transcripts constituted 1.39%, 1.79%, and 2.24% of the mitogenomes, respectively. Phylogenetic reconstruction based on mitochondrial PCGs robustly resolved Q. kongshanensis and Q. tungmaiensis as sister species, with all three forming a distinct clade separate from other Quercus species. This study provides comprehensive mitogenomic resources essential for elucidating Quercus evolutionary biology and supporting germplasm development.
Keywords: Quercus; mitogenome; repeated sequences; genome recombination; phylogenetic relationship Quercus; mitogenome; repeated sequences; genome recombination; phylogenetic relationship

Share and Cite

MDPI and ACS Style

Xiao, Z.-T.; Song, Y.; Liu, L.-T.; Chen, B.; Xu, Y.; Huang, L.-J.; Li, H.; Jiang, X.-L.; Liu, X.-S.; Deng, M. Mitochondrial Genome Assembly and Comparative Analysis of Three Closely Related Oaks. Horticulturae 2025, 11, 1231. https://doi.org/10.3390/horticulturae11101231

AMA Style

Xiao Z-T, Song Y, Liu L-T, Chen B, Xu Y, Huang L-J, Li H, Jiang X-L, Liu X-S, Deng M. Mitochondrial Genome Assembly and Comparative Analysis of Three Closely Related Oaks. Horticulturae. 2025; 11(10):1231. https://doi.org/10.3390/horticulturae11101231

Chicago/Turabian Style

Xiao, Zhi-Tong, Ying Song, Lu-Ting Liu, Bo Chen, Yue Xu, Li-Jun Huang, He Li, Xiao-Long Jiang, Xiong-Sheng Liu, and Min Deng. 2025. "Mitochondrial Genome Assembly and Comparative Analysis of Three Closely Related Oaks" Horticulturae 11, no. 10: 1231. https://doi.org/10.3390/horticulturae11101231

APA Style

Xiao, Z.-T., Song, Y., Liu, L.-T., Chen, B., Xu, Y., Huang, L.-J., Li, H., Jiang, X.-L., Liu, X.-S., & Deng, M. (2025). Mitochondrial Genome Assembly and Comparative Analysis of Three Closely Related Oaks. Horticulturae, 11(10), 1231. https://doi.org/10.3390/horticulturae11101231

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Article metric data becomes available approximately 24 hours after publication online.
Back to TopTop