Next Article in Journal
Effects of Utilizing Plasma-Activated Water as a Nitrate Source on Growth and Flowering of Vanda Orchids
Previous Article in Journal
Efficient Identification and Classification of Pear Varieties Based on Leaf Appearance with YOLOv10 Model
 
 
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 5
10.3390/horticulturae11050488
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

Whole-Genome Resequencing Reveals Phylogenetic Relationships and Sex Differentiation Mechanisms Among Fujian Cycas Species

by
Xinyu Xu
1,2,
Yousry A. El-Kassaby
2,
Sijia Liu
4,
Juan Zhang
3,
Lanqi Zhang
3,
Junnan Li
3,
Wenkai Li
3,
Kechang Zhang
5,
Minghai Zou
6,
Zhiru Lai
7,
Likuang Lin
7,
Yongdong Zhang
7,
Shasha Wu
1,* and
Bihua Chen
3,*
1
The Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province, National Long-Term Scientific Research Base for Fujian Orchid Conservation, Fujian Agriculture and Forestry University, Fuzhou 350002, China
2
Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
3
The Key Laboratory of Timber Forest, Breeding and Cultivation for Mountainous Areas in Southern China of China National Forestry and Grassland Bureau and the Key Laboratory of Forest Culture and Forest Product Processing Utilization of Fujian Province, Fujian Academy of Forestry Sciences, Fuzhou 350012, China
4
Fujian Satellite Data Development Co., Ltd., Fuzhou 350025, China
5
Zhao’an County Forestry Bureau, Zhao’an 363500, China
6
Sanming City Shaxian District Wildlife Center, Shaxian 365500, China
7
Yongtai County Forestry Bureau, Yongtai 350700, China
*
Authors to whom correspondence should be addressed.
Horticulturae 2025, 11(5), 488; https://doi.org/10.3390/horticulturae11050488 (registering DOI)
Submission received: 26 March 2025 / Revised: 26 April 2025 / Accepted: 29 April 2025 / Published: 30 April 2025
(This article belongs to the Section Genetics, Genomics, Breeding, and Biotechnology (G2B2))
Versions Notes

Abstract

Cycads, renowned as “living fossils”, are among the most ancient extant seed plants, playing a crucial role in understanding plant evolution and sex differentiation. Despite their importance, research on their genetics and sex differentiation remains scarce. This study investigates three species, represented by six samples, collected from various regions in Fujian Province, China, using whole-genome resequencing on the Illumina platform. The sequence data underwent rigorous quality control, alignment, and variant detection, focusing on SNP and InDel distribution and annotation. Among the studied species, Cycas revoluta exhibited the highest number of SNPs and the greatest heterozygosity values. Based on SNP data, phylogenetic trees and principal component analysis revealed distinct clusters, with the three C. revoluta samples forming one cluster, while the two C. szechuanensis samples and the C. taiwaniana sample were grouped separately. Gene function using COG and GO annotations, and KEGG enrichment analysis, all highlighted differences in genomic structure and functional gene distribution between male and female cycads. Notably, genes associated with sex differentiation, such as MADS-box and auxin-responsive protein genes, were shown, while other transcription factors showed distinct annotations and enrichment patterns based on sex. This study improves our understanding of genetic variation, evolutionary relationships, and gene enrichment in cycads, providing a foundation for conservation, cultivation, and insights into sex differentiation mechanisms in these ancient plants.
Keywords: SNP; InDel; sex differentiation; genetic diversity SNP; InDel; sex differentiation; genetic diversity

Share and Cite

MDPI and ACS Style

Xu, X.; A. El-Kassaby, Y.; Liu, S.; Zhang, J.; Zhang, L.; Li, J.; Li, W.; Zhang, K.; Zou, M.; Lai, Z.; et al. Whole-Genome Resequencing Reveals Phylogenetic Relationships and Sex Differentiation Mechanisms Among Fujian Cycas Species. Horticulturae 2025, 11, 488. https://doi.org/10.3390/horticulturae11050488

AMA Style

Xu X, A. El-Kassaby Y, Liu S, Zhang J, Zhang L, Li J, Li W, Zhang K, Zou M, Lai Z, et al. Whole-Genome Resequencing Reveals Phylogenetic Relationships and Sex Differentiation Mechanisms Among Fujian Cycas Species. Horticulturae. 2025; 11(5):488. https://doi.org/10.3390/horticulturae11050488

Chicago/Turabian Style

Xu, Xinyu, Yousry A. El-Kassaby, Sijia Liu, Juan Zhang, Lanqi Zhang, Junnan Li, Wenkai Li, Kechang Zhang, Minghai Zou, Zhiru Lai, and et al. 2025. "Whole-Genome Resequencing Reveals Phylogenetic Relationships and Sex Differentiation Mechanisms Among Fujian Cycas Species" Horticulturae 11, no. 5: 488. https://doi.org/10.3390/horticulturae11050488

APA Style

Xu, X., A. El-Kassaby, Y., Liu, S., Zhang, J., Zhang, L., Li, J., Li, W., Zhang, K., Zou, M., Lai, Z., Lin, L., Zhang, Y., Wu, S., & Chen, B. (2025). Whole-Genome Resequencing Reveals Phylogenetic Relationships and Sex Differentiation Mechanisms Among Fujian Cycas Species. Horticulturae, 11(5), 488. https://doi.org/10.3390/horticulturae11050488

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

Article Metrics

Back to TopTop