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Volume 14
Issue 19
10.3390/plants14193094
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

First Insights into Ploidy and Genome Size Estimation in Choerospondias axillaris (Anacardiaceae) Using Flow Cytometry and Genome Survey Sequencing

by
Fangdi Li
1,†,
Zhuolong Shen
1,†,
Tianhe Zhang
1,
Xiaoge Gao
1,
Huashan Ling
2,
Hequn Gu
2,
Zhigao Liu
2,
Jiyan Liu
2,
Chaokai Lin
3 and
Qirong Guo
1,*
1
Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry and Grassland College of Soil and Water Conservation, Nanjing Forestry University, Nanjing 210037, China
2
Jiangxi Qiyunshan Food Co., Ltd., Ganzhou 341300, China
3
Forestry Bureau of Chongyi County Jiangxi Province, Ganzhou 341300, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work as co-first author.
Plants 2025, 14(19), 3094; https://doi.org/10.3390/plants14193094
Submission received: 25 July 2025 / Revised: 23 September 2025 / Accepted: 6 October 2025 / Published: 7 October 2025
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
Review Reports Versions Notes

Abstract

For the Choerospondias axillaris (Roxb.) B.L.Burtt & A.W.Hill, a significant economic tree in the Anacardiaceae family with industrial, medicinal, and ecological value, the genome size remains unreported. Here, we optimized the flow cytometry-based method for ploidy analysis, finding that WPB lysis solution proved to be the most effective. Analysis of 58 C. axillaris accessions identified 47 diploids and 11 triploids. The average genome size of diploids was estimated at 450.36 Mb. Illumina sequencing of a diploid (No.22) generated 81.98 Gb of high-quality data (224.44X depth). K-mer analysis estimated the genome size at 365.25 Mb, with 0.91% genome heterozygosity, 34.17% GC content, and 47.74% repeated sequences, indicating high heterozygosity and duplication levels in the genome. Genome assembly may necessitate a combination of second- and third-generation sequencing technologies. Comparative analysis with the NT database revealed that C. axillaris exhibited the highest similarity to C. axillaris (3.01%) and Pistacia vera (2.5%). This study establishes a crucial theoretical framework for C. axillaris genome sequencing and molecular genetics.
Keywords: Choerospondias axillaris; genome size; flow cytometry; K-mer Choerospondias axillaris; genome size; flow cytometry; K-mer

Share and Cite

MDPI and ACS Style

Li, F.; Shen, Z.; Zhang, T.; Gao, X.; Ling, H.; Gu, H.; Liu, Z.; Liu, J.; Lin, C.; Guo, Q. First Insights into Ploidy and Genome Size Estimation in Choerospondias axillaris (Anacardiaceae) Using Flow Cytometry and Genome Survey Sequencing. Plants 2025, 14, 3094. https://doi.org/10.3390/plants14193094

AMA Style

Li F, Shen Z, Zhang T, Gao X, Ling H, Gu H, Liu Z, Liu J, Lin C, Guo Q. First Insights into Ploidy and Genome Size Estimation in Choerospondias axillaris (Anacardiaceae) Using Flow Cytometry and Genome Survey Sequencing. Plants. 2025; 14(19):3094. https://doi.org/10.3390/plants14193094

Chicago/Turabian Style

Li, Fangdi, Zhuolong Shen, Tianhe Zhang, Xiaoge Gao, Huashan Ling, Hequn Gu, Zhigao Liu, Jiyan Liu, Chaokai Lin, and Qirong Guo. 2025. "First Insights into Ploidy and Genome Size Estimation in Choerospondias axillaris (Anacardiaceae) Using Flow Cytometry and Genome Survey Sequencing" Plants 14, no. 19: 3094. https://doi.org/10.3390/plants14193094

APA Style

Li, F., Shen, Z., Zhang, T., Gao, X., Ling, H., Gu, H., Liu, Z., Liu, J., Lin, C., & Guo, Q. (2025). First Insights into Ploidy and Genome Size Estimation in Choerospondias axillaris (Anacardiaceae) Using Flow Cytometry and Genome Survey Sequencing. Plants, 14(19), 3094. https://doi.org/10.3390/plants14193094

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