Genome Size and Characteristics Analysis of Xanthopappus subacaulis Based on Flow Cytometry and Genome Survey

doi:10.11983/CBB24161

Abstract

Abstract: INTRUDUCTION: Xanthopappus subacaulis, endemic to the Qinghai-Xizang Plateau, is a perennial medicinal plant from the genus Xanthopappus of the family Asteraceae, with important economic, ecological and medicinal values. However, genomic information for this species remains limited, hindering further genetic studies and resource utilization. Determining an appropriate sequencing strategy for its whole genome is a key prerequisite for subsequent genomic studies.
RATIONALE: In order to determine the appropriate sequencing strategy for the whole genome of X. subacaulis, we analyzed and evaluated its genome size, heterozygosity, repeat and GC content using flow cytometry and genome survey analysis based on BGI sequencing.
RESULTS: Flow cytometry analyses using Opisthopappus longilobus and Solanum lycopersicum as reference genomes indicated that X. subacaulis was a diploid, with an estimated genome size of 1.94 G and 1.75 G respectively, and a DNA-C value of 0.99 pg. We generated approximately 100.3 G of clean short read sequencing data, with a GC content of 38.5%. K-mer analysis indicated that the genome size of X. subacaulis was 2 198.50 Mb, with a heterozygosity rate of 0.69%, and repeat content of 80.15%. The analysis of the long terminal repeat retrotransposons (LTR-RTs) indicated that the LTR/Copia was the most abundant LTR family, accounting for 30.72% of the whole genome, while the Gypsy family and the unknown LTRs accounted for 33.66% and 16.54%, respectively. Moreover, their peak insertion time began approximately three million years ago (Mya), with a marked amplification occurring within the last 1 Mya. These results suggested that the large-scale insertion of LTR elements was (most) likely one of the important factors leading to the genomic complexity of X. subacaulis.
CONCLUSION: This study clarifies the key genomic characteristics of X. subacaulis, which provides valuable reference data resources for subsequent genetic map construction and functional gene mining of X. subacaulis, and also lays a foundation for determining its whole-genome sequencing strategy.

Growth morphology and genomic characteristics of Xanthopappus subacaulis. (A) Growth morphology of X. subacaulis (bar=5 cm); (B) Depth and frequency distribution of K-mer and insertion time analysis of long terminal repeat retrotransposons (LTR-RTs)

Key words: Xanthopappus subacaulis, flow cytometry, C value, genome survey, long terminal repeat retrotransposons (LTR-RTs)

Jiarui Jin, Yuping Liu, Xu Su, Tao Liu, Mingjun Yu, Qian Yang, Rongju Qu, Penghui Zhang, Zhaxi Cairang, Cuojia Nan, Leyi Zhou. Genome Size and Characteristics Analysis of Xanthopappus subacaulis Based on Flow Cytometry and Genome Survey[J]. Chinese Bulletin of Botany, 2025, 60(6): 888-900.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24161

https://www.chinbullbotany.com/EN/Y2025/V60/I6/888

Figures/Tables 6

Figure 1 Flow cytometry (FCM) fluorescence pattern of different samples (A) Xanthopappus subacaulis; (B) Opisthopappus longilobus; (C) Solanum lycopersicum

Table 1 Squencing data statistics of Xanthopappus subacaulis

Date type	Library name	Read number	Base count (bp)	Read length (bp)	Q20 (%)	Q30 (%)	GC content (%)
Raw data	Xanthopappus subacaulis	710885064	106632759600	150; 150	98.7; 97.2	95.4; 91.0	38.6; 38.5
Clean data	X. subacaulis	669190080	100378512000	150; 150	98.6; 97.1	95.3; 90.8	38.5; 38.5

Figure 2 Sequencing quality evaluation for Xanthopappus subacaulis (A), (B) Base distribution plot; (C), (D) Base quality distribution plot; (E), (F) GC content density plot

Table 2 NCBI nucleotide database BLAST

Species	Comparison rate (%)
Dolomiaea souliei	2.36
Cynara cardunculus	1.96
Gynoxys mandonii	0.97
Sonchus asper	0.58
D. edulis	0.48

Figure 3 Genomic characterization analysis of Xanthopappus subacaulis (A) Depth frequency distribution of K-mer; (B) Insertion time estimation of long terminal repeat retrotransposons (LTR-RTs)

Table 3 Classification and characterization of long terminal repeat retrotransposons (LTR-RTs) in the genome of Xanthopappus subacaulis

Transposable element	Class	Number	Base count (bp)	Percent (%)
LTR-RTs	Copia	95073	674533731	30.72
LTR-RTs	Gypsy	73190	739177424	33.66
LTR-RTs	Unknown	70092	363196738	16.54

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