基于流式细胞术和基因组Survey的黄缨菊基因组大小及特征分析

doi:10.11983/CBB24161

植物学报 ›› 2025, Vol. 60 ›› Issue (6): 888-900.DOI: 10.11983/CBB24161 cstr: 32102.14.CBB24161

基于流式细胞术和基因组Survey的黄缨菊基因组大小及特征分析

靳佳瑞¹^,², 刘玉萍¹^,²^,³, 苏旭¹^,²^,³^,^*(), 刘涛⁴^,^*(), 余明君¹^,², 杨倩¹^,², 曲荣举¹^,², 张朋辉¹^,², 才让扎西¹^,², 南措加¹, 周乐怡¹

¹ 青海师范大学生命科学学院, 西宁 810008
² 青海师范大学青海省青藏高原生物多样性形成机制与综合利用重点实验室, 西宁 810008
³ 青海师范大学高原科学与可持续发展研究院, 西宁 810016
⁴ 青海理工学院生态与环境科学学院, 西宁 810016

收稿日期:2024-10-23 接受日期:2025-01-20 出版日期:2025-11-10 发布日期:2025-01-21
通讯作者: 苏旭,刘涛
基金资助:
青海理工大学(筹)“昆仑英才”人才引进科研项目(2023-QLGKLYCZX-012);青海省重大科技专项(2023-SF-A5);国家自然科学基金(32360305);2023年中央林业草原生态保护恢复资金野生动植物保护项目(QHSY-2023-016);青海省省财政林业改革发展资金林草新技术推广项目(QSCZ-2023-001)

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

Jiarui Jin¹^,², Yuping Liu¹^,²^,³, Xu Su¹^,²^,³^,^*(), Tao Liu⁴^,^*(), Mingjun Yu¹^,², Qian Yang¹^,², Rongju Qu¹^,², Penghui Zhang¹^,², Zhaxi Cairang¹^,², Cuojia Nan¹, Leyi Zhou¹

¹ School of Life Sciences, Qinghai Normal University, Xining 810008, China
² Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Xizang Plateau in Qinghai Province, Qinghai Normal University, Xining 810008, China
³ Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810016, China
⁴ School of Ecology and Environmental Science, Qinghai Institute of Technology, Xining 810016, China

Received:2024-10-23 Accepted:2025-01-20 Online:2025-11-10 Published:2025-01-21
Contact: Xu Su, Tao Liu

摘要/Abstract

摘要： 黄缨菊(Xanthopappus subacaulis)是菊科(Asteraceae)黄缨菊属(Xanthopappus)多年生高原特有单属种药用植物, 具有重要的经济、生态和药用价值。为确定适合黄缨菊全基因组测序的技术策略, 利用流式细胞术和基因组Survey分析评估黄缨菊基因组大小、杂合率、重复序列比例、GC含量和长末端重复反转录转座子(long terminal repeat retrotransposons, LTR-RTs)等信息。结果表明: (1) 以长裂太行菊(Opisthopappus longilobus)和番茄(Solanum lycopersicum)为参考物种, 采用流式细胞术预估黄缨菊为二倍体, 基因组大小分别为1.94 G和1.75 G, DNA-C值为0.99 pg; (2) 高通量测序得到约100.3 G的Clean reads, 其Q20均大于97.1%, Q30均高于90.8%, AT和GC碱基含量无明显分离, GC含量为38.5%, 测序质量良好; (3) K核苷酸序列分析(K-mer analysis, K-mer)显示黄缨菊基因组大小为2 198.50 Mb, 杂合度为0.69%, 重复序列占比为80.15%, 属于微杂合、高重复序列的复杂基因组; (4) LTR-RTs鉴定表明Copia家族数量最多, 占全基因组的30.72%, Gypsy家族和Unknown分别占全基因组的33.66%和16.54%, 插入时间始于约3 Mya, 在1 Mya内产生大量扩增。综上, 研究结果表明LTR的大量插入是导致黄缨菊基因组复杂化的重要原因之一; 测序数据和研究结果可为黄缨菊高质量基因组遗传图谱构建和关键功能基因挖掘提供重要参考。

关键词: 黄缨菊, 流式细胞术, C值, 基因组Survey, 长末端重复反转录转座子(LTR-RTs)

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)

靳佳瑞, 刘玉萍, 苏旭, 刘涛, 余明君, 杨倩, 曲荣举, 张朋辉, 才让扎西, 南措加, 周乐怡. 基于流式细胞术和基因组Survey的黄缨菊基因组大小及特征分析. 植物学报, 2025, 60(6): 888-900.

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. Chinese Bulletin of Botany, 2025, 60(6): 888-900.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB24161

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

图/表 6

图1 流式细胞术(FCM)荧光信号图 (A) 黄缨菊; (B) 长裂太行菊; (C) 番茄

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

表1 黄缨菊测序数据统计

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

图2 黄缨菊测序质量检测与评估 (A), (B) Reads碱基分布图; (C), (D) Reads碱基质量分布图; (E), (F) Reads GC含量密度图

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

表2 NCBI核苷酸数据库比对

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

图3 黄缨菊基因组特征分析 (A) K-mer深度频率分布图; (B) 长末端重复反转录转座子(LTR-RTs)插入时间分析

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)

表3 黄缨菊基因组长末端重复反转录转座子(LTR-RTs)分类与特征

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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基于流式细胞术和基因组Survey的黄缨菊基因组大小及特征分析

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

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