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
收稿日期: 2024-10-23
录用日期: 2025-01-20
网络出版日期: 2025-01-22
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
Received date: 2024-10-23
Accepted date: 2025-01-20
Online published: 2025-01-22
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)
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[J]. 植物学报, 2025 , 60(6) : 888 -900 . DOI: 10.11983/CBB24161
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)
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