植物学报2025，Vol.60Issue(6)：888-900,13.DOI:10.11983/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
Genome Size and Characteristics Analysis of Xanthopappus subacaulis Based on Flow Cytometry and Genome Survey
摘要
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.Deter-mining 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 ap-proximately 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.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)Key words
Xanthopappus subacaulis/flow cytometry/C value/genome survey/long terminal repeat retrotransposons(LTR-RTs)引用本文复制引用
靳佳瑞,南措加,周乐怡,刘玉萍,苏旭,刘涛,余明君,杨倩,曲荣举,张朋辉,才让扎西..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):888-900,13.基金项目
青海理工大学(筹)"昆仑英才"人才引进科研项目(No.2023-QLGKLYCZX-012)、青海省重大科技专项(No.2023-SF-A5)、国家自然科学基金(No.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(No.QHSY-2023-016)和青海省省财政林业改革发展资金林草新技术推广项目(No.QSCZ-2023-001) （筹）
