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

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, 青海西宁 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 修回日期:2025-01-02 出版日期:2025-01-21 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(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)

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

Jiarui Jin^{1, 2}, Yuping Liu^{1, 2, 3}, Xu Su^{1, 2, 3*}, Tao Liu^4*, Mingjun Yu^{1, 2}, Qian Yang^{1, 2}, Rongju Qu^{1, 2}, Penghui Zhang^{1, 2}, Zhaxi Cairang ^{1, 2}, Cuojia Nan ¹, Leyi Zhou ¹

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

Received:2024-10-23 Revised:2025-01-02 Online:2025-01-21 Published:2025-01-21
Contact: Xu Su, Tao Liu

摘要/Abstract

摘要： 黄缨菊(Xanthopappus subacaulis C. Winkl.)是菊科(Asteraceae)、黄缨菊属(Xanthopappus)的一种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。为了确定适合黄缨菊全基因组测序的技术策略, 本研究利用流式细胞术和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LTR-REs等信息。结果表明: (1) 以长裂太行菊和番茄为参考物种, 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106.6 G下机数据, 经质控后Clean reads的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-mer分析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-REs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。因此, 本研究认为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, 全基因组de novo测序建议采用二代与三代混合测序组装策略, 这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了重要参考数据。

关键词: 黄缨菊, 流式细胞术, C值, Survey分析, LTR-REs

Abstract:

Xanthopappus subacaulis C. Winkl., endemic to the Qinghai-Xizang Plateau, is a perennial medicinal plant from the genus Xanthopappus of the family Asteraceae, with the important economic, ecological and medicinal values. In order to determine the appropriate sequencing strategy for the whole genome of X. subacaulis, we analyzed and evaluated the genome size, heterozygosity, repeatability and GC content based on the flow cytometry and survey analysis method in the present study. The result was as follows: (1) Using Opisthopappus longilobus and Solanum lycopersicum as reference species, flow cytometry was used to estimate that X. subacaulis is a diploid, with genome sizes of 1.94 G or 1.75 G, and a DNA-C value of 0.99 pg. The genome size (G) of approximately was 0.99 pg, which was estimated through flow cytometry. (2) The high-throughput sequencing generated approximately 106.6 GB of raw data. After quality control, the Q20 and Q30 of the clean reads were greater than 97.1% and 90.8%, respectively. Besides, there was no significant separation of base contents within AT and GC, and the proportion of GC content was 38.5%. It indicated that the second-generation sequencing quality was good. (3) Based on K-mer analysis, the genome size of X. subacaulis was 2198.50 Mb, the heterozygosity was 0.69%, and the proportion of repeat sequences was 80.15%, which suggested that it belonged to the complex genome with micro-heterozygosity and high repeat sequence. (4) The identification results of LTR-REs indicate that the Copia family is the most abundant, accounting for 30.72% of the whole genome, while the Gypsy family and Unknown account for 33.66% and 16.54%, respectively. Moreover, their insertion time began approximately 3 Mya, with a significant amplification occurring within the last 1 Mya. Therefore, this study suggests that the large-scale insertion of LTR elements is one of the important factors leading to the genomic complexity of X. subacaulis. Thus, we thought that the de novo whole-genome sequencing of X. subacaulis should be adopted the sequencing and assembly strategy with the mixture of the second and third generation sequencing. This study provided the reference data for the genetic map construction of high-quality and key functional gene-mining for X. subacaulis.

Key words: Xanthopappus subacaulis, flow cytometry, C value, Survey analysis, LTR-REs

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, DOI: 10.11983/CBB24161.

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, DOI: 10.11983/CBB24161.

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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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