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草业学报 ›› 2022, Vol. 31 ›› Issue (12): 133-145.DOI: 10.11686/cyxb2021491

• 研究论文 • 上一篇    

基于流式细胞法和K-mer分析法检测沙鞭基因组大小

刘涛1(), 刘玉萍2,3(), 富贵1, 吕婷1, 刘峰2, 张雨2, 苏丹丹2, 王亚男2, 郑长远2, 苏旭2,3,4()   

  1. 1.青海师范大学地理科学学院,青海 西宁 810008
    2.青海师范大学生命科学学院,青海 西宁 810008
    3.高原科学与可持续发展研究院,青海 西宁 810016
    4.青海师范大学青藏高原地表过程与生态保育教育部重点实验室,青海 西宁 810008
  • 收稿日期:2021-12-28 修回日期:2022-03-09 出版日期:2022-12-20 发布日期:2022-10-17
  • 通讯作者: 刘玉萍,苏旭
  • 作者简介:E-mail: xusu8527972@126.com
    E-mail: lyp8527970@126.com
    刘涛(1993-),男,甘肃酒泉人,在读博士。E-mail: 532226527@qq.com
  • 基金资助:
    国家自然科学基金(32160297);青海省自然科学基金面上项目(2022-ZJ-918)

Estimation of genome size for Psammochloa villosa by flow cytometry and K-mer analysis

Tao LIU1(), Yu-ping LIU2,3(), Gui FU1, Ting LV1, Feng LIU2, Yu ZHANG2, Dan-dan SU2, Ya-nan WANG2, Chang-yuan ZHENG2, Xu SU2,3,4()   

  1. 1.School of Geography Sciences,Qinghai Normal University,Xining 810008,China
    2.School of Life Sciences,Qinghai Normal University,Xining 810008,China
    3.Academy of Plateau Science and Sustainability,Xining 810016,China
    4.Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau,the Ministry of Education,Qinghai Normal University,Xining 810008,China
  • Received:2021-12-28 Revised:2022-03-09 Online:2022-12-20 Published:2022-10-17
  • Contact: Yu-ping LIU,Xu SU

摘要:

禾本科沙鞭属仅包含沙鞭一个种。沙鞭具有根茎繁殖、克隆整合等典型沙生植物特征,是我国内蒙古高原非固定沙地的建群种。本研究采用流式细胞术和K-mer分析方法测定沙鞭基因组大小,建立和优化以芨芨草为内参物种、青海固沙草和方穗山羊草为外参物种的二倍体植物DNA含量(DNA C值)测定体系。研究结果表明:1)沙鞭流式细胞峰值荧光是青海固沙草的2.54倍,是芨芨草的1.35倍,峰值信号远小于方穗山羊草,推测沙鞭基因组大小约为1580.10±5.02 Mb;2)K-mer分析结果表明,沙鞭基因组大小为1563.54 Mb,杂合率1.15%,重复序列比例为66.27%,基因组GC含量为43.4%,属于高杂合、高重复的复杂基因组;3)沙鞭基因组可使用PacBio平台CLR或HiFi模式进行三代测序,测序深度应不低于20×。沙鞭基因组大小的准确测定不仅补充了禾本科针茅族植物的DNA含量数据,同时也为沙鞭基因组测序、进化基因组研究、种质资源开发和利用以及遗传资源保护提供了数据参考,可为针茅族近缘物种基因组大小测定提供借鉴。

关键词: 基因组大小, DNA C值, 流式细胞术, 基因组survey测序, K-mer分析

Abstract:

The genus Psammochloa belongs to Poaceae and contains only one species (Psammochloa villosa). P. villosa has characteristics typical of sand-plants, including a rhizomatous growth habit and clonal integration, and is a dominant species in non-fixed sand dunes on the Inner Mongolia Plateau in China. The present study measured the genome size of P. villosa by combing flow cytometry and K-mer analysis, built an optimized system for determination of DNA content (C value) in diploid species via selecting Achnatherum splendens as an internal standard, and Orinus kokonoricaand Aegilops squarrosa as external standards. We found that: 1) The P. villosa fluorescence peak in flow cytometry was 2.54 times that of O. kokonorica, and 1.35 times that of A. splendens. Relative fluorescence intensity of P. villosa was much smaller than for A. squarrosa. The genome size of P. villosa was estimated to 1580.10±5.02 Mb. 2) Using K-mer analysis, the genome size of P. villosa was estimated to be about 1563.54 Mb, the hybridity rate was 1.15%, and the proportion of repeated sequences was 66.27%. Therefore, the genome of P. villosa is a complex genome with high heterozygosity and high repetition. 3) It is recommended that the sequencing strategy should be based on CLR or HiFi mode from the PacBio platform, and sequencing depth should be higher than 20×. The accurate determination of genome size of P. villosa has both added to knowledge of DNA content in a member of the tribe Stipeae (Poaceae), and provided data useful for genome sequencing, evolutionary genomics research, germplasm resource development and utilization, and species conservation. The result may provide an indication of genomic size for closely related species of Stipeae.

Key words: genome size, DNA C value, flow cytometry, genome survey sequencing, K-mer analysis