Analysis of Genome Size and Characteristics of Nekemias grossedentata Based on Flow Cytometry and Genomic Survey

doi:10.3969/j.issn.1009-7791.2025.06.002

Subtropical Plant Science ›› 2025, Vol. 54 ›› Issue (6): 613-620.DOI: 10.3969/j.issn.1009-7791.2025.06.002

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Analysis of Genome Size and Characteristics of Nekemias grossedentata Based on Flow Cytometry and Genomic Survey

LI Meng-lu¹, YANG Meng-si¹, LIU Liang¹, ZHAO Bo², LIU Hua-ying³, LIU Jiang-jun⁴, XIONG Chao^1*

(1. School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, Hubei China; 2. School of Pharmacy, Guilin Medical University, Guilin 541199, Guangxi China; 3. Hubei Laifeng Tengsheng Spice Chemical Co., Ltd., Enshi 445701, Hubei China; 4. Zhangjiajie Xinlin Biotechnology Co., Ltd., Zhangjiajie 427306, Hunan China)

Received:2025-07-16 Accepted:2025-08-09 Online:2025-12-31 Published:2025-12-31
Contact: XIONG Chao

基于流式细胞术与基因组Survey的大齿牛果藤基因组大小及特征分析

李梦露¹，杨梦思¹，刘梁¹，赵博²，刘华英³，刘将军⁴，熊超^1*

(1. 武汉轻工大学生命科学与技术学院，湖北武汉 430023；2. 桂林医科大学药学院，广西桂林 541199；3. 湖北来凤腾升香料化工有限公司，湖北恩施 445701；4. 张家界鑫林生物科技有限公司，湖南张家界 427306)

通讯作者: 熊超
基金资助:
湖北省恩施州“赶超计划”科技计划项目(D20230091)；武汉轻工大学校立科研项目(2025Y24)

Abstract

Abstract: Nekemias grossedentata, a member of the genus Nekemias in Vitaceae, is a dual-purpose plant for both food and medicine with significant economic, edible and medicinal value. To determine an optimal technical strategy for its whole-genome sequencing, this study employed flow cytometry and genome survey analysis to evaluate key genomic characteristics, including genome size, heterozygosity rate, proportion of repetitive sequences, and GC content of N. grossedentata. The results showed that: (1) Using corn B73 as the reference species, flow cytometry predicted that N. grossedentata was diploid, with genomic sizes of approximately 0.677 G and DNA-C values of approximately 0.707 pg; (2) After quality control of high-throughput sequencing data, the Q20 and Q30 values of clean reads reached 98.74% and 96.34%, respectively, with a GC content of 35.3%, demonstrating excellent sequencing quality; (3) k-mer analysis revealed that the genome size of N. grossedentata was 706.01 Mb, with a heterozygosity rate of 0.57% and a repetitive sequence proportion of 59.76%, classifying it as a genome with relatively high heterozygosity and high repeat content. These findings provide an important reference for subsequent whole-genome de novo sequencing, assembly, and structural annotation, as well as for constructing of high-quality genome genetic maps and mining key functional genes in N. grossedentata.

Key words: Nekemias grossedentata, genome size, flow cytometry, survey analysis, k-mer analysis

摘要： 大齿牛果藤Nekemias grossedentata为葡萄科药食两用植物，具有重要的经济、食用和药用价值。为明确其全基因组测序的技术策略，采用流式细胞术与基因组Survey分析，系统评估该种基因组大小、杂合率、重复序列占比及GC含量等特征。结果表明：(1)以玉米B73为参考物种，流式细胞术检测显示大齿牛果藤为二倍体，基因组大小约为0.677 G，DNA-C值约为0.707 pg；(2)高通量测序经质控后，有效测序序列(clean reads)的Q20值为98.74%，Q30值为96.34%，GC含量35.3%，测序质量优良；(3) k-mer分析结果显示，该种基因组大小为706.01 Mb，杂合度为0.57%，重复序列占比59.76%，属于较高杂合、高重复型基因组。研究结果可为大齿牛果藤全基因组de novo测序、组装、注释及高质量基因组遗传图谱构建、关键功能基因挖掘提供参考。

关键词: 大齿牛果藤, 基因组大小, 流式细胞术, Survey分析, k-mer分析

CLC Number:

Q943

LI Meng-lu1, YANG Meng-si, LIU Liang, ZHAO Bo, LIU Hua-ying, LIU Jiang-jun, XIONG Chao. Analysis of Genome Size and Characteristics of Nekemias grossedentata Based on Flow Cytometry and Genomic Survey[J]. Subtropical Plant Science, 2025, 54(6): 613-620.

李梦露, 杨梦思, 刘梁, 赵博, 刘华英, 刘将军, 熊超. 基于流式细胞术与基因组Survey的大齿牛果藤基因组大小及特征分析[J]. 亚热带植物科学, 2025, 54(6): 613-620.

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Analysis of Genome Size and Characteristics of Nekemias grossedentata Based on Flow Cytometry and Genomic Survey

基于流式细胞术与基因组Survey的大齿牛果藤基因组大小及特征分析

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