热带胎生睡莲保罗蓝基因组大小及Survey测序分析

Genome size and Survey sequencing of tropical viviparous Nymphaea ‘Paul Stetson’

  • 摘要: 【目的】 研究热带胎生睡莲保罗蓝基因组大小等特征,为开展睡莲全基因组图谱绘制、重要性状功能基因挖掘及加快热带胎生睡莲分子育种进程提供参考依据。【方法】 以保罗蓝睡莲2~3 cm长的幼嫩根尖和3~5 cm长幼嫩未展开的叶片为试验材料,以已知基因组大小的玉米为内参植物,采用流式细胞术检测并估算保罗蓝睡莲的基因组大小,并与已公开发表的二倍体睡莲蓝星进行比较,初步判断保罗蓝睡莲的染色体倍型。采用荧光原位杂交法分析保罗蓝睡莲染色体数目、长度等,并结合基于K-mer分析的全基因组Survey测序和生物信息学方法,进一步明确保罗蓝睡莲基因组大小、倍性、杂合率、重复率等信息。【结果】 流式细胞术估算保罗蓝睡莲基因组大小为0.82 Gb,对比二倍体蓝星睡莲基因组,可初步判断出其为四倍体。利用基因组DAPI荧光染色及荧光原位杂交进一步证明保罗蓝睡莲基因组为四倍体,具有56条染色体,长度为0.45~1.50μm,核型公式为2n=4x=56。利用BGI测序平台对保罗蓝睡莲进行Survey测序分析,获得原始序列615552560条,有效碱基共92.33 Gb,其中GC含量为39.45%,Q20为97.08%,Q30为91.97%;有效序列(Cleanreads)615552500条,有效碱基共89.17Gb,其中Cleanreads中GC含量为39.00%,Q20为97.11%,Q30为92.05%。Survey总测序深度为106.9X,通过K-mer(K=19)分析修正后的保罗蓝睡莲基因组大小为834.12Mb,杂合率为1.95%,重复率为68.48%。Smudgeplot分析结果也表明保罗蓝睡莲为四倍体,其中以四倍体AAAB出现的频率最高,为0.43。【结论】 保罗蓝睡莲基因组属于高杂合高重复的复杂四倍体基因组,推测其基因组结构为AAAB,具有3套同源单倍型基因组,组装难度较高。

     

    Abstract: 【Objective】 The study aimed to investigate the genome size and related characteristics of the tropical viviparous Nymphaea ’Paul Stetson’ and thereby provide reference for constructing a whole-genome map, mining functional genes for key traits, and accelerating the molecular breeding of tropical viviparous water lilies. 【Method】Young root tips(2-3 cm) and young and unfolded leaves(3-5 cm) of Nymphaea ’Paul Stetson’ were used as experimental materials, with maize—whose genome size was known—serving as an internal reference. Flow cytometry was employed to estimate the genome size of Nymphaea ’Paul Stetson’, and the results were compared with those of the diploid Nymphaea colorata to preliminarily assess its ploidy. In addition, fluorescence in situ hybridization(FISH) was used to analyze the chromosome number and length. The genome size, ploidy, heterozygosity rate and repetition rate of Nymphaea ’Paul Stetson’ were further clarified combined with K-mer analysis on whole-genome survey sequencingbioinformatics and bioinformatics information. 【Result】 Flow cytometry estimated the genome size of Nymphaea ’Paul Stetson’ to be 0.82 Gb, and compared with the genome of diploid Nymphaea ’Paul Stetson’, it could be preliminatively identified as tetraploid. Genomic DAPI fluorescence staining and FISH further confirmed that the genome of Nymphaea ’Paul Stetson’ was tetraploid, comprising 56 chromosomes with lengths ranging from 0.45 to 1.50 μm and a karyotype formula of 2n=4x=56. BGI sequencing platform was used to carry out Survey sequencing analysis of Nymphaea ’Paul Stetson’, and 615552560 raw data were obtained, with a total of 92.33 Gb, in which GC content was 39.45%, Q20 was 97.08%, and Q30 was 91.97%. There were 615552500 clean reads(89.17 Gb), of which the GC content was 39.00%, Q20 was 97.11% and Q30 was 92.05%. The total sequencing depth of Survey was 106.9X. The genome size of the revised Nymphaea ’Paul Stetson’ was 834.12Mb, the heterozygous rate was 1.95%, and the repetition rate was 68.48%. The results of Smudgeplot analysis also showed that Nymphaea ’Paul Stetson’ was tetraploid, and the frequency of tetraploid AAAB was the highest(0.43). 【Conclusion】 The genome of Nymphaea ’Paul Stetson’ is a complex tetraploid characterized by high heterozygosity and a high repetition rate. Its structure is hypothesized to be of the AAAB type, comprising 3 sets of homologous haploid genomes, which presents great challenges for genome assembly.

     

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