南方农业学报2025，Vol.56Issue(2)：407-415,9.DOI:10.3969/j.issn.2095-1191.2025.02.006
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
Abstract
[Objective]The study aimed to investigate the genome size and related characteristics of the tropical vivipa-rous 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 colora-ta to preliminarily assess its ploidy.In addition,fluorescence in situ hybridization(FISH)was used to analyze the chro-mosome number and length.The genome size,ploidy,heterozygosity rate and repetition rate of Nymphaea'Paul Stet-son'were further clarified combined with K-mer analysis on whole-genome survey sequencingbioinformatics and bioin-formatics 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 tetra-ploid,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 ge-nomes,which presents great challenges for genome assembly.关键词
保罗蓝睡莲/流式细胞术/荧光原位杂交/Survey测序/K-mer分析Key words
Nymphaea'Paul Stetson'/flow cytometry/fluorescence in situ hybridization(FISH)/Survey sequen-cing/K-mer analysis分类
农业科技引用本文复制引用
苏群,王凌云,赵家惠,王虹妍,喇燕菲,方明雅,盛威,石林,唐毓玮,田敏..热带胎生睡莲保罗蓝基因组大小及Survey测序分析[J].南方农业学报,2025,56(2):407-415,9.基金项目
广西自然科学基金项目(2023GXNSFAA026279,2023GXNSFBA026347) （2023GXNSFAA026279,2023GXNSFBA026347）
广西农业科学院科技发展基金和基本科研业务专项(桂农科2025YP105,桂农科2024YP133) Guangxi Natural Science Foundation(2023GXNSFAA026279,2023GXNSFBA026347) （桂农科2025YP105,桂农科2024YP133）
Scien-ce and Technology Development Fund and Basic Research Project of Guangxi Academy of Agricultural Sciences(Guinong-ke 2025YP105,Guinongke 2024YP133) （Guinong-ke 2025YP105,Guinongke 2024YP133）
