醋栗番茄染色体水平基因组组装

doi:10.16420/j.issn.0513-353x.2022-0578

摘要/Abstract

摘要：

利用HiFi长片段测序技术对醋栗番茄PI365967的基因组进行测序和从头组装,共构建了924个连续的重叠群序列,N50长度高达12.8 Mb,获得了PI365967染色体水平长度为834 M的高质量基因组序列。与栽培番茄Heinz1706基因组进行比较分析发现,二者存在倒位、缺失等大量结构变异。GO富集分析揭示了发生结构变异的基因可能的生物学功能。

关键词: 醋栗番茄, 三代测序, 基因组组装, 结构变异

Abstract:

In this study,the genome of Solanum pimpinellifolium PI365967 was sequenced by HiFi long sequencing technology and de novo assembled. A total of 924 contigs were constructed,and the length of N50 was up to 12.8 MB. A 834 M high-quality genome at the chromosome-level of PI365967 was obtained. Compared with the reference genome of cultivated tomato Heinz1706,a large number of structural variations are existed in PI365967,including inversion,deletion and so on. GO enrichment analysis revealed the possible biological functions of the genes with structural variation.

Key words: Solanum pimpinellifolium, third genome sequencing, genome assembly, structural variation

中图分类号:

S641.2

刘志强, 蔡和序, 崔霞. 醋栗番茄染色体水平基因组组装[J]. 园艺学报, 2022, 49(10): 2263-2272.

LIU Zhiqiang, CAI Hexu, and CUI Xia. A Chromosome-level Genome Assembly of Solanum pimpinellifolium[J]. Acta Horticulturae Sinica, 2022, 49(10): 2263-2272.

图/表 8

表1 引物列表

Table 1 List of primers

标记名称 Marker name	染色体 Chromosome	物理位置/bp Position	正向引物（5′-3′） Forward primer	反向引物（5′-3′） Reverse primer
Insertion1	2	23799464	TACTTGCTAACAGTGTTGAAGG	CTACTTGACAGTCGGCTCTC
Insertion2	3	3620314	ACACCTCGTTACTTGACTAA	AGATAGGAGAGTGACAAACA
Insertion3	8	54793793	TTGGACTTGCTCAACATCAGAA	TTGTTCACTATGCCTAGATCCTAC
Deletion1	1	18838033	TTTAGGTGCTGAGGTTCTTTCT	AACTAGACTGCCAAGGTATGC
Deletion2	9	65541719	TGACCCTCGTACTCCAATGAA	GGTTGAAATTCCTCTGTCCTTAATC
INV-F1/R1	9	15652525	GAGACTTAATAAGTGTGCACG	GATAGATTGTTGTGCCTCATTCCA
INV-F2/R2	9	15653722	GAAGAAGAGCACGAAGGTCAAG	CGCACTCAACAAGAATCACATTAC

图1 醋栗番茄PI365967的HiFi读长片段长度（A）及K-mer（B）分布

Fig. 1 Distribution of Solanum pimpinellifolium PI365967 HiFi reads length（A）and K-mer analysis（B）

表2 HiFi读长片段及从头组装重叠群数统计结果

Table 2 Count of HiFi reads and de novo assembly contigs

项目 Term	HiFi读长片段数 HiFi reads count	从头组装重叠群数 De novo assembly contigs count
总数目Total number	936 162	924
总碱基数/ bp Total bases	15 560 290 479	848 409 336
最小长度/ bp Minimum length	804	14 243
最大长度/ bp Maximum length	36 414	45 069 587
平均长度/ bp Average length	16 621	918 192
N50长度/ bp N50	16 665	12 818 588
N90长度/ bp N90	15 110	3 172 915

表3 使用BUSCO对醋栗番茄PI365967基因组的评估结果

Table 3 PI365967 genome assessed by BUSCO pipeline

评估类型 Type of assessment	有胚植物（1 614 BUSCOs） Embryophyta		茄科植物（5 950 BUSCOs） Solanaceae
评估类型 Type of assessment	数量Number	百分比Percent	数量Number	百分比Percent
完整的BUSCO片段Complete BUSCOs	1 591	98.6	5 849	98.3
完整的单拷贝BUSCO片段Complete and single-copy BUSCOs	1 580	97.9	5 741	96.5
完整的重复BUSCO片段Complete and duplicated BUSCOs	11	0.7	108	1.8
不完整的BUSCO片段Fragmented BUSCOs	8	0.5	12	0.2
缺失的BUSCO片段Missing BUSCOs	15	0.9	89	1.5

图2 醋栗番茄PI365967基因组概况

Fig. 2 Genomic landscape of PI365967

图3 醋栗番茄PI365967和栽培番茄Heinz1706基因组序列比较 A:两基因组之间5种结构变异类型统计;B:插入和缺失两种类型变异大小的分布;C:两基因组之间共线性分析结果（红色星号表示倒位变异）。

Fig. 3 Comparative analysis of PI365967 and Heinz1706 genome sequences A:The count of five types structure variations between PI365967 and Heinz1706 genome;B:Size distribution of insertions and deletions in the genome;C:Co-linearity analysis of two genome（The red asterisk indicates an inversion for experimental verification）.

图4 醋栗番茄PI365967和栽培番茄Heinz1706倒位、插入和缺失变异的验证 A:9号染色体上倒位序列验证。B:3个插入变异和2个缺失变异的验证。

Fig. 4 Validation of the inversion,insertion and deletion between PI365967 and Heinz1706 A:Validation of inversion on chromosome 09;B:Validation of three insertions and two deletions.

图5 醋栗番茄PI365967插入和缺失变异在全基因组的分布（A）和编码区发生变异基因的功能富集（B）

Fig. 5 The distribution of variation in PI365967 genome（A）and GO enrichment analysis of genes with variation at the CDS region（B）

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