A Chromosome-level Genome Assembly of Solanum pimpinellifolium

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

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (10): 2263-2272.doi: 10.16420/j.issn.0513-353x.2022-0578

• Research Papers • Previous Articles Next Articles

A Chromosome-level Genome Assembly of Solanum pimpinellifolium

LIU Zhiqiang¹, CAI Hexu², and CUI Xia¹^,^**()

¹Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs,Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,Beijing 100081,China
²College of Horticulture,China Agricultural University,Beijing 100193,China

Received:2022-06-07 Revised:2022-08-15 Online:2022-10-25 Published:2022-10-31
Contact: and CUI Xia E-mail:cuixia@caas.cn

Abstract

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

CLC Number:

S641.2

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

Figures/Tables 8

References 20

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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

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

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

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

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

A Chromosome-level Genome Assembly of Solanum pimpinellifolium

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