杨树泛基因组构建与基因组变异分析

doi:10.12302/j.issn.1000-2006.202209037

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (6): 251-260.doi: 10.12302/j.issn.1000-2006.202209037

所属专题：南京林业大学120周年校庆特刊

杨树泛基因组构建与基因组变异分析

储陈辰(), 孙明升, 吴雨涵, 言震宇, 李婷, 冯洋帆, 国颖, 尹佟明, 薛良交()

江苏省杨树种质创新与品种改良重点实验室,南京林业大学林学院,南方现代林业协同创新中心, 江苏南京 210037

收稿日期:2022-09-19 修回日期:2022-10-19 出版日期:2022-11-30 发布日期:2022-11-24
通讯作者: 薛良交
基金资助:
国家自然科学基金项目(32171826)

Pan-genome and genomic variation analyses of Populus

CHU Chenchen(), SUN Mingsheng, WU Yuhan, YAN Zhenyu, LI Ting, FENG Yangfan, GUO Ying, YIN Tongming, XUE Liangjiao()

Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, College of Forestry, Co-Innovation Center for Sustainable Forestry in Sourthern China, Nanjing Forestry University, Nanjing 210037, China

Received:2022-09-19 Revised:2022-10-19 Online:2022-11-30 Published:2022-11-24
Contact: XUE Liangjiao

摘要/Abstract

摘要：

【目的】杨树是重要的速生用材、生态防护和碳汇造林树种,也是林木遗传研究的模式树种。开展杨树泛基因组构建与基因组变异分析,可为杨树精准育种和林木泛基因组研究提供理论先导。【方法】以公开发表的高质量杨树基因组序列为基础,分析不同类型的序列变异,总结变异特征,并构建基于基因和图形结构的杨树泛基因组。【结果】本研究收集到8个杨属树种和3个二倍体或三倍体杨树杂交品种的基因组序列,3个杂交品种包含7个单倍型亚基因组序列,较好地代表了杨树4个组派的基因组特征。分析结果表明,杨树基因组间存在较多大的结构变异。在基于基因的泛基因组中,共线核心基因、非共线核心基因、次核心基因、非必需基因、特异基因占比分别为12.5%、34.9%、31.4%、16.5%、4.7%。其中,非必需基因在功能上具有较高的多样性。以基因组序列变异为基础构建杨树图形结构泛基因组,大幅提升2代测序数据的变异检测效果。通过泛基因组变异热点分析,鉴定出2个与物候关联的基因位点。【结论】杨属基因组中存在大量染色体重排,进而增加了基因调控的多样性。杨树组/派间的基因组结构变异可能与物候适应存在关联。基于林木基因组序列的复杂性,在林木泛基因组研究中应注意基因组整合范围与研究目标相匹配,结合基因泛基因组和图形结构泛基因组结果,综合解析林木的遗传变异规律和物种演化特征。

关键词: 杨属, 泛基因组, 结构变异, 物候关联基因

Abstract:

【Objective】Poplar trees are important for timber production, ecological protection and carbon sequestration, and also serve as a model for forest genetic research. The construction of poplar pangenome and analysis of genomic variations will provide a theoretical guidance for poplar precision breeding and pan-genome research of forest trees. 【Method】All published high-quality poplar genome sequences were collected for a comparative genomic analysis. Both small genomic variations and large structural variations were identified and compared. Gene-based and graph-based pan-genomes were constructed, respectively. 【Result】Genomic sequences of eight poplar species and three diploid or triploid poplar hybrids were collected. The three hybrids contained seven haplotype subgenome sequences. These sequences represented the genomic characteristics of the four poplar Sections well. The comparative genomic analysis showed that there were many structural variations among poplar genomes. In the gene-based Populus pan-genomes, syntenic core genes, nonsyntenic core genes, softcore genes, dispensable genes, and private genes account for 12.5%, 34.9%, 31.4%, 16.5% and 4.7% of the total genes, respectively. Among them, dispensable genes exhibit a high functional diversity. Based on the variations of genome sequences, the graph-based poplar pangenome was constructed, which greatly improved the efficiency of variation detection using NGS data. Two genomic loci associated with phenology were identified through variation hotspot analysis of pan-genome. 【Conclusion】A large amount of genomic structural variations were observed in the genomes of Populus genus, which increase the diversity of gene regulation and thus affect the growth traits of poplar trees. The genomic structural variations among poplar Sections may be related to phenological adaptation. Due to the genomic complexity of forest trees, several aspects need to be considered during the construction of forest pangenomes, such as the agreement of included genomes and research objectives. The results from gene- and graph-based pan-genomes can be combined to explore the genomic variation and evolution of forest trees.

Key words: Populus, pan-genome, structural variation, phenological candidate genes

中图分类号:

S718

储陈辰,孙明升,吴雨涵,等. 杨树泛基因组构建与基因组变异分析[J]. 南京林业大学学报（自然科学版）, 2022, 46(6): 251-260.

CHU Chenchen, SUN Mingsheng, WU Yuhan, YAN Zhenyu, LI Ting, FENG Yangfan, GUO Ying, YIN Tongming, XUE Liangjiao. Pan-genome and genomic variation analyses of Populus[J].Journal of Nanjing Forestry University (Natural Science Edition), 2022, 46(6): 251-260.DOI: 10.12302/j.issn.1000-2006.202209037.

图/表 8

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种/品种 species/cultivar	单倍型 haplotype	简称 short name	基因组大小/Mb genome size	组装质量评估/% BUSCO	基因数量 number of genes	平均基因长度/bp average gene length	平均CDS 长度/bp average CDS length
银白杨 P. alba		P.alba	417.1	94.0	33 472	3 850	2 077
新疆杨 P. alba var. pyramidalis		P.alba pyr	408.1	89.8	40 214	3 646	1 115
美洲黑杨‘2-2’ P. deltoides‘2-2’		P.del2	431.9	96.4	37 900	3 289	1 401
美洲黑杨‘I-69’ P. deltoides‘I-69’		P.delI	424.6	97.1	31 722	3 561	1 740
胡杨P. euphratica		P.eup	574.3	96.7	36 606	3 454	1 128
小叶杨P. simonii		P.sim	441.4	96.2	45 127	3 138	1 075
欧洲山杨P. tremula		P.tre	408.8	97.6	37 184	4 131	2 353
毛果杨 P. trichocarpa		P.tri	392.2	97.9	34 699	3 646	2 163
银腺杨P. alba × P. tremula var. glandulosa	hapA	P.ag hA	356.0	97.5	38 368	3 164	1 286
银腺杨P. alba × P. tremula var. glandulosa	hapG	P.ag hG	354.0	96.5	38 471	3 121	1 257
毛白杨 P. tomentosa	hapA	P.tom hA	336.7	96.3	28 863	3 543	1 301
毛白杨 P. tomentosa	hapD	P.tom hD	344.4	94.3	28 951	3 528	1 292
三倍体毛白杨 P.× tomentosa clone 741	hap1	P.tom T h1	352.4	96.8	27 173	3 905	1 544
	hap2	P.tom T h2	329.7	97.7	24 987	3 866	1 539
	hap3	P.tom T h3	382.9	96.2	29 382	3 877	1 540

种/品种 tree species/ cultivar	变异类型 variant type	基因组变异数目 variant number from genome assemblies	图泛基因组检测变异数目 variants number of called using graph-base pan-genome	变异重叠数目 number of common variantion	变异比值/% ratio of variantion
	SNP	5 105 506	8 049 509	4 197 301	157.66
银白杨 P.alba	InDel	1 001 519	1 456 832	646 141	145.46
	PAV	2 241	4 684	1 985	209.00
	SNP	7 057 106	10 763 171	6 257 596	152.52
美州黑杨‘2-2’ P.del 2	InDel	1 374 430	2 044 506	1 086 692	148.75
	PAV	3 009	5 563	2 825	184.88
	SNP	4 968 151	10 122 781	4 106 298	203.75
胡杨 P.eup	InDel	909 977	1 859 804	647 873	204.38
	PAV	1 605	4 820	1 406	300.29
	SNP	4 561 434	8 065 104	4 057 224	176.81
欧洲山杨 P.tre	InDel	795 356	1 524 214	656 397	191.64
	PAV	1 658	4 767	1 487	287.49

杨树泛基因组构建与基因组变异分析

Pan-genome and genomic variation analyses of Populus

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