Pan-genome and genomic variation analyses of Populus

doi:10.12302/j.issn.1000-2006.202209037

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (6): 251-260.doi: 10.12302/j.issn.1000-2006.202209037

Special Issue: 南京林业大学120周年校庆特刊

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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 E-mail:8200110010@njfu.edu.cn;lxue@njfu.edu.cn

Abstract

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

CLC Number:

S718

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, 2022, 46(6): 251-260.

Figures/Tables 8

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References 44

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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

Pan-genome and genomic variation analyses of Populus

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