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

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (6) : 251-260.

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

Pan-genome and genomic variation analyses of Populus

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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.

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Populus / pan-genome / structural variation / phenological candidate genes

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CHU Chenchen , SUN Mingsheng , WU Yuhan , et al . Pan-genome and genomic variation analyses of Populus[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2022, 46(6): 251-260 https://doi.org/10.12302/j.issn.1000-2006.202209037

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