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. 2019 Feb;17(2):451-460.
doi: 10.1111/pbi.12989. Epub 2018 Oct 24.

Genome sequence and genetic transformation of a widely distributed and cultivated poplar

Jianchao Ma  1 , Dongshi Wan  1 , Bingbing Duan  1 , Xiaotao Bai  1 , Qiuxian Bai  1 , Ningning Chen  1 , Tao Ma  1   2
Affiliations

Genome sequence and genetic transformation of a widely distributed and cultivated poplar

Jianchao Ma et al. Plant Biotechnol J. 2019 Feb.

Abstract

Populus alba is widely distributed and cultivated in Europe and Asia. This species has been used for diverse studies. In this study, we assembled a de novo genome sequence of P. alba var. pyramidalis (= P. bolleana) and confirmed its high transformation efficiency and short transformation time by experiments. Through a process of hybrid genome assembly, a total of 464 M of the genome was assembled. Annotation analyses predicted 37 901 protein-coding genes. This genome is highly collinear to that of P. trichocarpa, with most genes having orthologs in the two species. We found a marked expansion of gene families related to histone and the hormone auxin but loss of disease resistance genes in P. alba if compared with the closely related P. trichocarpa. The genome sequence presented here represents a valuable resource for further molecular functional analyses of this species as a new tree model, poplar breeding practices and comparative genomic analyses across different poplars.

Keywords: Populus alba; Populus bolleana; comparative genomics; gene families; transformation efficiency.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Populus alba var. pyramidalis genome. From the outer edge inward, circles represent the 50 largest DNA sequence scaffolds (green), the genes on each scaffold (blue), repeat density at 10 kb intervals (orange), GC density at 10 kb intervals (green), and the sequenced reads density at 10 kb intervals (grey). Links in the core connect duplicated sets of genes (E‐value threshold of <1e−10 and 85% similarity).
Figure 2
Figure 2
Genome characteristics. (a) Distribution of synonymous nucleotide substitutions (Ks). (b) Circos plots showing synteny between the Populus alba var. pyramidalis (left) and P. trichocarpa (right) genomes. (c) Venn diagram showing the number of gene families shared between P. alba var. pyramidalis and P. trichocarpa. (d) Expansion and contraction of gene families in ten species. (e) Phylogenetic trees of HFO3 genes in Arabidopsis, P. alba var. pyramidalis and P. trichocarpa.
Figure 3
Figure 3
Phylogenetic tree of NBS genes and it's contraction in Populus alba var. pyramidalis. (a) Phylogenetic tree of NBS genes in P. alba var. pyramidalis and P. trichocarpa. (b) Numbers of NBS genes subfamilies in P. alba var. pyramidalis and P. trichocarpa.
Figure 4
Figure 4
The genetic transformation process and results of transient transformation. (a) Simultaneous selection and regeneration on WPM‐reg plates. (b) Multiple green transgenic calli. (c) Transformed shoots regenerated from calli on WPM‐elo media. (d) A regenerated transgenic whole plant on rooting medium. (e) A transgenic plant under greenhouse conditions. (f–i) Transient GFP fusion protein expression assay in nucleus. (f) bright field; (g) DAPI; (h) green fluorescence; (i) overlay. Scale bar = 20 μm.
See this image and copyright information in PMC

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