The genome of Populus alba x Populus tremula var. glandulosa clone 84K

Qiu, Deyou; Bai, Shenglong; Ma, Jianchao; Zhang, Lisha; Shao, Fenjuan; Zhang, Kaikai; Yang, Yongqiang; Sun, Taixiang; Huang, Jinling; Zhou, Yun; Galbraith, David W.; Wang, Zhaoshan; Sun, Guiling

doi:10.1093/dnares/dsz020

Cited by 68 publications

(67 citation statements)

References 45 publications

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“…However, this case is very similar to the genome of a hybrid poplar (84K) recently published, which was subdivided into two subgenomes (P. alba and P. tremula var. glandulosa ) with a total genome size of 747.5 Mb (Qiu et al, 2019) (Table S7).…”

Section: Discussionmentioning

confidence: 99%

“…Diverse well-assembled reference genomes would also provide a fundamental tool for functional genomics, genetic engineering, and molecular breeding in this economically important genus (L. . It would also improve phylogenomic analyses of thePopulus pan-genome (Pinosio et al, 2016;L. Zhang et al, 2019), without the need for reliance on reference-guided mapping and variant calling based solely on the P. trichocarpa reference.…”

Section: Introductionmentioning

confidence: 99%

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High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species that is widespread in Asia

Gao

Chen

et al. 2021

Preprint

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Populus has a wide ecogeographical range spanning the Northern Hemisphere, and exhibits abundant distinct species and hybrids globally. Populus tomentosa Carr. is widely distributed and cultivated in the eastern region of Asia, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. Reference genomes are available for several Populus species, however, our goals were to produce a very high quality de novo, chromosome-level genome assembly in P. tomentosa genome that could serve as a reference for evolutionary and ecological studies of hybrid speciation. Here, combining long-read sequencing and Hi-C scaffolding, we present a high-quality, haplotype-resolved genome assembly. The genome size was 740.2 Mb, with a contig N50 size of 5.47 Mb and a scaffold N50 size of 46.68 Mb, consisting of 38 chromosomes, as expected with the known diploid chromosome number (2n=2x=38). A total of 59,124 protein-coding genes were identified. Phylogenomic analyses revealed that P. tomentosa is comprised of two distinct subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female parent and Populus alba var. pyramidalis as the male parent, approximately 3.93 Mya. Although highly colinear, significant structural variation was also found between the two subgenomes. Our study provides a valuable resource for ecological genetics and forest biotechnology.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species that is widespread in Asia

Gao

Chen

et al. 2021

Preprint

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“…To confirm the gene expression levels of the RNA-Seq assay, 1 μg total RNA mixed equally from 3 plants for each RNA-Seq sample was used for the qRT-PCR assay as previously described [62]. The RNA, following elimination of residual genomic DNA using DNase I, was reverse transcribed into cDNA using the PrimeScript RT reagent Kit with gDNA Eraser (Perfect Real Time) (Takara, Japan).…”

Section: Quantitative Real-time Pcr Analysis (Qrt-pcr)mentioning

confidence: 99%

Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Qin

Bai

et al. 2020

BMC Plant Biol

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Background: Nicotiana tabacum is an important economic crop. Topping, a common agricultural practice employed with flue-cured tobacco, is designed to increase leaf nicotine contents by increasing nicotine biosynthesis in roots. Many genes are found to be differentially expressed in response to topping, particularly genes involved in nicotine biosynthesis, but comprehensive analyses of early transcriptional responses induced by topping are not yet available. To develop a detailed understanding of the mechanisms regulating nicotine biosynthesis after topping, we have sequenced the transcriptomes of Nicotiana tabacum roots at seven time points following topping.Results: Differential expression analysis revealed that 4830 genes responded to topping across all time points. Amongst these, nine gene families involved in nicotine biosynthesis and two gene families involved in nicotine transport showed significant changes during the immediate 24 h period following topping. No obvious preference to the parental species was detected in the differentially expressed genes (DEGs). Significant changes in transcript levels of nine genes involved in nicotine biosynthesis and phytohormone signal transduction were validated by qRT-PCR assays. 549 genes encoding transcription factors (TFs), found to exhibit significant changes in gene expression after topping, formed 15 clusters based on similarities of their transcript level time-course profiles. 336 DEGs involved in phytohormone signal transduction, including genes functionally related to the phytohormones jasmonic acid, abscisic acid, auxin, ethylene, and gibberellin, were identified at the earliest time point after topping. Conclusions:Our research provides the first detailed analysis of the early transcriptional responses to topping in N. tabacum, and identifies excellent candidates for further detailed studies concerning the regulation of nicotine biosynthesis in tobacco roots.

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“…To explore this we isolated an NBR1 gene from Poplar 84 K clone ( Populus alba × P. tremula var. glandulosa ; PagNBR1 ), a hybrid poplar introduced from Korea that has been extensively cultivated in northern China ( Qiu et al, 2019 ). Transgenic poplars were generated to evaluate the potential tolerance mechanism mediated by the NBR1 gene in response to salt stress.…”

Section: Introductionmentioning

confidence: 99%

Poplar Autophagy Receptor NBR1 Enhances Salt Stress Tolerance by Regulating Selective Autophagy and Antioxidant System

Bao

Lǚ

et al. 2021

Front. Plant Sci.

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Salt stress is an adverse environmental factor for plant growth and development. Under salt stress, plants can activate the selective autophagy pathway to alleviate stress. However, the regulatory mechanism of selective autophagy in response to salt stress remains largely unclear. Here, we report that the selective autophagy receptor PagNBR1 (neighbor of BRCA1) is induced by salt stress in Populus. Overexpression of PagNBR1 in poplar enhanced salt stress tolerance. Compared with wild type (WT) plants, the transgenic lines exhibited higher antioxidant enzyme activity, less reactive oxygen species (ROS), and higher net photosynthesis rates under salt stress. Furthermore, co-localization and yeast two-hybrid analysis revealed that PagNBR1 was localized in the autophagosome and could interact with ATG8 (autophagy-related gene). PagNBR1 transgenic poplars formed more autophagosomes and exhibited higher expression of ATG8, resulting in less accumulation of insoluble protein and insoluble ubiquitinated protein compared to WT under salt stress. The accumulation of insoluble protein and insoluble ubiquitinated protein was similar under the treatment of ConA in WT and transgenic lines. In summary, our results imply that PagNBR1 is an important selective autophagy receptor in poplar and confers salt tolerance by accelerating antioxidant system activity and autophagy activity. Moreover, the NBR1 gene is an important potential molecular target for improving stress resistance in trees.

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The genome of Populus alba x Populus tremula var. glandulosa clone 84K

Cited by 68 publications

References 45 publications

High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species that is widespread in Asia

High quality haplotype-resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species that is widespread in Asia

Transcriptome analysis reveals key genes involved in the regulation of nicotine biosynthesis at early time points after topping in tobacco (Nicotiana tabacum L.)

Poplar Autophagy Receptor NBR1 Enhances Salt Stress Tolerance by Regulating Selective Autophagy and Antioxidant System

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