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

Ma, Jianchao; Wan, Dongshi; Duan, Bingbing; Bai, Xiaotao; Bai, Qiuxian; Chen, Ningning; Ma, Tao

doi:10.1111/pbi.12989

Cited by 74 publications

(103 citation statements)

References 75 publications

(99 reference statements)

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“…We have previously reported the assembly of the genomes of a male P. euphratica (Zhang et al , 2020) and a male P. alba var. pyramidalis (a variety of P. alba ) (Ma et al , 2019). Here we further sequenced and de novo assembled female genomes for both species using Oxford Nanopore reads.…”

Section: Resultsmentioning

confidence: 99%

“…We have previously reported the reference genome of a male P. euphratica (Zhang et al , 2020) and a male P. alba (Ma et al , 2019). In this study, we further collected the fresh leaves of a female P. euphratica and a female P. alba for genome sequencing and assembly.…”

Section: Methodsmentioning

confidence: 99%

“…Transposable elements in our assembled Y and W contigs were identified and classified using the software RepeatMasker (Tarailo-Graovac and Chen, 2009). Gene annotation was conducted by combining the results of de novo prediction from the program Augustus v.3.2.1 (Stanke et al , 2006), homology-based prediction using the protein sequences of A. thaliana , P. trichocarpa and S. purpurea downloaded from Phytozome 12 (https://phytozome.jgi.doe.gov/), as well as transcriptome data of P. euphratica and P. alba generated from our previously studies (Ma et al , 2019; Hu et al , 2020; Zhang et al , 2020). The predicted genes were searched against predicted proteins from P. trichocarpa , S. suchowensis and A. thaliana to find the closest homologous annotation.…”

Section: Methodsmentioning

confidence: 99%

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A general model to explain repeated turnovers of sex determination in the Salicaceae

Yang

Zhang

Wang

et al. 2020

Preprint

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0Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly 3 1 in multiple plant lineages. However, the specific mechanisms through which sex 3 2 systems evolve and their commonalities among plant species remain poorly 3 3 understood. With both XY and ZW sex systems, the family Salicaceae provides a 3 4 system to uncover the evolutionary forces driving sex chromosome turnovers. In this 3 5 study, we performed a genome-wide association study to characterize sex 3 6 determination in two Populus species, P. euphratica and P. alba. Our results reveal an 3 7XY system of sex determination on chromosome 14 of P. euphratica, and a ZW 3 8 system on chromosome 19 of P. alba. We further assembled the corresponding sex 3 9 determination regions, and found that their sex chromosome turnovers may be driven 4 0 by the repeated translocations of a Helitron-like transposon. During the translocation, 4 1 this factor may have captured partial or intact sequences that are orthologous to a 4 2 type-A cytokinin response regulator gene. Based on results from this and other 4 3recently published studies, we hypothesize that this gene may act as a master regulator 4 4 of sex determination for the entire family. We propose a general model to explain how 4 5 the XY and ZW sex systems in this family can be determined by the same RR gene. 6Our study provides new insights into the diversification of incipient sex chromosome 4 7 in flowering plants by showing how transposition and rearrangement of a single gene 4 8 can control sex in both XY and ZW systems. 4 9 5 0

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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A general model to explain repeated turnovers of sex determination in the Salicaceae

Yang

Zhang

Wang

et al. 2020

Preprint

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“…Over the past two decades, a large number of genomic and molecular biology resources of this model plant have been developed. For example, the genomes of various poplar species, including Populus trichocarpa, Populus euphratica, Populus tremula and so on, have been sequenced (Tuskan et al, 2006;Ma et al, 2013;Yang et al, 2017;Lin et al, 2018;Liu et al, 2019;Ma et al, 2019). At the same time, poplars have also been extensively studied at the transcriptome (Qiu et al, 2011;Zhang et al, 2014), proteomics (Xiao et al, 2009), methylome (Song et al, 2015;Su et al, 2018), and population genomics levels (Evans et al, 2014;Ma et al, 2018;Wang et al, 2020), focusing on long-term perennial growth, wood development, flowering, sex determination, and adaptation to environmental stress.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing

Yang

Zheng

et al. 2020

Front. Genet.

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Poplars are worldwidely cultivated with ecologically and economically important value. Populus alba var. pyramidalis (= P. bolleana) is a main tree of the farmland shelter-belt system in the arid region of Northwest China due to its rapid growth, erect stems, and high biomass production. However, the full-length messenger RNA (mRNA) sequences and complete structure of P. alba var. pyramidalis remain unclear. In this study, using singlemolecular real-time (SMRT) and next-generation high-throughput sequencing (NGS) platform, we sequenced transcripts from leaf, root, xylem, and phloem of P. alba var. pyramidalis, to obtain the full-length mRNA transcripts and annotate the complete structure. In total, 86,327 mapped full-length non-chimeric (FLNC) reads were identified, with 705 previously unannotated loci and 3,410 long noncoding RNAs (lncRNAs) and 174 fusion genes found. Alternative spicing (AS) events were detected in 7,536 genes, of which 4,652 genes had multiple AS events. A total of 10,213 alternative polyadenylation (APA) sites were identified, with two or more APA sites observed in 2,212 genes. Our transcriptome data provided the full-length sequences and gene isoforms of transcripts for P. alba var. pyramidalis, which will be helpful in improving our understanding for the genome annotation and gene structures of P. alba var. pyramidalis.

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“…The whole genome size of P. tomentosa is 740.2 Mb, which 331 is comprised of the sum of subgenome A (P. alba var. pyramidalis) and subgenome D (P. (416.0 Mb), which respectively consist of 19 chromosomes as they were resolved into a 335 single haploid genome rather than two diploid subgenomes (Liu et al, 2019;Ma et al, 2019; 336 Ma et al, 2013;Tuskan et al, 2006;Yang et al, 2017). However, this case is very similar to 337 the genome of a hybrid poplar (84K) recently published, which was subdivided into two 338 subgenomes (P. alba and P. tremula var.…”

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Hybrid origin ofPopulus tomentosaCarr. identified through genome sequencing and phylogenomic analysis

Gao

Chen

et al. 2020

Preprint

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32Populus tomentosa is widely distributed and cultivated in the Northern and Central China, 33 where it is of great economic and ecological importance. However, the origin of P. tomentosa 34 remains controversial. Here, we used a PacBio+Hi-C+Illumina strategy to sequence and 35 assemble its 740.2 Mb (2n) genome. The assembly accounts for greater than 92.1% of the 36 800-megabase genome, comprises 38 chromosomes, and contains 59,124 annotated 37 protein-coding genes. Phylogenomic analyses elucidated dynamic genome evolution events 38 among its closely related white poplars, and revealed that tomentosa is comprised of two 39 subgenomes, which we deomonstrate is likely to have resulted from hybridization between 40 Populus adenopoda as the female, and Populus alba var. pyramidalis as the male, around 41 3.93 Mya. We also detected structural variations and allele-indels across genome. Our study 42 presents a high quality and well assembled genome, unveils the origin of the widely 43 distributed and planted P. tomentosa, and provides a powerful resource for comparative plant 44 biology, breeding, and biotechnology. 45 46

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

Cited by 74 publications

References 75 publications

A general model to explain repeated turnovers of sex determination in the Salicaceae

A general model to explain repeated turnovers of sex determination in the Salicaceae

Analysis of Alternative Splicing and Alternative Polyadenylation in Populus alba var. pyramidalis by Single-Molecular Long-Read Sequencing

Hybrid origin ofPopulus tomentosaCarr. identified through genome sequencing and phylogenomic analysis

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