Section Populus Research Articles

Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA.

Populus species play a foundational role in diverse ecosystems and are important renewable feedstocks for bioenergy and bioproducts. Hybrid aspen Populus tremula × P. alba INRA 717-1B4 is a widely used transformation model in tree functional genomics and biotechnology research. As an outcrossing interspecific hybrid, its genome is riddled with sequence polymorphisms which present a challenge for sequence-sensitive analyses. Here we report a telomere-to-telomere genome for this hybrid aspen with two chromosome-scale, haplotype-resolved assemblies. We performed a comprehensive analysis of the repetitive landscape and identified both tandem repeat array-based and array-less centromeres. Unexpectedly, the most abundant satellite repeats in both haplotypes lie outside of the centromeres, consist of a 147 bp monomer PtaM147, frequently span >1 megabases, and form heterochromatic knobs. PtaM147 repeats are detected exclusively in aspens (section Populus) but PtaM147-like sequences occur in LTR-retrotransposons of closely related species, suggesting their origin from the retrotransposons. The genomic resource generated for this transformation model genotype has greatly improved the design and analysis of genome editing experiments that are highly sensitive to sequence polymorphisms. The work should motivate future hypothesis-driven research to probe into the function of the abundant and aspen-specific PtaM147 satellite DNA.

Comparative Analysis of the Characteristics, Phylogenetic Relationships of the Complete Chloroplast Genome, and Maternal Origin Track of White Poplar Interspecific Hybrid GM107

White poplars are a dominant tree species in natural ecosystems throughout China, where they are also widely planted for agroforestry and industrial uses. However, the phylogenetic relationships among poplars in section Populus have a complex genetic background influenced by frequent hybridization events and, to date, only a few studies have attempted to clarify this background. In this study, we performed de novo assembly of the whole chloroplast (cp) genome of an elite individual GM107 with the size of 156,493 bp, which consists of a large single-copy (LSR) (84,610 bp), a small single-copy (SSC) (16,567 bp), and a pair of inverted repeats (27,658 bp). It comprises 127 genes, including 85 protein-coding genes, 36 tRNAs, and 6 rRNAs. Comparative analysis of the cp genomes was conducted among 7 poplars in section Populus and 4 cp DNA markers with >1% variable sites were detected. We found that Populus alba was the most closely related species to GM107 by phylogenetic analyses. RNA sequencing detected 66 genes that participated in translation, transcription, and photosynthesis. The expression levels of almost all 66 genes were higher in leaves than in other tissues, except for PtatpF and PtatpH. In all tissues, we detected higher transcript abundances of PtndhF, PtpsbA, PtpsbB, Ptrps14, PtatpF, and PtatpH than of other genes. Both cp genome and transcriptome data help understand evolution events in section Populus and unravel the origin of Chinese white poplars, and may contribute to the molecular genetic improvement of wood properties and carbon sink capacities in the breeding of poplars in this section.

Assembly and analysis of the Populus deltoides mitochondrial genome: the first report of a multicircular mitochondrial conformation for the genus Populus

Genomics research of Populus deltoides, an important timber species that is widely planted worldwide, is an important part of poplar breeding. Currently, the nuclear and chloroplast genome of P. deltoides have been sequenced, but its mitochondrial genome (mitogenome) has not been reported. To further explore the evolution and phylogeny of P. deltoides, the mitogenome of P. deltoides I-69 was assembled using reads from Nanopore and Illumina sequencing platforms and found to consist of 802,637 bp and three circular chromosomes (336,205, 280,841, and 185,591 bp) containing 58 genes (34 protein-coding genes, 21 tRNA genes, and 3 rRNA genes). RNA analysis in combination with several species showed significantly fewer RNA editing sites in the mitogenomes of poplar and other angiosperms than in gymnosperms. Sequence transfer analysis showed extensive mitogenome rearrangements in Populus species, and with evolution from lower to higher plants, tRNA transfer from chloroplasts to mitochondria became increasingly frequent. In a phylogenetic analysis, the evolutionary status of P. deltoides was determined, and the section Populus was supported. Our results based on the first report of a multi-circular conformation of the Populus mitogenome provide a basis for further study of the evolution and genetics of P. deltoides and other Populus species and for breeding programs.

A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination.

Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.

Identification and Comparative Analysis of Conserved and Species-Specific microRNAs in Four Populus Sections

The conservation and diversity of microRNA (miRNA) families provide insights into the evolution of miRNA genes. However, there are few studies to explore the miRNA genes at the genus level in plants. Here, we identified 1194 miRNA loci in four Populus species P. deltoides, P. euphratica, P. tremula, and P. trichocarpa from Aigeiros, Turanga, Populus, and Tacamahaca sections, respectively, by combining de novo and homolog-based approaches. Our results indicated that a similar number of miRNA loci exist in each species (296–301 miRNA loci). Among the identified 143 miRNA families, 68 families are shared by the studied four species, and 31 families are species-specific, which might be related to local adaptation. Additionally, multiple miRNA-related single nucleotide polymorphisms (SNPs) were found, indicating that polymorphisms in pre-miRNA hairpins were likely to affect miRNA biogenesis. This study expanded the breadth and depth of miRNA annotations and provided valuable resources for further exploring the diversity and function of poplar miRNAs.

In vitro amphidiploid induction of a distant hybrid Populus simonii × P. euphratica cv. ‘Xiaohuyang-2’ and its effect on plant morphology and anatomy

Abstract Highly gametic sterility of a distant hybrid Populus simonii × P. euphratica cv. ‘Xiaohuyang-2’ restricts its utilization in breeding programs of Populus. Amphidiploid induction by somatic chromosome doubling is expected to restore its gametic fertility. In this study, nodal-segment and leaf explants of ‘Xiaohuyang-2’ were used to induce chromosome doubling with colchicine in vitro. Although chromosome doubling of the nodal-segment explants only produced mixoploids, the treatments of leaf explants on adventitious bud regeneration medium successfully produced 4 amphidiploids, which might be attributed to the direct organogenesis of the adventitious buds on the leaf explants. This is the first report of amphidiploid induction in a distant hybrid between Populus section Tacamahaca and sect. Turanga. The highest amphidiploid induction frequency was 16.7 %. Both the explant survival rate and polyploidization frequency were significantly affected by colchicine concentration and exposure time. The amphidiploid plants significantly differed from the diploid and mixoploid plants in morphological and anatomical characteristics. They had larger, thicker, and greener leaves than the diploids and mixoploids. The increase in ploidy level also resulted in changes in stomatal features. The induced amphidiploid plants of the distant hybrid ‘Xiaohuyang-2’ are expected to play important roles in breeding programs of Populus in the future, which can be used as a bridge parent with the ability of unreduced gamete formation to cross with fast-growth germplasms to produce triploids pyramiding desirable traits of fast growth, easy cutting propagation, and salt and drought tolerances.

The genetic basis of sex determination in Populus provides molecular markers across the genus and indicates convergent evolution

Abstract Many dioecious angiosperms are trees, which only flower after years of vegetative development and do not usually exhibit marked secondary sexual dimorphism. Nevertheless, if the genetic basis of sex determination is known, the sex of an individual can be determined using molecular markers. Here, we report that in the genus Populus sect. Populus an XY system of sex determination, which is found in P. tremula and P. tremuloides, likely re-evolved from a ZW system present in P. alba, P. adenopoda and P. qiongdaoensis. Strikingly, this new XY system is mechanistically identical to the older system found in several species of the Populus sections Tacamahaca, Aigeiros and Turanga demonstrating a remarkable example of convergent evolution. In both XY systems, male-specific inversely repeated sequences appear to silence the ARR17 gene, which functions as a sex switch, via small interfering RNAs and DNA methylation. In the ZW system, female-specific copies of ARR17 appear to regulate dioecy. With this detailed information on the genetic basis of sex determination it was possible to develop molecular markers that can be utilized to determine the sex in seedlings and non-flowering trees of different poplar species. We used the female-specific ARR17 gene to develop a sex marker for P. alba and P. adenopoda. For P. grandidentata, we employed the male-specific ARR17 inverted repeat. Finally, we summarize previously described markers for P. tremula, P. tremuloides, P. trichocarpa, P. deltoides and P. nigra. These markers can be useful for poplar ecologists, geneticists and breeders.

Effect of Micromelalopha sieversi (Staudinger) Oviposition Behavior on the Transcriptome of Two Populus Section Aigeiros Clones

Research Highlights: The molecular mechanisms underlying woody plant resistance upon oviposition by herbivores remain unclear, as studies have focused on herbaceous plants. The effect of oviposition on gene expression in neighboring plants has also not been reported. Elucidating these molecular responses can help cultivate insect-resistant trees. Background and Objectives: Oviposition by herbivorous insects acts as an early warning signal, inducing plant resistance responses. Here, we employed poplar as a model woody plant to elucidate gene expression and the molecular mechanisms underlying plant resistance after oviposition by Micromelalopha sieversi (Staudinger) (Lepidoptera: Notodontidae). Materials and Methods: The differences in gene expression of two Populus section Aigeiros clones (‘108’ (Populus × euramericana ‘Guariento’) and ‘111’ (Populus × euramericana ‘Bellotto’)) were analyzed via high-throughput sequencing of oviposited, neighboring, and control plants. Results: We obtained 304,526,107 reads, with an average length of 300 bp and a total size of 40.77 Gb. Differentially expressed genes (DEGs) in gene ontology terms of biological process, cellular component, and molecular function were mainly enriched in the “cell part”, “catalytic”, and “metabolic process” functions. Moreover, DEGs were mainly enriched in the following pathways: plant-pathogen interaction, linoleic acid metabolism, and cyanoamino acid metabolism (108-O vs. 108-C); metabolic pathways, photosynthesis, photosynthesis-antenna proteins, nitrogen metabolism, and linoleic acid metabolism (111-O vs. 111-C); metabolic pathways and biosynthesis of secondary metabolites (111-N vs. 111-C); no pathways were significantly enriched in 108-N vs. 108-C. Up-regulated defense genes were associated with pathogenesis-related protein function, innate immune regulation, and biological stress response, with differences in specific genes. All genes related to photosynthetic activity were significantly down-regulated in oviposited and neighboring leaves of the two clones. Conclusions: Oviposited and neighboring ‘108’ and ‘111’ plants exhibited varying degrees of resistance upon oviposition, involving the up-regulation of various defense genes, decreased photosynthesis and nutrient accumulation, and increased secondary metabolic synthesis.

The response of the species diversity pattern of Populus to climate change in China

Increasing evidence shows that climate has already triggered species’ range and species diversity patterns shifting on the large scale, while the underlying mechanisms about it yet no consensus has been researched, due to various species focused and different scales researches performed. Based on the findings that the species diversity pattern supported niche conservatism between the sections (subgenus) of genus Populus, by exhaustively searching the herbarium specimen records, we investigated the species diversity patterns of genus Populus and projected their potential range and diversity pattern in the future scenarios of climate in China, using a geographic information system (GIS) and Gaussian model. Our analyses showed that (1) under the condition of contemporary climate, the species diversity center of Populus was distributed in a transitional region of arid-semiarid areas, near the “Heihe-Tengchong Line”, within which species diversity increased from northeast to southwest China along the line; (2) in the future scenarios of climate, the species distribution range of Populus will expand to the eastern and northern directions; and (3) the species diversity center of Populus tends to enlarge to northeast and northwest in the future scenarios of climate.

Использование признаков петиолярной анатомии для идентификации гибридов и видов секции Aigeiros и Tacamahaca рода Populus

Использование признаков петиолярной анатомии для идентификации гибридов и видов секции Aigeiros и Tacamahaca рода Populus

Comparative analysis of the complete chloroplast genomes of seven Populus species: Insights into alternative female parents of Populus tomentosa.

Populus tomentosa, of section Populus, is distributed mainly in northern China. This species has high resistance to many diseases and insects, and it plays key roles in shelterbelts and urban afforestation in northern China. It has long been suspected to be a hybrid, but its parents remain unknown. In the present study, we report four newly sequenced complete cp genomes from section Populus and comparative genomic analyses of these new sequences and three published cp genome sequences. The seven cp genomes ranged from 155,853 bp (P. tremula var. davidiana) to 156,746 bp (P. adenopoda) in length, and their gene orders, gene numbers and GC contents were similar. We analyzed SNPs, indels, SSRs and repeats among the seven cp genomes, and eight small inversions were detected in the ndhC-trnV, rbcL-accD, petA-psbJ, trnW-trnP, rpl16-rps3, trnL-ycf15, ycf15-trnL, and ndhF-trnL intergenic regions. Furthermore, seven divergent regions (trnH-psbA, matK, psbM-psbD, ndhC-trnV, ycf1, ndhF-ccsA and ccsA-ndhD) were found in more highly variable regions. The phylogenetic tree reveals that P. tomentosa is closely related to P. alba and P. alba var. pyramidalis. Hence, P. alba was involved in the formation of P. tomentosa.

Comparative genomic and phylogenetic analyses of Populus section Leuce using complete chloroplast genome sequences

Species of Populus section Leuce are distributed throughout most parts of the Northern Hemisphere and have important economic and ecological significance. However, due to frequent hybridization within Leuce, the phylogenetic relationship between species has not been clarified. The chloroplast (cp) genome is characterized by maternal inheritance and relatively conservative mutation rates; thus, it is a powerful tool for building phylogenetic trees. In this study, we used the PacBio SEQUEL software to determine that the cp genome of Populus tomentosa has a length of 156,558 bp including a long single-copy region (84,717 bp), a small single-copy region (16,555 bp), and a pair of inverted repeat regions (27,643 bp). The cp genome contains 131 unique genes, including 37 transfer RNAs, 8 ribosomal RNAs, and 86 protein-coding genes. We compared the cp genomes of seven species of section Leuce and identified five cp DNA markers with > 1% variable sites. Phylogenetic analyses revealed two evolutionary branches for section Leuce. The species with the closest relationship with P. tomenstosa was P. adenopoda, followed by P. alba. These cp genome data will help to determine the cp evolution of section Leuce and further elucidate the origin of P. tomentosa.

Enhancement of Populus alba tolerance to Venturia tremulae upon inoculation with endophytes showing in vitro biocontrol potential

Several studies have provided evidence that endophytes of forest trees can provide the trees with protection against pests and pathogens, but more experimental evidence is still needed to better understand if endophytes could be utilized in biocontrol of forest diseases. Here, we tested the hypothesis that fungal endophytes of Populus alba L. contribute to tree tolerance to Venturia tremulae Aderh., causal agent of shoot dieback in trees within Populus section. Fungal endophytes were isolated from twigs of two healthy P. alba trees, and classified according to their morphology and ITS sequence. Pleosporales, Dothideales and Eurotiales were the main fungal orders represented. Twelve isolates were challenged by the pathogen in in vitro dual assays and 10 of them reduced the growth rate of the pathogen. A mixed cell suspension from these endophytes was applied as a preventive treatment to P. alba seedlings growing in the greenhouse with the exception of positive control plants. Fifteen days later, plants were treated with a V. tremulae spore suspension. An additional control group of Populus x canescens (Aiton) Sm. seedlings were also inoculated with V. tremulae. Although the overall incidence of symptoms was low, both the incidence and severity of damages were lower in P. alba plants pretreated with endophytes than in controls (43.18 and 12.16% of incidence and severity reduction, respectively). Incidence of symptoms was higher in P. x canescens than in P. alba seedlings, evidencing the higher tolerance of P. alba to Venturia shoot blight. The results suggest that P. alba endophyte community may reinforce the host’s tolerance to the pathogen.

Populus luzae (Salicaceae), a new species of white poplar endemic to the western Transmexican Volcanic Belt, in Zapopan, Jalisco, Mexico

Populus luzae, a new species of white poplar from the western Transmexican Volcanic Belt, Zapopan, Jalisco, Mexico, is described and illustrated. Populus luzae belongs to section Populus and is morphologically close to P. guzmanantlensis, but it differs from the latter in having smaller size and soboliferous habit, narrower twigs and petioles, ovate to ovate-deltoid and chartaceous leaf blades, adaxial leaf surface with less depressed veins, abaxial surface puberulent, thrice smaller ovate male bracteoles with entire margin, twice longer female bracteoles sparsely denticulate but none lobed, smaller number of pistillate flowers, capsules pubescent, twice longer mature male inflorescence, and a lax and longer infrutescence.

Immunolocalization in Secondary Xylem of Populus.

Immunolocalization can be used to precisely visualize the location of specific proteins, cell wall components, or any other molecules within cells or tissues for which specific antibodies are available. Here we describe an immunolocalization protocol for tissue sections of woody Populus stems. The protocol includes descriptions of the required sectioning, fixation, probing, detection, and imaging parameters, as well suggested controls useful in interpreting results.

Disease biology and histopathology of bronze leaf disease: a threat to cultivated aspens, white poplars and their hybrids

SummaryBronze leaf disease (BLD) of species and hybrids of aspens, grey and white poplars (Genus Populus, section Populus) is a systemic disease incited by the fungus Apioplagiostoma populi (E.K. Cash & A.M. Waterman) M.E. Barr that results in a characteristic bronze to dark brown pigmentation of infected leaves in late summer and early fall. Branches on affected trees die over a period of several years, disfiguring trees and eventually leading to mortality of susceptible trees planted in landscapes. In this study, we describe the histopathology of the disease and fungus development relative to external symptoms on affected trees. A. populi hyphae were observed in leaf vessels, lateral veins and xylem vessels of stems and roots of affected trees. Hyphae were also observed in veins and vessels of asymptomatic leaves. Xylem vessels of growth rings on dead branches were completely occluded with A. populi near the vascular cambium and together with the ray parenchyma were stained a bronze colour. Evidence of putative toxin damage to mesophyll cells, not colonized by hyphae, was observed and may contribute to the characteristic tissue staining observed. The development of the fungus was consistent with previous reports, but in this study, we report additional details including perithecial development and ascospore release from predominantly abaxial leaf surfaces. We also report for the first time the isolation and growth of the pathogen in pure culture and systemic infection of roots.

Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding

Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.

Investigation of gas exchange and biometric parameters in isogenic lines of poplar differing in ploidy

Abstract Three poplar clones of section Populus (Brauna 11 [Populus tremula], L447 [Populus canescens] and Esch 5 [Populus tremula × Populus tremuloides]) were used to analyse the effects of ploidy levels on primary productivity and water use efficiency. The clones were established in tissue culture (2N) and lines with different ploidy levels (2N/4N and 4N) were generated via colchicine treatment. Light response curves were modelled based on gas exchange measurements carried out three times during the growing season on the 1st fully developed leaf under controlled conditions. The plants were harvested in September to analyse biometric parameters. The photosynthetic capacity was greatest in May, decreased throughout the season and increased slightly again in September. The decrease in Brauna 11 and Esch 5 varied from 20-50% compared with values in May and it was not as pronounced in L 447. Photosynthesis and intrinsic water use efficiency differed between clones, but not among the single isogenic lines within each clone. The seasons in which the experiments were conducted influenced the rankings of the 9 variants in physiological measurements, but these rankings were not uniform during the growing period. Differences in biometric parameters were detected between the clones and variants, e.g.; leaf masses were greater in all of the polyploid variants and lowest in the diploid variants. All of the L 447 lines showed the highest wood densities, which were higher in the mixoploid and lower in the tetraploid variants within each clone. A compact wood structure could prevent damage to the water-conducting system under drought stress.

Differential transcriptome analysis between Populus and its synthesized allotriploids driven by second-division restitution.

In this report, we compared transcriptomic differences between a synthetic Populus section Tacamahaca triploid driven by second-division restitution and its parents using a high-throughput RNA-seq method. A total of 4,080 genes were differentially expressed between the high-growth vigor allotriploids (SDR-H) and their parents, and 719 genes were non-additively expressed in SDR-H. Differences in gene expression between the allotriploid and male parent were more significant than those between the allotriploid and female parent, which may be caused by maternal effects. We observed 3,559 differentially expressed genes (DEGs) between the SDR-H and male parent. Notably, the genes were mainly involved in metabolic process, cell proliferation, DNA methylation, cell division, and meristem and developmental growth. Among the 1,056 DEGs between SDR-H and female parent, many genes were associated with metabolic process and carbon utilization. In addition, 1,789 DEGs between high- and low-growth vigor allotriploid were mainly associated with metabolic process, auxin poplar transport, and regulation of meristem growth. Our results indicated that the higher poplar ploidy level can generate extensive transcriptomic diversity compared with its parents. Overall, these results increased our understanding of the driving force for phenotypic variation and adaptation in allopolyploids driven by second-division restitution.

Breeding triploid aspen and poplar clones for biomass production

AbstractEnriched diploid pollen was applied for in vitro pollinations and crossbreeding in the greenhouse to produce high performance triploid aspen and aspen hybrids for cultivation in medium rotation plantations. In addition to crossings within the section Populus, intersectional crossbreeding was performed to combine benefits of intersectional hybridization with those derived from triploidisation.Both the enrichment of diploid pollen by size fractionation of naturally unreduced pollen and heat treatment of microspore mother cells resulted in a distinct increase of diploid pollen. Using this pollen, six triploid plants were obtained from in vitro pollinations and twenty from crossbreeding in the greenhouse. The triploid plants displayed a high variability in growth performance. Two clones from in vitro pollination and five from crossbreeding in the greenhouse were chosen to estimate growth characteristics. A first assessment of clone performance in an outdoor container test con - ducted over one growing season revealed two triploid clones with a same stem height and a significantly increased basal stem diameter in comparison to the fast-growing triploid reference clone “Astria”. Crossbreeding experiments also resulted in two fast-growing mixoploid clones, which have already been stable for several years.All in all, in this study, crossbreeding using enriched diploid pollen is proved to be a reliable and applicable approach for an effective breeding of triploid poplars.