Analysis of synonymous codon usage in chloroplast genome of Populus alba

The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis （a commonly used multivariate statistical approach） and method of effective number of codons （ENc）-plot were conducted to analyze synonymous codon usage. The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G＋C in synonymously variable third position of sense codon （GC3S）, （r=0.349）, and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI （r=-0.348, p〈0.01 and r=0.602, p〈0.01）. The ENc for most genes was similar to that for the expected ENc based on the GC3s, but several genes with low ENc values were lying below the expected curve. All of these data indicated that codon usage was dominated by a mutational bias in chloroplast gcnome ofP. alba. The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome ofP alba.

Radial profile of sap flow velocity in mature Xinjiang poplar(Populus alba L. var. pyramidalis) in Northwest China

Estimation of the transpiration rate for a tree is generally based on sap flow measurements within the hydro-active stem xylem. In this study, radial variation of sap flow velocity（Js） was investigated at five depths of the xylem（1, 2, 3, 5 and 8 cm under the cambium） in three mature Xinjiang poplar（Populus alba L. var. pyramidalis） trees grown at the Gansu Minqin National Studies Station for Desert Steppe Ecosystem from May to October 2011. Thermal dissipation probes of various lengths manufactured according to the Granier＇s design were installed into each tree for simultaneous observation of the radial patterns of Js through the xylem. The radial patterns were found to fit the four-parameter GaussAmp equation. The peak Js was about 27.02±0.95 kg/（dm2？d） at approximately 3 to 5 cm deep from the cambium of the three trees,and the lowest Js appeared at 1 cm deep in most of the time. Approximately 50% of the total sap flow in Xinjiang poplar occurred within one-third of the xylem from its outer radius, whereas 90% of the total sap flow occurred within two-fifth of the xylem. In addition, the innermost point of the xylem（at 8-cm depth）, which appeared as the penultimate sap flow in most cases during the study period, was hydro-active with Js,8 of 7.55±3.83 kg/（dm2？d）. The radial pattern of Js was found to be steeper in midday than in other time of the day, and steeper diurnal fluctuations were recorded in June, July and August（the mid-growing season）. Maximum differences between the lowest Js（Js,1 or Js,8） and the highest Js（Js,3 or Js,5） from May through October were 12.41, 17.35, 16.30, 18.52, 12.60 and 16.04 g/（cm2？h）, respectively. The time-dependent changes of Js along the radial profile（except at 1-cm depth） were strongly related to the reference evapotranspiration（ET0）. Due to significant radial variability of Js, the mean daily sap flow at the whole-tree level could be over-estimated by up to 29.69% when only a single probe at depth of 2 cm was used. However, the accuracy of the estimation of sap flow in Xinjiang poplar could be significantly improved using a correction coefficient of 0.885.

Effects of pruning intensity on nonstructural carbohydrates of Populus alba×P.talassica in the arid desert region of Northwest China

Although pruning is important to obtain highquality,large-diameter timber,the effects of pruning on nonstructural carbohydrates(NSC)in aboveground organs of many timber species are not well understood.Three intensities of pruning(none,moderate and severe)were tested on poplars(Populus alba×P.talassica)in the arid desert region of northwest China to compare the concentrations of soluble sugar(SS),starch(ST)and total nonstructural carbohydrate(TNC)in leaves,branches and trunks during the growing season.The concentration of NSC components after different pruning intensities varied similarly in seasonal patterns,increasing slowly at the beginning of the growing season,continuously declining in the middle,then gradually recovering by the end of the growing season.The monthly mean NSC concentration in poplar differed significantly among the three pruning intensities(p<0.05).The SS concentration in pruned trees was higher than in unpruned trees(p<0.05).For moderately pruned trees,the concentrations of ST and TNC in trunks and branches were higher than in unpruned and in severely pruned trees(p<0.05).Compared with no pruning,pruning changed the seasonal variation in NSC concentration.The orders of SS and TNC concentrations in aboveground organs were leaf>branch>trunk,while the order of ST concentration was trunk>leaf>branch,which was related to functional differences of plant organs.The annual average growth in height of unpruned,moderately pruned,and severely pruned poplars was 0.21±0.06,0.45±0.09 and 0.24±0.05 m,respectively,and the annual average growth in DBH were 0.92±0.04,1.27±0.06 and 1.02±0.05 cm,respectively.Our results demonstrate that moderate pruning may effectively increase the annual growth in tree height and DBH while avoiding damage caused by excessive pruning to the tree body.Therefore,moderate pruning may increase the NSC storage and improve the growth of timber species.

An improved draft genome sequence of hybrid Populus alba×Populus glandulosa

Populus alba × P.glandulosa clone 84 K,derived from South Korea,is widely cultivated in China and used as a model in the molecular research of woody plants because of hi gh gene transformation efficiency.Here,we combined63-fold coverage Illumina short reads and 126-fold coverage PacBio long reads to assemble the genome.Due to the hi gh heterozygosity level at 2.1% estimated by k-mer analysis,we exploited TrioCanu for genome assembly.The PacBio clean subreads of P.alba × P.glandulosa were separated into two parts according to the similarities,compared with the parental genomes of P.alba and P.glandulosa.The two parts of the subreads were assembled to two sets of subgenomes comprising subgenome A(405.31 Mb,from P.alba)and subgenome G(376.05 Mb,from P.glandulosa) with the contig N50 size of 5.43 Mb and 2.15 Mb,respectively.A high-quality P.alba × P.glandulosa genome assembly was obtained.The genome size was 781.36 Mb with the contig N50 size of 3.66 Mb and the longest contig was 19.47 Mb.In addition,a total of 176.95 Mb(43.7%),152.37 Mb(40.5%)of repetitive elements were identified and a total of 38,701 and 38,449 protein-coding genes were predicted in subgenomes A and G,respectively.For functional annotation,96.98% of subgenome A and 96.96% of subgenome G genes were annotated with public databases.This de novo assembled genome will facilitate systematic and comprehensive study,such as multi-omics analysis,in the model tree P.alba X P.glandulosa.

Experimental study on characteristic curves of restoring forces of Populus alba var. pyramidalis

Static tests under cyclic loading were carried out on Populus alba var. pyramidalis to determine its characteristic curves of restoring forces. The results show that P alba var. pyramidalis had good elastic performance. There was degradation of strength and stiffness under cyclic loading and unloading, where characteristic curves of restoring forces ofP. alba var. pyrarnidalis assumed a ＂flat and contrary S-shape＂ form. Simultaneously, P alba vat. pyramidalis showed typical characteristics of brittle destruction under large high peak loading and unloading. Furthermore, dynamic tests were carried out under wind loads to obtain dynamic displacement curves and dynamic strain curves. P alba var. pyramidalis reflected its stochastic dynamic performance in building up its resistance to the stochastic wind loads and its dynamically hysteretic properties. The dynamic response of this species was random and fuzzy under stochastic wind loads. This study has theoretical significance and reference value to research on the static characteristics and wind-induced dynamic performance of forests.

Waterlogging tolerance and wood properties of transgenic Populus alba×glandulosa expressing Vitreoscilla hemoglobin gene(Vgb)

Because overexpression of Vitreoscilla hemoglobin gene(Vgb)gene in plants can enhance tolerance to waterlogging,here Vgb was inserted into Populus alba×glandulosa to investigate its expression and effects on growth and physiological responses to waterlogging stress in the transgenic poplars.Southern blotting and RT-PCR analysis of Vgb-transgenic P.alba×glandulosa showed that the Vgb gene was integrated into the genome of the V13-81 and V13-85 transgenic lines and expressed.In greenhouse waterlogging stress tests,mortality of the transgenic poplar was significant lower than that of nontransgenic plants with increasing treatment time from 2 to 22 days.The transgenic plants had higher chlorophyll content and less chloroplast damage than in the control plants.Additionally,starch accumulation increased,and growth was enhanced in the transgenic plants,suggesting that the Vgb-expressing lines had improved energy reserves.Field trials of the transgenic poplar suggested that Vgb expression promotes growth and influences wood quality.Taken together,our results suggest that the expression of Vgb can increase the accumulation of chlorophyll and starch in the transgenic poplar,improve its ability to endure flooding,and improve growth and wood quality of the transgenic plants.

The complete chloroplast genomic landscape and phylogenetic analyses of Populus alba L.

Populus alba is a foundation species in evolutionary and ecological studies in the northern hemisphere.In this study,the chloroplast genome and gene map of P.alba were constructed.The P.alba chloroplast genome is 156,505 bp in length comprising a large single-copy region,two inverted repeat regions and a small single-copy region.The genome contains 131 genes,including 86 protein-coding genes(77 PCG species),eight ribosomal RNA genes(four rRNA species)and 37 transfer RNA genes(30 tRNA species).Phylogenetic analysis indicates that all Populus chloroplast genome sequences are clustered together and divided into three large branches.Among reported Populus chloroplast genomes,the leuce section formed monophyletic,indicating that all Populus spp.have a common maternal ancestor.P.rotundifolia and P.tremula are closely related and are sisters to P.davidiana.P.alba is closely related to P.adenopoda.Population genetic research in ecology and evolution may be easily developed through chloroplast genomes as they are conserved.This research will benefit future studies related to Populus,one of the world’s most ecologically and economically important genera.

Vital Parameters Assessments of Starvation Tolerance of in vitro Populus alba Culture

Populus alba is a large woody deciduous plant.The plant has been introduced to shooting,then multiplication of rooting on Murashige and Skoog(MS)medium.This work was designed to estimate the effect of two factors(low levels of 1-Naphthaleneacetic acid NAA and sucrose)on P.alba response resulting in 6 treatments compared to the control,with twelve measured responses.There was a significant difference in some measurements in morphology,like plantlets fresh-weight,shoot-,root-length,and leaf number.In the physiological measurements,there were significant differences in all the measured parameters.The low concentrations of sucrose and media composition/power(MS grams/L)led to starvation in plants;however,these conditions led to enhancement in some morphological and physiological parameters to overcome the starvation effect,compared to the control.The RAPD-PCR molecular marker(four decamers)was used to evaluate the new individuals’genetic variation(instability),resulting in a total polymorphism percentage of 50.83%.It was formerly known that the plantlets were identical to each other and to the mother plant.In this study,however,the use of distinct media power,hormonal and sucrose levels resulted in molecular variation reflected in P.alba’s morphological and physiological responses.

Survival and development of immature Harmonia axyridis (Pallas) feeding on Chaitophorus populeti (Panzer) propagated on transgenic Populus alba × P. glandulosa

Laboratory feeding experiments with the poplar aphid, Chaitophorus populeti （Panzer）, feeding on transgenic poplar （P. alba × P. glandulosa） varieties C13-5 and C013-5, were carried out to study the effect of transgenic poplar on the ladybird Harmonia axyridis （Pallas）. The mortality and development time of the immature stages, the eclosion rate and body mass of H. axyridis were measured. The results indicated that C. populeti feeding on different varieties of transgenic plants had no statistically significant ef- fect on the mortality ofH. axyridis larvae. The development time of larval and pupal stages were not significantly different between the two transgenic poplars and a non-transgenic poplar. Furthermore, the body mass and eclosion rate did not show any difference between the H. axyridis feeding on aphids reared on transgenic plants and those from non-transgenic plants. It is suggested that transgenic plants have no deleterious effect on the predatory ladybird.

Effects of Different Afforestation Techniques on Soil Nutrients in Populus alba Woodland

[Objective] The research aimed to study the influence of different afforestation technology measures on soil nutrients of P. alba wood-land in arid valley region of Rikaze, Tibet. It aimed to improve afforestation technology measure in arid valley region of Rikaze, Tibet, and provide theoretic basis for restoring the degraded ecosystem at upper reaches of the Yarlung Zangbo River. [ Method] In arid valley region of Duojiao Vil-lage, Nanmulin County, Rikaze City, the planted land using rooting powder, egg shell, leaves, mud and water retention agent was taken as re-search object, while the land without any afforestation measures was taken as the control, to determine soil nutrients under different afforestation measures. [Result] Under different afforestation measures, the contents of various soil nutrients were all obviously higher than control, in which available potassium, available phosphorus, alkali hydrolysable nitrogen and organic matter in soil obviously increased than control, but there was no similar rule among different measures. [Conclusion] Vegetation restoration in dry valley belt of Rikaze by different afforestation measures is favorable for improving physical-chemical properties of soil and increasing soil fertility.

银腺杨不同部位叶片形态、生理及转录差异分析

本研究以银腺杨成年树木为对象,测定了不同类型叶片形态、生理和基因表达差异,为揭示银腺杨的成熟效应提供参考。主要研究结果如下:(1)长枝叶和短枝叶的叶片形态差异显著,不同部位的叶片有很大程度的重叠。(2)不同部位叶片所含化合物差异显著,即:下部叶片的叶绿素a和叶绿素总含量显著大于上部和中部;下部叶片的SOD酶活性显著高于上部和中部,MDA含量表现为中部>上部>下部;下部叶片的淀粉含量显著低于上部和中部;不同部位叶片的IAA含量随着高度的降低而上升,ABA含量表现为中部>上部>下部;长枝叶的IAA和IAA/ABA显著大于短枝叶,ZR含量呈现相反的变化趋势。(3)基于转录组数据对差异显著基因进行筛选,不同部位叶片之间的差异显著基因数量少于不同类型叶片之间差异显著基因数量。(4)对各比较组的差异显著基因进行GO和KEGG富集分析,结果显示上部长枝叶相对于下部长枝叶(SC-vs-XC)、上部短枝叶相对于下部短枝叶(SD-vs-XD)差异显著基因显著富集到光合作用通路上,对其中的2个基因进行基因注释,发现这2个基因均编码PsbR蛋白,且下部叶片中基因表达量上调;对生长素转导过程进行分析,发现短枝叶中相关基因表达量均上调。

Early differentiation in biomass production and carbon sequestration of white poplar and its two hybrids in Central Iran

We assessed the potential of white poplar（Populus alba L.） and its inter-sectional hybridization with euphrates poplar（P. euphratica Oliv.） for carbon storage and sequestration in central Iran. Trials were established at planting density of 2,500 trees per hectare in block randomized design with three replicates. After 6 years, we measured the above-ground biomass of tree components（trunk, branch, bark, twig and leaf）, and assessed soil carbon at three depths. P. alba 9 euphratica plantation stored significantly more carbon（22.3 t ha-1） than P. alba（16.7 t ha-1） and P. euphratica 9 alba（13.1 t ha-1）.Most of the carbon was accumulated in the above-ground biomass（61.1 % in P. alba, 72.4 % in P. alba 9 euphratica and 56.0 % in P. euphratica 9 alba）. There was no significant difference in soil carbon storage. Also, biomass allocation was different between white poplar P. alba and its inter-sectional hybridization. Therefore, there was a yield difference due to genomic imprinting, which increased the possibility that paternally and maternally inherited wood production alleles would be differentially expressed in the new crossing.

Stand structure and yield of the mixed white poplar and black locust plantations on sandy ridges between the Danube and Tisza rivers in Hungary

The paper deals with the stand structure and yield of black locust (Robinia pseudoacacia L.) forests mixed with white (Populus alba L.) in various proportions, partly applying a new methodological approach. The main stand structure and yield factors were determined separately for each species, measured stem by stem, using the volume functions prepared for each species. The ratio of the volumes of the species (A and B) in mixed and in pure stands (based on volume tables) was determined. A close relationship has been found between the ratio by relative total volume and the proportion (by the number of stems) of the species. The relative surplus in the volume of the mixed stands varied between 1.24-1.55 at the age of 16 compared to the control, i.e. the yield of pure stands of the species concerned. The trial has also proven that if two species have a fast initial growth rate and a similar rotation age, they can be planted in mixed stands resulting in mutual advantages.

Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus

High-throughputsingle-cellRNAsequencing(sc RNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa. The sc RNA-seq profiled9,798 cells, which were grouped into 12 clusters.Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations,we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type(cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.

De novo assembly of white poplar genome and genetic diversity of white poplar population in Irtysh River basin in China

The white poplar(Populus alba) is widely distributed in Central Asia and Europe. There are natural populations of white poplar in Irtysh River basin in China. It also can be cultivated and grown well in northern China. In this study, we sequenced the genome of P. alba by single-molecule real-time technology. De novo assembly of P. alba had a genome size of 415.99 Mb with a contig N50 of 1.18 Mb. A total of 32,963 protein-coding genes were identified. 45.16% of the genome was annotated as repetitive elements. Genome evolution analysis revealed that divergence between P. alba and Populus trichocarpa(black cottonwood)occurred ～5.0 Mya(3.0, 7.1). Fourfold synonymous third-codon transversion(4 DTV) and synonymous substitution rate(ks)distributions supported the occurrence of the salicoid WGD event(～ 65 Mya). Twelve natural populations of P. alba in the Irtysh River basin in China were sequenced to explore the genetic diversity. Average pooled heterozygosity value of P. alba populations was 0.170±0.014, which was lower than that in Italy(0.271±0.051) and Hungary(0.264±0.054). Tajima's D values showed a negative distribution, which might signify an excess of low frequency polymorphisms and a bottleneck with later expansion of P.alba populations examined.