Comparative genomic analysis of the Growth-Regulating Factors-Interacting Factors (GIFs) in six Salicaceae species and functional analysis of PeGIF3 reveals their regulatory role in Populus heteromorphic leaves.

BACKGROUND: The growth-regulating factor-interacting factor (GIF) gene family plays a vital role in regulating plant growth and development, particularly in controlling leaf, seed, and root meristem homeostasis. However, the regulatory mechanism of heteromorphic leaves by GIF genes in Populus euphratica as an important adaptative trait of heteromorphic leaves in response to desert environment remains unknown. RESULTS: This study aimed to identify and characterize the GIF genes in P. euphratica and other five Salicaceae species to investigate their role in regulating heteromorphic leaf development. A total of 27 GIF genes were identified and characterized across six Salicaceae species (P. euphratica, Populus pruinose, Populus deltoides, Populus trichocarpa, Salix sinopurpurea, and Salix suchowensis) at the genome-wide level. Comparative genomic analysis among these species suggested that the expansion of GIFs may be derived from the specific Salicaceae whole-genome duplication event after their divergence from Arabidopsis thaliana. Furthermore, the expression data of PeGIFs in heteromorphic leaves, combined with functional information on GIF genes in Arabidopsis, indicated the role of PeGIFs in regulating the leaf development of P. euphratica, especially PeGIFs containing several cis-acting elements associated with plant growth and development. By heterologous expression of the PeGIF3 gene in wild-type plants (Col-0) and atgif1 mutant of A. thaliana, a significant difference in leaf expansion along the medial-lateral axis, and an increased number of leaf cells, were observed between the overexpressed plants and the wild type. CONCLUSION: PeGIF3 enhances leaf cell proliferation, thereby resulting in the expansion of the central-lateral region of the leaf. The findings not only provide global insights into the evolutionary features of Salicaceae GIFs but also reveal the regulatory mechanism of PeGIF3 in heteromorphic leaves of P. euphratica.

Multi-omics analysis reveals spatiotemporal regulation and function of heteromorphic leaves in Populus.

Despite the high economic and ecological importance of forests, our knowledge of the adaptive evolution of leaf traits remains very limited. Euphrates poplar (Populus euphratica), which has high tolerance to arid environment, has evolved four heteromorphic leaf forms, including narrow (linear and lanceolate) and broad (ovate and broad-ovate) leaves on different crowns. Here, we revealed the significant functional divergence of four P. euphratica heteromorphic leaves at physiological and cytological levels. Through global analysis of transcriptome and DNA methylation across tree and leaf developmental stages, we revealed that gene expression and DNA epigenetics differentially regulated key processes involving development and functional adaptation of heteromorphic leaves, such as hormone signaling pathways, cell division, and photosynthesis. Combined analysis of gene expression, methylation, ATAC-seq, and Hi-C-seq revealed longer interaction of 3D genome, hypomethylation, and open chromatin state upregulates IAA-related genes (such as PIN-FORMED1 and ANGUSTIFOLIA3) and promotes the occurrence of broad leaves while narrow leaves were associated with highly concentrated heterochromatin, hypermethylation, and upregulated abscisic acid pathway genes (such as Pyrabactin Resistance1-like10). Therefore, development of P. euphratica heteromorphic leaves along with functional divergence was regulated by differentially expressed genes, DNA methylation, chromatin accessibility, and 3D genome remodeling to adapt to the arid desert. This study advances our understanding of differential regulation on development and functional divergence of heteromorphic leaves in P. euphratica at the multi-omics level and provides a valuable resource for investigating the adaptive evolution of heteromorphic leaves in Populus.

Bna.EPF2 Enhances Drought Tolerance by Regulating Stomatal Development and Stomatal Size in Brassica napus.

Drought stress severely affects global plant growth and production. The enhancement of plant water-use efficiency (WUE) and drought tolerance by the manipulation of the stomata is an effective strategy to deal with water shortage. However, increasing the WUE and drought tolerance by manipulation on the stomata has rarely been tested in Brassica napus. Here, we isolated Bna.EPF2, an epidermal patterning factor (EPF) in Brassica napus (ecotype Westar), and identified its role in drought performance. Bna.EPF2 overexpression lines had a reduction average of 19.02% in abaxial stomatal density and smaller stomatal pore size, leading to approximately 25% lower transpiration, which finally resulted in greater instantaneous WUE and enhanced drought tolerance. Interestingly, the reduction in stomatal density did not affect the CO2 assimilation or yield-related agronomic traits in Bna.EPF2 overexpression plants. Together with the complementation of Bna.EPF2 significantly decreasing the stomatal density of Arabidopsis epf2, and Bna.EPF2 being expressed in mature guard cells, these results suggest that Bna.EPF2 not only functions in stomatal density development, but also in stomatal dimension in Brassicas. Taken together, our results suggest that Bna.EPF2 improves WUE and drought tolerance by the regulation of stomatal density and stomatal size in Brassica without growth and yield penalty, and provide insight into the manipulation of this gene in the breeding of drought tolerant plants with increased production under water deficit conditions.

Ki-67 index of 5% could better predict the clinical prognosis of well-differentiated pancreatic neuroendocrine tumours.

BACKGROUND: The pathological classification of well-differentiated pancreatic neuroendocrine tumour (pNET) is based largely upon Ki-67 index. However, current controversies abound about the classification of pNETG1/pNETG2. PATIENTS AND METHODS: Clinicopathological data were retrospectively analysed for 153 pNETG1/pNETG2 patients hospitalized at China-Japan Friendship Hospital. The critical values of pNETG1/pNETG2 were examined by using the area under the receiver operating characteristic curve and survival analysis was used to compare the clinical prognosis of pNETG1/G2. RESULTS: Among them, 52.3% were males. The median age was 49 (18-81) years and the clinical types were pNETG1 (n = 38) and pNETG2 (n = 115). According to the receiver operating characteristic curve, the optimal cut-off value was 5.5% for classifying pNETG1/pNETG2. Significant differences between pNETG1 (n = 101) and pNETG2 (n = 52) existed in overall survival (P = 0.001) and disease-free survival (P = 0.013) when Ki-67 index was 5%. Yet no significant differences existed in overall survival (P = 0.378) or disease-free survival (P = 0.091) between pNETG1 and pNETG2 when Ki-67 index was 3%. Furthermore, multivariate analysis indicated that the revised pathological grade was an independent risk factor for mortality and post-operative recurrence of pNET patients (P = 0.003 and 0.014; hazard ratio (HR) = 4.005 and 2.553). CONCLUSION: Thus, differentiating pNETG1/pNETG2 with Ki-67 index (5%) is proposed as the cut-off value and a new Ki-67 index (5%) is a better predictor of pNET mortality and post-operative recurrence than Ki-67 index (3%).

Transcriptomic and metabolomic analysis reveals the role of CoA in the salt tolerance of Zygophyllum spp.

BACKGROUND: Zygophyllum is an important medicinal plant, with notable properties such as resistance to salt, alkali, and drought, as well as tolerance of poor soils and shifting sand. However, the response mechanism of Zygophyllum spp. to abiotic stess were rarely studied. RESULTS: Here, we aimed to explore the salt-tolerance genes of Zygophyllum plants by transcriptomic and metabolic approaches. We chose Z. brachypterum, Z. obliquum and Z. fabago to screen for salt tolerant and sensitive species. Cytological observation showed that both the stem and leaf of Z. brachypterum were significantly thicker than those of Z. fabago. Then, we treated these three species with different concentrations of NaCl, and found that Z. brachypterum exhibited the highest salt tolerance (ST), while Z. fabago was the most sensitive to salt (SS). With the increase of salt concentration, the CAT, SOD and POD activity, as well as proline and chlorophyll content in SS decreased significantly more than in ST. After salt treatment, the proportion of open stomata in ST decreased significantly more than in SS, although there was no significant difference in stomatal number between the two species. Transcriptomic analysis identified a total of 11 overlapping differentially expressed genes (DEGs) in the leaves and roots of the ST and SS species after salt stress. Two branched-chain-amino-acid aminotransferase (BCAT) genes among the 11 DEGs, which were significantly enriched in pantothenate and CoA biosynthesis, as well as the valine, leucine and isoleucine biosynthesis pathways, were confirmed to be significantly induced by salt stress through qRT-PCR. Furthermore, overlapping differentially abundant metabolites showed that the pantothenate and CoA biosynthesis pathways were significantly enriched after salt stress, which was consistent with the KEGG pathways enriched according to transcriptomics. CONCLUSIONS: In our study, transcriptomic and metabolomic analysis revealed that BCAT genes may affect the pantothenate and CoA biosynthesis pathway to regulate the salt tolerance of Zygophyllum species, which may constitute a newly identified signaling pathway through which plants respond to salt stress.

[Preparation of Human Serum Albumin Micro/Nanotubes].

In this research, protein micro/nanotubes were fabricated by alternate layer-by-layer (LbL) assembly of human serum albumin (HSA) and polyethyleneimine (PEI) into polycarbonate (PC) membranes. The experimental conditions of pH values, ionic strength, the depositions cycles and the diameter of porous membrane were discussed. The morphology and composition of tubes were characterized by scanning electron microscope (SEM), transmission electron microscope (TEM), fourier transform infrared spectroscopy (FTIR) and energy dispersive spectroscopy (EDS). The results show that pH and ionic strength of the solution are the key factors that influence the effect of assembly. Micro/nanotubes with good opening hollow tubular structure were obtained when pH 7.4 HSA solution and pH 10.3 PEI solution without NaCl were used in synthesis procedure. The outer diameter of tube was dependent on the PC template, thus the micro/nanotubes size was controlled by the wall thickness, which can be adjusted by the number of layers of the HSA and PEI deposited along the pore walls. To avoid the thin wall being damaged in dissolving the template and vacuum drying, the PEI/HSA bilayer number should not be less than 3. The polar solvent N,N-dimethylformamide (DMF) can dissolve PC template to release the micro/nanotubes.

Chromosome-scale assemblies of the male and female Populus euphratica genomes reveal the molecular basis of sex determination and sexual dimorphism.

Reference-quality genomes of both sexes are essential for studying sex determination and sex-chromosome evolution, as their gene contents and expression profiles differ. Here, we present independent chromosome-level genome assemblies for the female (XX) and male (XY) genomes of desert poplar (Populus euphratica), resolving a 22.7-Mb X and 24.8-Mb Y chromosome. We also identified a relatively complete 761-kb sex-linked region (SLR) in the peritelomeric region on chromosome 14 (Y). Within the SLR, recombination around the partial repeats for the feminizing factor ARR17 (ARABIDOPSIS RESPONSE REGULATOR 17) was potentially suppressed by flanking palindromic arms and the dense accumulation of retrotransposons. The inverted small segments S1 and S2 of ARR17 exhibited relaxed selective pressure and triggered sex determination by generating 24-nt small interfering RNAs that induce male-specific hyper-methylation at the promoter of the autosomal targeted ARR17. We also detected two male-specific fusion genes encoding proteins with NB-ARC domains at the breakpoint region of an inversion in the SLR that may be responsible for the observed sexual dimorphism in immune responses. Our results show that the SLR appears to follow proposed evolutionary dynamics for sex chromosomes and advance our understanding of sex determination and the evolution of sex chromosomes in Populus.

Complete chloroplast genome sequence of Tamarix taklamakanensis (Tamaricaceae).

Tamarix taklamakanensis M. T. Liu, belonging to the genus Tamarix (family Tamaricaceae), is an endangered shrub endemic to arid basins in northwestern China. Most of species in this genus have high medicinal value. The complete chloroplast genome was reported in this study. The chloroplast genome with a total size of 156,177 bp consists of two inverted repeats (IR, 26,571 bp) separated by a large single-copy region (LSC, 84,778 bp) and a small single-copy region (SSC, 18,257 bp). Further annotation revealed the chloroplast genome contains 106 genes, including 73 protein coding genes, 29 tRNA genes, and 4 rRNA genes. A total of 64 simple sequence repeats (SSRs) were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of T. taklamakanensis in the future.

Complete chloroplast genome sequence of Peganum harmala (Zygophyllaceae).

Peganum harmala L. is a perennial herbaceous plant belonging to the family of Zygophyllaceae, and is grows in semi-arid climates, such as Xinjiang, Gansu, Ningxia, Qinghai, and Inner Mongolia in China, and also Middle East and North Africa. This species is of high medicinal value. The complete chloroplast genome was reported in this study. The chloroplast genome with a total size of 159,957 bp consists of two inverted repeats (IR, 26,550 bp) separated by a large single-copy region (LSC, 88,098 bp) and a small single-copy region (SSC, 18,759 bp). Further annotation revealed the chloroplast genome contains 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. A total of 90 simple sequence repeats (SSRs) were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of Peganum harmala in the future.

Phylogeography Reveals Geographic and Environmental Factors Driving Genetic Differentiation of Populus sect. Turanga in Northwest China.

Populus sect. Turanga (hereafter referred to as "Populus"), including Populus euphratica and Populus pruinosa, are the predominant tree species in desert riparian forests in northwestern China. These trees play key roles in maintaining ecosystem balance, curbing desertification, and protecting biodiversity. However, the distribution area of Populus forests has been severely diminished and degraded in recent years due to increased habitat destruction and human activity. Understanding the genetic diversity among Populus individuals and populations is essential for designing conservation strategies, but comprehensive studies of their genetic diversity in northwest China are lacking. Here, we assessed the population structures and genetic diversity of 1,620 samples from 85 natural populations of Populus (59 P. euphratica and 26 P. pruinosa populations) covering all of northwestern China using 120 single nucleotide polymorphism (SNP) markers. Analysis of population structure revealed significant differentiation between these two sister species and indicated that strong geographical distribution patterns, a geographical barrier, and environmental heterogeneity shaped the extant genetic patterns of Populus. Both P. euphratica and P. pruinosa populations in southern Xinjiang had higher genetic diversity than populations in other clades, perhaps contributing to local geographic structure and strong gene flow. Analysis of molecular variance (AMOVA) identified 15% variance among and 85% variance within subpopulations. Mantel tests suggested that the genetic variation among P. euphratica and P. pruinosa populations could be explained by both geographical and environmental distance. The genetic diversity of P. euphratica showed a significant negative correlation with latitude and longitude and a positive correlation with various environmental factors, such as precipitation of warmest quarter and driest month, temperature seasonality, and annual mean temperature. These findings provide insights into how the genetic differentiation of endangered Populus species was driven by geographical and environmental factors, which should be helpful for designing strategies to protect these genetic resources in the future.

Complete chloroplast genome sequence of Oxytropis glabra (Leguminosae).

Oxytropis glabra DC. is a perennial poisonous plant to livestock belonging to the genus Oxytropis, Leguminosae, mainly distributed in Northwestern China. As a poisonous grass, this species protects plant diversity in degraded grasslands by sheltering adjacent plants. In this study, the complete chloroplast genome with a total size of 122,094 bp was reported. Our annotations showed that the chloroplast genome contains 109 genes, including 76 protein-coding genes, 29 tRNA genes, and four rRNA genes. This work presents complete chloroplast genome information, which will be valuable for studying the evolution and genetic diversity of O. glabra.

Complete plastid genome sequence of Halimodendron halodendron (Leguminosae).

Halimodendron halodendron (Pall.) Voss. is a deciduous shrub belonging to the genus Halimodendron, Leguminosae, and is mainly distributed in dry areas. This species can be used for saline-alkali soil improvement and sand fixation. The complete plastid genome of H. halodendron first reported here is 129,342 bp in length, and contains 110 genes, including 76 protein coding genes, 30 tRNA genes, and 4 rRNA genes. A total of 105 simple sequence repeats (SSRs) were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of Halimodendron halodendron in the future.

Complete chloroplast genome sequence of Thermopsis turkestanica Gand. (Leguminosae).

Thermopsis turkestanica Gand. is a perennial herbaceous plant belonging to the genus Thermopsis, Leguminosae, and is mainly distributed in dry areas. Most of the species in this genus have high medicinal value. The complete chloroplast genome was reported in this study. The chloroplast genome with a total size of 149,551 bp consists of two inverted repeats (IRs, 24,159 bp) separated by a large single-copy region (LSC, 83,692 bp) and a small single-copy region (SSC, 17,541 bp). Further annotation revealed the chloroplast genome contains 110 genes, including 77 protein coding genes, 29 tRNA genes, and four rRNA genes. This information will be useful for study on the evolution and genetic diversity of Thermopsis turkestanica in the future.

Complete chloroplast genome sequence of Populus euphratica from PacBio Sequel platform.

Populus euphratica Oliv., one of tall arbors growing in desert areas, has great stress resistance. The complete chloroplast genome was reported in this study using the PacBio Sequel Platform. The chloroplast genome with a total size of 157,881 bp consisted of two inverted repeats (IRs) (27,666 bp) separated by a large single-copy region (85,906 bp) and a small single-copy region (16,643 bp). Further annotation revealed the chloroplast genome contains 111 genes, including 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. The information of the chloroplast genome will be useful for study on the evolution of P. euphratica in the future.

Complete chloroplast genome sequence of Sphaerophysa salsula (Leguminosae).

Sphaerophysa salsula (Pall.) DC. is a perennial herbaceous plant belonging to the genus Sphaerophysa, Galegeae, Leguminosae, and is mainly distributed in dry areas in Central Asia and Northwest China. The complete chloroplast genome with a total size of 123,300 bp was reported in this study. Further annotation revealed the chloroplast genome contains 109 genes, including 76 protein coding genes, 29 tRNA genes, and four rRNA genes. A total of 107 simple sequence repeats (SSRs) from mononucleotide to hexa-nucleotide repeat motif were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of Sphaerophysa salsula in the future.

The complete chloroplast genome of Alhagi sparsifolia Shap. (Leguminosae).

Alhagi sparsifolia Shap. is a perennial herbaceous plant belonging to the genus Alhagi, Leguminosae. This species is of high nutritional, medicinal and ecological values. The complete chloroplast genome was 128,418 bp and lost an IR (inverted repeat) region. Further annotation revealed the chloroplast genome contains 108 genes, including 75 protein coding genes, 29 tRNA genes, and 4 rRNA genes. A total of 103 simple sequence repeats (SSRs) were identified in the chloroplast genome. This chloroplast genome resource will be useful for study on the evolution and genetic diversity of A. sparsifolia in the future.

Structural dynamics of Populus euphratica forests in different stages in the upper reaches of the Tarim River in China.

We selected four Populus euphratica Oliv. forest plots (100 m × 100 m) in the upper reaches of the Tarim River in the Xinjiang Uygur Autonomous Region of China. Each of the four forest plots was chosen to represent a different growth and death stage of P. euphratica forest: juvenile forest, mature forest, dying forest, and dead forest. In each plot, we measured the coordinates, DBH, height, and status of all P. euphratica individuals. We used (1) spatial pattern analysis to explore spatial distribution patterns and associations of live trees and dead trees, (2) a random mortality model to test whether the tree death was random or non-random, and (3) a generalized linear mixed-effect model (GLMM) to analyse factors related to tree survival (or death). In the juvenile plot, live trees were significantly aggregated at all scales (p < 0.05); while in the mature and dying plots, live trees were more aggregated at small scales and randomly distributed at larger scales. Live trees and dead trees showed a significantly positive association at all scales in the juvenile plot (p < 0.05). While in the mature and dying plots, live trees and dead trees only showed a significantly positive association at scales of 0-3 m (p < 0.05). There was significant density-dependent mortality in the juvenile plot; while mortality was spatially random at all scales in the mature and dying plots. The distance from the river showed significantly negative correlations with tree survival (p < 0.01). DBH and height had significantly positive associations with tree survival in the juvenile, mature, and dying plots (p < 0.05). In extreme drought, dying trees appeared to be shape-shifting into more shrub-like forms with clumps of root sprouts replacing the high canopies. The shift under extreme drought stress to more shrub-like forms of P. euphratica may extend their time to wait for a favourable change.

Complete chloroplast genome sequence of Populus pruinosa Schrenk from PacBio Sequel II Platform.

Populus pruinosa Schrenk plays an important role on ecological services in desert areas. The complete chloroplast genome was reported in this study using the PacBio Sequel II Platform. The chloroplast genome with a total size of 157,856 bp consists of two inverted repeats (IR, 27,673 bp) separated by a large single-copy region (LSC, 85,867 bp) and a small single-copy region (SSC, 16,645 bp). Further annotation revealed the chloroplast genome contains 111 genes, including 78 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. A total of 151 simple sequence repeats (SSRs) were identified in the chloroplast genome. This information will be useful for study on the evolution and genetic diversity of P. pruinosa in the future.

Heterologous expression of antifreeze protein gene AnAFP from Ammopiptanthus nanus enhances cold tolerance in Escherichia coli and tobacco.

Antifreeze proteins are a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival under the subzero environments. Ammopiptanthus nanus is the unique evergreen broadleaf bush endemic to the Mid-Asia deserts. It survives at the west edge of the Tarim Basin from the disappearance of the ancient Mediterranean in the Tertiary Period. Its distribution region is characterized by the arid climate and extreme temperatures, where the extreme temperatures range from -30 °C to 40 °C. In the present study, the antifreeze protein gene AnAFP of A. nanus was used to transform Escherichia coli and tobacco, after bioinformatics analysis for its possible function. The transformed E. coli strain expressed the heterologous AnAFP gene under the induction of isopropyl ß-D-thiogalactopyranoside, and demonstrated significant enhancement of cold tolerance. The transformed tobacco lines expressed the heterologous AnAFP gene in response to cold stress, and showed a less change of relative electrical conductivity under cold stress, and a less wilting phenotype after 16 h of -3 °C cold stress and thawing for 1h than the untransformed wild-type plants. All these results imply the potential value of the AnAFP gene to be used in genetic modification of commercially important crops for improvement of cold tolerance.