Genome-Wide Identification and Analysis of the EIN3/EIL Transcription Factor Gene Family in Doubled Haploid (DH) Poplar.

Ethylene (ET) is an important phytohormone that regulates plant growth, development and stress responses. The ethylene-insensitive3/ethylene-insensitive3-like (EIN3/EIL) transcription factor family, as a key regulator of the ET signal transduction pathway, plays an important role in regulating the expression of ET-responsive genes. Although studies of EIN3/EIL family members have been completed in many species, their role in doubled haploid (DH) poplar derived from another culture of diploid Populus simonii × P. nigra (donor tree, DT) remains ambiguous. In this study, a total of seven EIN3/EIL gene family members in the DH poplar genome were identified. Basic physical and chemical property analyses of these genes were performed, and these proteins were predicted to be localized to the nucleus. According to the phylogenetic relationship, EIN3/EIL genes were divided into two groups, and the genes in the same group had a similar gene structure and conserved motifs. The expression patterns of EIN3/EIL genes in the apical buds of different DH poplar plants were analyzed based on transcriptome data. At the same time, the expression patterns of PsnEIL1, PsnEIN3, PsnEIL4 and PsnEIL5 genes in different tissues of different DH plants were detected via RT-qPCR, including the apical buds, young leaves, functional leaves, xylem, cambium and roots. The findings presented above indicate notable variations in the expression levels of PsnEIL genes across various tissues of distinct DH plants. Finally, the PsnEIL1 gene was overexpressed in DT, and the transgenic plants showed a dwarf phenotype, indicating that the PsnEIL1 gene was involved in regulating the growth and development of poplar. In this study, the EIN3/EIL gene family of DH poplar was analyzed and functionally characterized, which provides a theoretical basis for the future exploration of the EIN3/EIL gene function.

BpWOX11 promotes adventitious root formation in Betula pendula.

Adventitious root formation is a key step in vegetative propagation via cuttings. It is crucial for establishing birch plantations and preserve birch varieties. Although previous studies have highlighted role of WOX11 in controlling adventitious root formation, no such study has been conducted in birch. Understanding the mechanism of adventitious root formation is essential for improvement of rooting or survival rate using stem cuttings in birch. In this study, we cloned BpWOX11 and produced BpWOX11 overexpression (OE) transgenic lines using the Agrobacterium-mediated plant transformation. OE lines exhibited early initiated adventitious root formation, leading to increase the rooting rate of stem cuttings plants. RNA sequencing analysis revealed that OE lines induced the gene expression related to expansin and cell division pathway, as well as defense and stress response genes. These may be important factors for the BpWOX11 gene to promote adventitious root formation in birch cuttings. The results of this study will help to further understand the molecular mechanisms controlling the formation of adventitious roots in birch.

Characterization of the F-Box Gene Family and Its Expression under Osmotic Stress in Birch.

The F-box gene family is abundant in plants and crucial for plant growth and development. However, two questions prevail: Which F-box genes are involved in regulating plant biological processes? How do these genes regulate such biological processes? In this study, we characterized the F-box family and identified 240 F-box genes in birch (Betula platyphylla Suk.) via HMMER analysis. According to the C-terminal conserved domains, the F-box members were divided into 10 subfamilies. Through phylogenetic analysis, the F-box proteins were clustered into eight evolutionary branches. Synteny analyses suggested that the birch F-box gene family exhibits tandem and segmental duplication events. GO annotation analysis revealed that BpF-box proteins respond to stimuli, and regulate the defense response. According to RNA-Seq analysis, we found that 11 differentially expressed genes (DEGs) are responsive to osmotic stress. We performed co-expression analysis on the representative genes, and GO enrichment analysis further revealed that representative plant genes participate in the regulation of hormones, growth, and development. Through qRT-PCR, we found that the representative BpF-box genes are mainly involved in hormone response signaling pathways. It appears that the F-box gene family plays a significant role in the regulation of birch osmotic stress responses through the regulation of different hormones. Our results provided novel insights into the biological function of BpF-box proteins.

Functional study of BpCOI1 reveals its role in affecting disease resistance in birch.

Plants interact with biotic and abiotic environments. Some of these interactions are detrimental including herbivory consumption and infections by microbial pathogens. The COI1 (coronatine insensitive 1) protein is the master controller of JA-regulated plant responses and plays a regulatory role in the plant defense response. However, there is little information on COI1 function in birch (Betula platyphylla × Betula pendula). Herein, we studied the F-box protein BpCOI1 which is located in the nucleus. To validate the function of this protein, we developed transgenic birch plants with overexpression or repression of BpCOI1 gene. Growth traits, such as tree height, ground diameter, number of lateral branches, did not change significantly among transgenic lines. Alternaria alternata treatment experiments indicated that low expression of BpCOI1 reduced disease resistance in birch. Furthermore, our results showed that low expression of BpCOI1 significantly reduced the sensitivity of plants to exogenous MeJA. Co-expression analysis showed gene expression patterns with similar characteristics. These genes may be closely related in function, or members involved in the same signaling pathway or physiological process with BpCOI 1. The results of transcriptome sequencing and co-expression analysis showed that BpCOI1 affects plant defense against Alternaria alternata by regulating jasmonates. This study reveals the role of BpCOI1 in disease resistance and proposes the possibility of controlling diseases through molecular breeding in birch.

Arabidopsis pollen-specific glycerophosphodiester phosphodiesterase-like genes are essential for pollen tube tip growth.

In angiosperms, pollen tube growth is critical for double fertilization and seed formation. Many of the factors involved in pollen tube tip growth are unknown. Here, we report the roles of pollen-specific GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE-LIKE (GDPD-LIKE) genes in pollen tube tip growth. Arabidopsis thaliana GDPD-LIKE6 (AtGDPDL6) and AtGDPDL7 were specifically expressed in mature pollen grains and pollen tubes and green fluorescent protein (GFP)-AtGDPDL6 and GFP-AtGDPDL7 fusion proteins were enriched at the plasma membrane at the apex of forming pollen tubes. Atgdpdl6 Atgdpdl7 double mutants displayed severe sterility that was rescued by genetic complementation with AtGDPDL6 or AtGDPDL7. This sterility was associated with defective male gametophytic transmission. Atgdpdl6 Atgdpdl7 pollen tubes burst immediately after initiation of pollen germination in vitro and in vivo, consistent with the thin and fragile walls in their tips. Cellulose deposition was greatly reduced along the mutant pollen tube tip walls, and the localization of pollen-specific CELLULOSE SYNTHASE-LIKE D1 (CSLD1) and CSLD4 was impaired to the apex of mutant pollen tubes. A rice pollen-specific GDPD-LIKE protein also contributed to pollen tube tip growth, suggesting that members of this family have conserved functions in angiosperms. Thus, pollen-specific GDPD-LIKEs mediate pollen tube tip growth, possibly by modulating cellulose deposition in pollen tube walls.

Populus D-type cyclin gene PsnCYCD1;1 accelerates cell division and participates in secondary growth of vascular bundles.

Plant growth and development rely heavily on cyclins, which comprise an important class of cell division regulators. D-type cyclins (CYCDs) are responsible for the rate-limiting step of G1 cells. In the plant kingdom, despite the importance of CYCDs in herbaceous plants, there is little knowledge of these proteins in perennial woody plants. Here, the gene of a nucleus-localized cyclin, PsnCYCD1;1, was cloned from Populus simonii × P. nigra. PsnCYCD1;1 was highly expressed in tissues with active cell division, especially the leaf buds, and could be induced by sucrose and phytohormones. Moreover, overexpression of PsnCYCD1;1 in poplar could stimulate cell division, resulting in the generation of small cells and causing severe morphological changes in the vascular bundles, resulting in 'S'-shaped tortuous stems and curled leaves. Furthermore, transcriptomic analysis revealed that endogenous genes related to cell division and vascular cambium development were significantly up-regulated in the transgenic plants. In addition, using yeast two-hybrid and bimolecular fluorescence complementation assays PsnCDKA1, PsnICK3, and PsnICK5 were identified as proteins interacting with PsnCYCD1;1. Our study demonstrates that PsnCYCD1;1 accelerates plant cell division and participates in secondary growth of vascular bundles in poplar.

Genome-wide identification of the TIFY family reveals JAZ subfamily function in response to hormone treatment in Betula platyphylla.

BACKGROUND: The TIFY family is a plant-specific gene family and plays an important role in plant growth and development. But few reports have been reported on the phylogenetic analysis and gene expression profiling of TIFY family genes in birch (Betula platyphylla). RESULTS: In this study, we characterized TIFY family and identified 12 TIFY genes and using phylogeny and chromosome mapping analysis in birch. TIFY family members were divided into JAZ, ZML, PPD and TIFY subfamilies. Phylogenetic analysis revealed that 12 TIFY genes were clustered into six evolutionary branches. The chromosome distribution showed that 12 TIFY genes were unevenly distributed on 5 chromosomes. Some TIFY family members were derived from gene duplication in birch. We found that six JAZ genes from JAZ subfamily played essential roles in response to Methyl jasmonate (MeJA), the JAZ genes were correlated with COI1 under MeJA. Co-expression and GO enrichment analysis further revealed that JAZ genes were related to hormone. JAZ proteins involved in the ABA and SA pathways. Subcellular localization experiments confirmed that the JAZ proteins were localized in the nucleus. Yeast two-hybrid assay showed that the JAZ proteins may form homologous or heterodimers to regulate hormones. CONCLUSION: Our results provided novel insights into biological function of TIFY family and JAZ subfamily in birch. It provides the theoretical reference for in-depth analysis of plant hormone and molecular breeding design for resistance.

Genome-wide identification of glutamate synthase gene family and expression patterns analysis in response to carbon and nitrogen treatment in Populus.

Glutamate synthase (GOGAT) is a key enzyme in glutamine synthetase (GS)/GOGAT cycle and at the hub of carbon and nitrogen metabolism, catalyzing the formation of glutamate from α-oxoglutarate and glutamine. In this study, members of GOGAT family in Populus trichocarpa were identified and analyzed by bioinformatics. The four PtGOGATs were divided into two subgroups: subgroup A (Fd-GOGAT1 and Fd-GOGAT2) and subgroup B (NADH-GOGAT1 and NADH-GOGAT2). Many important elements have been identified in the promoters of different PtGOGATs, including hormone- and light-responsive elements. Meanwhile, the transcript levels of PxGOGATs were affected by light and diurnal cycle. Quantitative real-time PCR showed PxFd-GOGATs and PxNADH-GOGATs were mainly expressed in leaves and roots in Populus × xiaohei T. S. Hwang et Liang, respectively. Under elevated CO2, PxGOGATs were suppressed in all tissues except the stem. And PxFd-GOGATs and PxNADH-GOGATs were strongly induced by nitrogen in leaves and roots, respectively. In addition, PxGOGATs were stimulated significantly in roots in response to NH4+and glutamine directly. Our results provide new insights about GOGATs in poplar and their expression patterns under exogenous substances, to lay molecular basis for studying gene function and provide a reference for exploring putative roles of GOGATs in carbon-nitrogen balance.

Molecular mechanism of leaf adaxial upward curling caused by BpPIN3 suppression in Betula pendula.

Leaves are one of the vegetative organs of plants that are essential for plant growth and development. PIN-FORMED (PINs) gene is an indoleacetic acid (IAA) transporter that plays a critical role in leaf development. To determine the function of BpPIN3 in leaf polarity formation in Betula pendula, the transgenic lines with BpPIN3 overexpression (OE) and BpPIN3-reduced expression (RE) were analyzed using the Agrobacterium-mediated method. The RE lines displayed the characteristics of leaf margin adaxial upward curling, with lower expression of BpPIN3 resulting in greater rolling. Tissue localization of IAA in the auxin GUS reporter system proved that auxin in the RE was mainly distributed in the secondary veins, palisade tissues, and epidermal cells in the leaf margin area. The auxin content in the leaf margin area was significantly greater than that in the main vein tissue. The cell density of the palisade tissue and the ratio of palisade tissue to spongy tissue in the curled leaf margin of the RE lines were found to be significantly decreased. RNA-seq analysis revealed that the RE hormone-signaling pathway genes were significantly enriched compared with those of the OE and WT lines; in particular, the auxin response-related genes SAURs (i.e., SAUR23, SAUR24, SAUR28, and SAUR50) and GH3.10 were found to be significantly upregulated. qRT-PCR analysis indicated that BpPIN3 expression at the leaf margin was significantly lower than that near the main vein in the RE lines. In contrast, the expression levels of SAURs and GH3.10 were significantly higher than those near the midrib. In conclusion, BpPIN3 regulates the expression of auxin response-related genes and the polar transport of auxin to change the polar form of the proximal and distal axes of birch leaves.

Climate-responsive DNA methylation is involved in the biosynthesis of lignin in birch.

Lignin is one of the most important secondary metabolites and essential to the formation of cell walls. Changes in lignin biosynthesis have been reported to be associated with environmental variations and can influence plant fitness and their adaptation to abiotic stresses. However, the molecular mechanisms underlying this association remain unclear. In this study, we evaluated the relations between the lignin biosynthesis and environmental factors and explored the role of epigenetic modification (DNA methylation) in contributing to these relations if any in natural birch. Significantly negative correlations were observed between the lignin content and temperature ranges. Analyzing the transcriptomes of birches in two habitats with different temperature ranges showed that the expressions of genes and transcription factors (TFs) involving lignin biosynthesis were significantly reduced at higher temperature ranges. Whole-genome bisulfite sequencing revealed that promoter DNA methylation of two NAC-domain TFs, BpNST1/2 and BpSND1, may be involved in the inhibition of these gene expressions, and thereby reduced the content of lignin. Based on these results we proposed a DNA methylation-mediated lignin biosynthesis model which responds to environmental factors. Overall, this study suggests the possibility of environmental signals to induce epigenetic variations that result in changes in lignin content, which can aid to develop resilient plants to combat ongoing climate changes or to manipulate secondary metabolite biosynthesis for agricultural, medicinal, or industrial values.

Differences in Leaf Morphology and Related Gene Expression between Diploid and Tetraploid Birch (Betula pendula).

Plant polyploidization changes its leaf morphology and leaf development patterns. Understanding changes in leaf morphology and development patterns is a prerequisite and key to studying leaf development in polyploid plants. In this study, we quantified and analyzed the differences in leaf morphology, leaf growth polarity, and leaf size between diploid and tetraploid birches (Betula pendula subsp. pendula), and preliminarily investigated genes involved in leaf growth and development in birch. The results showed significant changes in leaf morphology in tetraploid birches, especially the basal part of the leaf. In addition, the proximal growth rate of tetraploid leaves was altered. The changed proximal growth rate did not affect the growth polarity pattern of tetraploid leaves. The leaf area of tetraploid was significantly larger than that of diploid birch. The difference in leaf size was mainly due to differences in their growth rates in the middle and late stages of leaf development. Increased cell expansion capacity was the major reason for the enormous leaves of tetraploid birch; however, cell proliferation did not contribute to the larger tetraploid leaf. The gene expression of ATHB12 was associated with cell size and leaf area, and may be a critical gene affecting the leaf size in diploid and tetraploid birches. The results will provide valuable insights into plant polyploid leaf development and a theoretical basis for later investigations into the molecular mechanisms underlying the gigantism of tetraploid birch leaves.

PsnWRKY70 Negatively Regulates NaHCO3 Tolerance in Populus.

Poplar is an important afforestation and ornamental tree species in Northeast China. The distribution area of saline-alkali land is approximately 765 hm2 in Northeast China. The breeding of saline-alkali-resistant transgenic trees could be an effective method of afforestation in saline-alkali land. WRKY transcription factors play a crucial role in abiotic stress. In this study, we analyzed the genetic stability of the two-year-old PsnWRKY70 transgenic poplars. The results showed that PsnWRKY70 of transgenic poplars had been expressed stably and normally at the mRNA level. The gene interference expression (RE) lines had no significant effect on the growth of PsnWRKY70 under NaHCO3 stress, and the alkali damage index of RE lines was significantly lower than that of WT and overexpression (OE) lines at day 15 under NaHCO3 stress. POD activity was significantly higher in RE lines than in WT. The MDA content of the RE line was lower than that of the WT line. Transcriptome analysis showed that RE lines up-regulated genes enriched in cell wall organization or biogenesis pathway-related genes such as EXPA8, EXPA4, EXPA3, EXPA1, EXPB3, EXP10, PME53, PME34, PME36, XTH9, XTH6, XTH23, CESA1, CESA3, CES9; FLA11, FLA16 and FLA7 genes. These genes play an important role in NaHCO3 stress. Our study showed that the interference expression of the PsnWRKY70 gene can enhance the tolerance of NaHCO3 in poplar.

The Poplar (Populus trichocarpa) Dehydrin Gene PtrDHN-3 Enhances Tolerance to Salt Stress in Arabidopsis.

Dehydrin (DHN), a member of the late embryogenesis abundant protein (LEA) family, was recently found to play a role in physiological responses to salt and drought stress. In this study, we identified and cloned the PtrDHN-3 gene from Populus trichocarpa. The PtrDHN-3 protein encoded 226 amino acids, having a molecular weight of 25.78 KDa and an isoelectric point of 5.18. It was identified as a SKn-type DHN and was clustered with other resistance-related DHN proteins. Real-time fluorescent quantitative PCR showed that transcription levels of PtrDHN-3 were induced by mannitol stress, and more significantly by salt stress. Meanwhile, in a yeast transgenic assay, salt tolerance increased in the PtrDHN-3 transgenic yeast, while the germination rate, fresh weight and chlorophyll content increased in PtrDHN-3-overexpressing transgenic Arabidopsis plants (OE) under salt stress. Significant increases in expression levels of six antioxidant enzymes genes, and SOD and POD enzyme activity was also observed in the OE lines, resulting in a decrease in O2- and H2O2 accumulation. The proline content also increased significantly compared with the wild-type, along with expression of proline synthesis-related genes P5CS1 and P5CS2. These findings suggest that PtrDHN-3 plays an important role in salt resistance in plants.

Aspartic proteases modulate programmed cell death and secondary cell wall synthesis during wood formation in poplar.

Programmed cell death (PCD) is essential for wood development in trees. However, the determination of crucial factors involved in xylem PCD of wood development is still lacking. Here, two Populus trichocarpa typical aspartic protease (AP) genes, AP17 and AP45, modulate xylem maturation, especially fibre PCD, during wood formation. AP17 and AP45 were dominantly expressed in the fibres of secondary xylem, as suggested by GUS expression in APpro::GUS transgenic plants. Cas9/gRNA-induced AP17 or AP45 mutants delayed secondary xylem fibre PCD, and ap17ap45 double mutants showed more serious defects. Conversely, AP17 overexpression caused premature PCD in secondary xylem fibres, indicating a positive modulation in wood fibre PCD. Loss of AP17 and AP45 did not alter wood fibre wall thickness, whereas the ap17ap45 mutants showed a low lignin content in wood. However, AP17 overexpression led to a significant decrease in wood fibre wall thickness and lignin content, revealing the involvement in secondary cell wall synthesis during wood formation. In addition, the ap17ap45 mutant and AP17 overexpression plants resulted in a significant increase in saccharification yield in wood. Overall, AP17 and AP45 are crucial modulators in xylem maturation during wood development, providing potential candidate genes for engineering lignocellulosic wood for biofuel utilization.

PtrHAT22, as a higher hierarchy regulator, coordinately regulates secondary cell wall component biosynthesis in Populus trichocarpa.

Homeodomain-leucine zipper (HD-Zip) II transcription factors (TFs) have been reported to play vital roles in diverse biological processes of plants. However, it remains unclear whether HD-Zip II TFs regulate secondary cell wall (SCW) in woody plants. In this study, we performed the functional characterization of a Populus trichocarpa HD-Zip II TF, PtrHAT22, which encodes a nuclear localized transcription repressor predominantly expressing in secondary developing tissues. Overexpression of PtrHAT22 showed arrested growths, including reduced heights and diameters above the ground, small leaves, and decreased biomass. Meanwhile, the contents of lignin, cellulose, and thickness of SCW significantly decreased, whilst the content of hemicellulose obviously increased in PtrHAT22 transgenic poplar. The expressions of some wood-associated TFs and structural genes significantly changed accordingly with the alternations of SCW characteristics in PtrHAT22 transgenic poplar. Furthermore, PtrHAT22 directly repressed the promoter activities of PtrMYB20, PtrMYB28, and PtrCOMT2, and bind two cis-acting elements that were specifically enriched in their promoter regions. Taken together, our results suggested that PtrHAT22, as a higher hierarchy TF like PtrWNDs, exerted coordination regulation of poplar SCW component biosynthesis through directly and indirectly regulating structural genes and different hierarchy TFs of SCW formation network.

Identification and expression analysis of the PtGATL genes under different nitrogen and carbon dioxide treatments in Populus trichocarpa.

Pectin is one of the most important components of the plant cell wall. Galacturonosyltransferase-like (GATL) is an important enzyme involved in forming pectin in Arabidopsis thaliana. In this study, 12 PtGATL genes were identified and characterized based on the Populus trichocarpa genome using bioinformatics methods. The results showed that the PtGATLs contained four typical motifs, including DXD, LPPF, GLG, and HXXGXXKPW. According to phylogenetic analysis, PtGATLs were divided into six groups. Chromosome distribution and genome synteny analysis showed that there were 11 segmental-duplicated gene pairs with repeated fragments on chromosomes 2, 5, 7, 8, 10, and 14. Tissue-specific expression profiles indicated that these PtGATLs had different expression patterns. The transcription level of PtGATLs was regulated by different carbon dioxide and nitrogen concentrations. In conclusion, the identification and analysis of PtGATL genes in poplar provide important information on the gene function. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03129-y.

Functional roles of the birch BpRAV1 transcription factor in salt and osmotic stress response.

RAV (Related to ABI3/VP1) transcription factors play vital roles in regulating plant response to abiotic stresses; however, the regulatory mechanisms underlying stress response are still poorly understood for most of the RAVgenes. In this study, a novel gene BpRAV1 was cloned from white birch (Betula platyphylla). BpRAV1 protein is localized in the nucleus and serves as a transcriptional activator. The expression of BpRAV1 was induced by salt and osmotic stress treatments. BpRAV1-overexpression birch seedlings exhibited dramatically less ROS accumulation and reduced cell death in response to salt and osmotic stresses. BpRAV1 can specifically bind to the known RAV1A element. In addition, a novel cis-acting element (termed RBS1) bound by BpRAV1 was identified by transcription factor (TF)- centered Y1H assay. BpRAV1 activated the RAV1A and RBS1 elements to induce the expression of SOD and POD genes, resulting in increased SOD and POD activities to enhance ROS scavenging ability, thus improving salt and osmotic stress tolerance. These results indicate that BpRAV1 is a positive regulator governing abiotic stress response.

Cas9/gRNA-Mediated Mutations in PtrFLA40 and PtrFLA45 Reveal Redundant Roles in Modulating Wood Cell Size and SCW Synthesis in Poplar.

Fasciclin-like arabinogalactan proteins (FLAs) play an important role in plant development and adaptation to the environment. However, the roles of FLAs in wood formation remain poorly understood. Here, we identified a total of 50 PtrFLA genes in poplar. They were classified into four groups: A to D, among which group A was the largest group with 28 members clustered into four branches. Most PtrFLAs of group A were dominantly expressed in developing xylem based on microarray and RT-qPCR data. The roles of PtrFLA40 and PtrFLA45 in group A were investigated via the Cas9/gRNA-induced mutation lines. Loss of PtrFLA40 and PtrFLA45 increased stem length and diameter in ptrfla40ptrfla45 double mutants, but not in ptrfla40 or ptrfla45 single mutants. Further, our findings indicated that the ptrfla40ptrfla45 mutants enlarged the cell size of xylem fibers and vessels, suggesting a negative modulation in stem xylem cell size. In addition, wood lignin content in the ptrfla40fla45 mutants was increased by nearly 9%, and the lignin biosynthesis-related genes were significantly up-regulated in the ptrfla40fla45 mutants, in agreement with the increase in wood lignin content. Overall, Cas9/gRNA-mediated mutations in PtrFLA40 and PtrFLA45 reveal redundant roles in modulating wood cell size and secondary cell wall (SCW) synthesis in poplar.

Bioinformatics analysis of PAE family in Populus trichocarpa and responsiveness to carbon and nitrogen treatment.

Plant Pectin acetylesterase (PAE) belongs to family CE13 of carbohydrate esterases in the CAZy database. The ability of PAE to regulate the degree of acetylation of pectin, an important polysaccharide in the cell wall, affects the structure of plant cell wall. In this study, ten PtPAE genes were identified and characterized in Populus trichocarpa genome using bioinformatics methods, and the physiochemical properties such as molecular weight, isoelectric points, and hydrophilicity, as well as the secondary and tertiary structure of the protein were predicted. According to phylogenetic analysis, ten PtPAEs can be divided into three evolutionary clades, each of which had similar gene structure and motifs. Tissue-specific expression profiles indicated that the PtPAEs had different expression patterns. Real-time quantitative PCR (RT-qPCR) analysis showed that transcription level of PtPAEs was regulated by different CO2 and nitrogen concentrations. These results provide important information for the study of the phylogenetic relationship and function of PtPAEs in Populus trichocarpa. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02918-1.