su Chen

• Doctor of Philosophy
• Northeast Forestry University

Background Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the divergence of species, RNA editin...

Birch (Betula platyphylla × B. pendula) is an important tree for landscaping due to its attractive white bark and straight trunk. In this study, we characterized a T-DNA yellow-green leaf mutant, yl. We identified six insertion sites (ISs) in the mutant by genome resequencing and found a 40-kb deletion containing BpGLK1 around IS2 on chromosome 2....

Flowering is a crucial process for plants that is under complex genetic control. AP1 acts as an organizer and a switch for the transition from vegetative to reproductive growth. In our previous study, we found that overexpression of BpAP1 significantly promoted the formation of male inflorescence in birch (Betula platyphlla × B. pendula). In this s...

MADS-box genes encode transcription factors involved in the control of many important developmental processes, especially the flower development of angiosperms. Analysis on gene regulatory relationship between MADS-box genes is useful for understanding the molecular mechanism of flower development. In this study, we focused on the regulatory relati...

Tetraploid plants always exhibit noticeable changes in tissue structure and stress tolerance, but the underlying physiological mechanisms remain poorly understood. Here, we generated a tetraploid plant of Populus davidiana using colchicine induction and performed phenotypic characterization. The results showed that the tetraploid plant had bigger g...

Abscisic acid (ABA) is a key phytohormone that participates in various plant biological processes, such as seed germination, senescence, stomatal movement, and flowering. In the ABA signal transduction pathway, Pyrabactin Resistance 1 (PYR1)/PYR1-Like (PYL)/Regulatory Component is the core module for ABA perception. In this study, a total of 12 PYL...

Populus species, particularly P. trichocarpa, have long served as model trees for genomics research, owing to fully sequenced genomes. However, the high heterozygosity, and the presence of repetitive regions, including centromeres and ribosomal RNA gene clusters, have left 59 unresolved gaps, accounting for approximately 3.32% of the P. trichocarpa...

This study, conducted in China in November 2020, was aimed at exploring the variations in growth traits among different provenances and families as well as to select elite materials of Juglans mandshurica. Thus, seeds of 44 families from six J. mandshurica provenances in Heilongjiang and Jilin provinces were sown in the nursery and then transplante...

Wood formation involves consecutive developmental steps, including cell division of vascular cambium, xylem cell expansion, secondary cell wall (SCW) deposition, and programmed cell death. In this study, we identified PagMYB31 as a coordinator regulating these processes in Populus alba × Populus glandulosa and built a PagMYB31-mediated transcriptio...

The Auxin/Indole acetic acid (Aux/IAA) family is an important class of auxin-response genes involved in leaf development in Arabidopsis . However, the biological function of these genes remains unclear in perennial wood plants. In this study, we identified an Aux/IAA10 gene ( BpIAA10 ) from birch ( Betula platyphylla) that is associated with growth...

Background Betula platyphylla Sukaczev is one of important tree species due to its ecological and economic value. It is a cold-tolerant tree species which also faces heat stress during summer. In the current study, RNA-Seq profiling of two-month-old B. platyphylla seedlings were conducted utilizing the MGISEQ-2000 platform. Results In total, 856,3...

In this study, the poplar doubled haploid (DH) plants were used as the experimental material to explore the huge phenotypic differences between homozygous DH plants and the paternal plants, and the molecular regulation mechanism of the differential phenotypes. In this experiment, through morphological and histological observation and statistics, we...

CBF (C-repeat binding factor) transcription factor subfamily belongs to AP2/ERF (Apetala 2/ethylene-responsive factor) transcription factor family, known for playing a vital role in plant abiotic stress response. Although some CBF transcription factors have been identified in several species, such as Arabidopsis, tobacco, tomato and poplar, researc...

Many studies have provided significant insights into polyploid breeding in recent years, but limited research has been carried out on trees. The genomic information needed to understand the growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to our forests imposed by climate chang...

Many studies have provided significant insights into polyploid breeding in recent years, but limited research has been carried out on trees. The genomic information needed to understand the growth and response to abiotic stress in polyploidy trees is largely unknown, but has become critical due to the threats to our forests imposed by climate chang...

Low temperature is an important environmental factor that affects the growth and development of trees and leads to the introduction of failure in the genetic improvement of trees. Acer pseudosieboldianum is a tree species that is well-known for its bright red autumn leaf color. These trees are widely used in landscaping in northeast China. However,...

The formation of adventitious roots (ARs) is vital for the vegetative propagation of poplars. However, the relevant mechanisms remain unclear. To reveal the underlying molecular mechanism, we used RNA-seq to investigate the transcriptional alterations of poplar cuttings soaked in water for 0, 2, 4, 6, 8, and 10 d; 3,798 genes were differentially ex...

Background Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturate...

Related studies have provided significant insights into polyploid breeding in recent years, but limited research was focused on trees. The genomic information for the growth and response to abiotic stress in polyploidy trees is still largely unknown. Populus alba ’ Berolinensis ’, also named “Yinzhong poplar”, is a triploid poplar in the northeast...

To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome du...

This article is a Commentary on Zheng et al. (2022), 235: 141–156.

Polycomb group (PcG) protein-mediated histone methylation (H3K27me3) controls the correct spatiotemporal expression of numerous developmental regulators in Arabidopsis. Epigenetic silencing of the stem cell factor WUS in floral meristems (FMs) depends on H3K27me3 deposition by PcG proteins. However, the role of H3K27me3 in silencing of other merist...

Müller-Xing et al. 2022 - Polycomb proteins control floral determinacy by H3K27me3-mediated repression of pluripotency genes in Arabidopsis thaliana - Supplementary Material

Aralia elata is a perennial woody plant of the genus Aralia in the family Araliaceae. It is rich in saponins and therefore has a wide range of pharmacological effects. Here, we report a high-quality reference genome of A. elata, with a genome size of 1.21 Gb and a contig N50 of 51.34 Mb, produced by PacBio HiFi sequencing technology. This is the fi...

Although many genes and biological processes involved in abiotic stress response have been identified, how they are regulated remains largely unclear. Here, to study the regulatory mechanism of birch (Betula platyphylla) responding to drought induced by polyethylene glycol (PEG) 6000 (20%, w/v), a partial correlation coefficient-based algorithm for...

Cold and freezing stress is one of the most harmful environmental stresses, especially in temperate and subtropical areas, that adversely affects plant growth, development, and yield production. Betula platyphylla Sukaczev, also known as white birch, is one of the most valuable, important, and widely distributed tree species in East Asia. This stud...

Related studies have provided significant insights into polyploid breeding in recent years, but limited research was focused on trees. The genomic information for the growth and response to abiotic stress in polyploidy trees is still largely unknown. Populus alba ’ Berolinensis ’, also named “Yinzhong poplar”, is a triploid poplar in the northeast...

RNA-editing is a post-transcriptional modification that can diversify genome-encoded information by modifying individual RNA bases. In contrast to the well-studied RNA-editing in organelles, little is known about nuclear RNA-editing in higher plants. We performed a genome-wide study of RNA-editing in Populus trichocarpa nuclei using the RNA-seq dat...

Increasing the vulnerability of plants especially crops to a wide range of cold stress reduces plant growth, development, yield production, and plant distribution. Cold stress induces physiological, morphological, biochemical, phenotypic, and molecular changes in plants. Transcription factor (TF) is one of the most important regulators that mediate...

Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 3...

Nowadays, crop insufficiency resulting from soil salinization is threatening the world. On the basis that soil salinization has become a worldwide problem, studying the mechanisms of plant salt tolerance is of great theoretical and practical significance to improve crop yield, to cultivate new salt-tolerant varieties, and to make full use of saline...

Poplar 84 K (Populus alba x P. tremula var. glandulosa) is a good resource for genetic engineering due to its rapid growth and wide adaptability, and it is also an excellent ornamental tree species. In this study, we used 84 K plantlets grown in the nitrogen-limited medium as experimental materials to explore the molecular mechanism in 84 K leaves...

Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis , rice, poplar, maize and Chinese pear, but there are no re...

With the global climate anomalies and the destruction of ecological balance, the water shortage has become a serious ecological problem facing all mankind, and drought has become a key factor restricting the development of agricultural production. Therefore, it is essential to study the drought tolerance of crops. Based on previous studies, we revi...

With the global climate anomalies and the destruction of ecological balance, water shortage has become a serious ecological problem facing all mankind, and drought has become a key factor restricting the development of agricultural production. Therefore, it is essential to study the drought tolerance of crops. On the basis of previous studies, we r...

Betula L. (birch) is a pioneer hardwood tree species with ecological, economic, and evolutionary importance in the Northern Hemisphere. We sequenced the Betula platyphylla genome and assembled the sequences into 14 chromosomes. The Betula genome lacks evidence of recent whole-genome duplication and has the same paleoploidy level as Vitis vinifera a...

Betula L. (birch) is a pioneer hardwood tree species with ecological, economic, and evolutionary importance in the Northern Hemisphere. We sequenced the Betula platyphylla genome and assembled the sequences into 14 chromosomes. The Betula genome lacks evidence of recent whole-genome duplication and has the same paleoploidy level as Vitis vinifera a...

Abiotic stress is one of the major factors in reducing plant growth, development, and yield production by interfering with various physiological, biochemical, and molecular functions. In particular, abiotic stress such as salt, low temperature, heat, drought, UV-radiation, elevated CO2, ozone, and heavy metals stress is the most frequent study in S...

Key message We identified 15 genes encoding enzymes for phenylpropanoid biosynthesis in the genome of birch by combining phylogenetic analysis and tissue-specific expression data. Abstract Lignin is one of the most abundant terrestrial biopolymers and is essential for plant structure and defense. An essential step in lignin formation is phenylprop...

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 high gene transformation efficiency. Here, we combined 63-fold coverage Illumina short reads and 126-fold coverage PacBio long reads to assemble the genome. Due to the high heteroz...

Low temperature is one of the common abiotic stresses that adversely affect the growth and development of plants. In this study, we used RNA-Seq to identify low-temperature-responsive genes in birch and further analyzed the underlying molecular mechanism. Birch seedlings were treated by the low temperature (6 °C) for 0, 1, 1.5, 2, 2.5, and 3 h, res...

Adventitious root (AR) formation is critically important in vegetative propagation through cuttings in some plants, especially woody species. However, the underlying molecular mechanisms remain elusive. Here, we report the identification of a poplar homeobox gene, PuHox52, which was induced rapidly (within 15 min) at the basal ends of stems upon cu...

Cellulose is an essential structural component of the plant cell wall and is an important resource for the production of paper, textiles, bioplastics and other biomaterials. The synthesis of cellulose is among the most important but poorly understood biochemical processes, which is precisely regulated by internal and external cues. Here we identifi...

Background Cellulose is an essential structural component of plant cell wall and is an important resource to produce paper, textiles, bioplastics and other biomaterials. The synthesis of cellulose is among the most important but poorly understood biochemical processes, which is precisely regulated by internal and external cues. Results Here, we ide...

Cellulose is an essential structural component of the plant cell wall and is an important resource for the production of paper, textiles, bioplastics and other biomaterials. The synthesis of cellulose is among the most important but poorly understood biochemical processes, which is precisely regulated by internal and external cues. Here we identifi...

Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis...

Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula , although it has been characterized in Arabidopsi...

Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis...

Background: Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. However, little is known about the POD genes in Betula pendula, although it has been characterized in Arabidopsis...

Previous studies have reported that low temperature (LT) constrains plant growth and restricts productivity in temperate regions. However, the underlying mechanisms are complex and not well understood. Over the past ten years, research on the process of adaptation and tolerance of plants during cold stress has been carried out. In molecular terms,...

Key message In this study, constructing BpEIN3 overexpression, inhibition expression vector, we transferred to birch to obtain BpEIN3 transgenic lines and study the function of this gene. Abstract EIN3 is an important transcription factor in the ethylene signal transduction pathway. It initiates the expression of a series of genes that regulate et...

Background: Pinus koraiensis is an evergreen tree species with strong cold resistance. However, the transcriptomic patterns in response to cold stress are poorly understood for P. koraiensis. In this study, global transcriptome profiles were generated for P. koraiensis under cold stress (- 20 °C) over time by high-throughput sequencing. Results:...

The AP2/ERF (APETALA2/ethylene-responsive factor) family of transcription factors (TF) is involved in regulating biotic and abiotic stress responses in plants. To explore the role of AP2/ERFs in cold tolerance in woody plants, BpERF13 was cloned and characterized in Betula platyphylla (white birch), a species primarily found in Asia in temperate an...

Background: Plant architecture, which is mostly determined by shoot branching, plays an important role in plant growth and development. Thus, it is essential to explore the regulatory molecular mechanism of branching patterns based on the economic and ecological importance. In our previous work, a multiple-branches birch mutant br was identified f...

Research Highlights: A rigorous genome survey helped us to estimate the genomic characteristics, remove the DNA contamination, and determine the sequencing scheme of Betula platyphylla. Background and Objectives: B. platyphylla is a common tree species in northern China that has high economic and medicinal value. However, there is a lack of complet...

NACs (NAM, ATAF1/2, and CUC2) are plant-specific transcription factors that play diverse roles in various plant developmental processes. In this study, we identified the NAC gene family in birch (Betula pendula) and further analyzed the function of BpNACs. Phylogenetic analysis reveals that the 114 BpNACs can be divided into seven subfamilies. We i...

Background Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in plant research. T-DNA integration in plants is complex and still largely unknown. In this work, we reported that multiple T-DNA...

Chlorophyll (Chl)-deficient mutants are ideal materials for the study of Chl biosynthesis, chloroplast development, and photosynthesis. Although the genes encoding key enzymes related to Chl biosynthesis have been well-characterized in herbaceous plants, rice (Oryza sativa L.), Arabidopsis (Arabidopsis thaliana), and maize (Zea mays L.), yellow-gre...

Betula platyphylla Sukaczev tetraploids have significantly larger leaf, fruit and stoma (gigantic phenotype) than diploids of the same species; however, the mechanism underlying this difference remains unclear. Tetraploid B. platyphylla transcriptome data have indicated that the expression of genes related to indole-3-acetic acid (IAA) biosynthesis...

Lesion mimic mutants (LMM) usually show spontaneous cell death and enhanced defence responses similar to hypersensitive response (HR) in plants. Many LMM have been reported in rice, wheat, maize, barley, Arabidopsis, etc., but little was reported in xylophyta. BpGH3.5 is an early auxin-response factor which regulates root elongation in birch. Here,...

SQUAMOSA promoter binding protein-like (SPL) genes encode plant-specific transcription factors and play vital roles in plant growth and development. The BpSPL gene family has not been systematically studied in Betula platyphylla Suk. (birch). In this study, we identified 12 full-length BpSPLs and analyzed their gene structure and distribution patte...

MicroRNAs (miRNAs) are short (~22 nucleotides) noncoding RNAs and disseminated throughout the genome, either in the intergenic regions or in the intronic sequences of protein-coding genes. MiRNAs have been proved to play important roles in regulating gene expression. Hence, understanding the transcriptional mechanism of miRNA genes is a very critic...

The establishment of a collaborative network of transcription factors (TFs) followed by decomposition and then construction of subnetworks is an effective way to obtain sets of collaborative TFs; each set controls a biological process or a complex trait. We previously developed eight gene association methods for genome-wide coexpression analysis be...

Background: Plant biologists frequently need to examine if a sequence motif bound by a specific transcription or translation factor is present in the proximal promoters or 3' untranslated regions (3' UTR) of a set of plant genes of interest. To achieve such a task, plant biologists have to not only identify an appropriate algorithm for motif searc...

Key message: Overexpression of BpAP1 could cause early flowering in birch. BpAP1 affected the expression of many flowering-related unigenes and diterpenoid biosynthesis in transgenic birch, and BpPI was a putative target gene of BpAP1. APETALA1 (AP1) is an MADS-box transcription factor that is involved in the flowering process in plants and has be...

The GH3 family comprises a set of early auxin-responsive genes. Several previous studies have proven that GH3 family proteins play important roles in various aspects of plant growth and development. Our previous studies have found that the overexpression or suppression of BpGH3.5 in birch tree can result in shorter primary and lateral root compared...

WRKY transcription factors play important roles in regulating biotic and abiotic stress responses in plants. Although a plethora of studies have revealed the functions and mechanisms of some WRKYs in various plants, the studies of WRKYs in woody plants especially tree species under different abiotic and biotic stress conditions are still not well c...

The GH3 family is an important class of early auxin-response genes involved in the development of the hypocotyls and roots in Arabidopsis thaliana, but the role of this gene family in woody plants is poorly understood. In this study, we cloned a GH3-like gene from Betula platyphylla × Betula pendula (birch) named BpGH3.5 and produced transgenic bir...

Development of transgenic plants with tolerance to environmental stress is an important goal of plant biotechnology. Late-embryogenesis-abundant (LEA) proteins accumulate in seeds during late embryogenesis, where they protect cellular membranes and macromolecules against drought. In this work, we transferred the Tamarix androssowii LEA gene into hy...

We cloned a Cinnamoyl-CoA Reductase gene (BpCCR1) from an apical meristem and first internode of Betula platyphylla and characterized its functions in lignin biosynthesis, wood formation, and tree growth through transgenic approaches. We generated overexpression and suppression transgenic lines and analyzed them in comparison with the wild-type in...

In our previous research, the Tamarix androssowii LEA gene (Tamarix androssowii late embryogenesis abundant protein Mrna, GenBank ID: DQ663481) was transferred into Populus simonii × Populus nigra. Among the eleven transgenic lines, one exhibited a dwarf phenotype compared to the wild type and other transgenic lines, named dwf1. To uncover the mech...

The involvement of APETALA1 (AP1) in the flowering transition has been the focus of much research. Here, we produced Betula platyphylla × Betula pendula (birch) lines that overexpressed BpAP1 using Agrobacterium-mediated transformation; we obtained five independent 35S::BpAP1 transgenic lines. PCR, Southern, northern and western analyses were used...

Induction and break of bud dormancy are important features for perennial plants surviving extreme seasonal variations in climate. However, the molecular mechanism of the dormancy regulation, still remain poorly understood. To better understand the molecular basis of poplar bud dormancy, we used a label-free quantitative proteomics method based on n...

A dwarf mutant (dwf1) was obtained among 15 transgenic lines, when TaLEA (Tamarix androssowii late embryogenesis abundant gene) was introduced into Populus simonii × Populus nigra by Agrobacterium tumefaciens-mediated transformation. Under the same growth conditions, dwf1 height was significantly reduced compared with the wild type and the other tr...

In this study, the dynamic transcriptome of poplar (Populus simonii × Populus nigra) was investigated under salt stress using Solexa/illumine digital gene expression (DGE) technique. A total of 5453, 2372, and 1770 genes were shown to be differentially expressed after exposure to NaCl for 3 days, 6 days and 9 days, respectively. Differential expres...