Xiaoming Song

• Professor
• Laboratory Head at North China University of Science and Technology

As some of the earliest evolving flowering plants, waterlilies can offer unique insights into angiosperm evolution. Giant Amazonian waterlilies (genus Victoria) are of particular interest: they produce the world’s largest floating leaves as well as gigantic flowers that entrap pollinating beetles. Here, we report chromosomal-level genomes of Victor...

This study assembled a high‐quality chromosome‐level genome of Prunus tomentosa, offering a vital resource for elucidating its genetic architecture, evolutionary relationships, and facilitating genome‐assisted breeding efforts. Multi‐omics integration revealed PtIMP3 and PtMIOX1L as key factors in cold tolerance of P. tomentosa. PtIMP3 drives the c...

This study reports the first high‐quality telomere‐to‐telomere (T2T) Rhododendron liliiflorum genome with 11 chromosomes that are gap free. The 24 telomeres and all 13 centromeres detected in this genome, which reached the highest quality gold level. In addition, other three Rhododendron species were sequenced and assembled to the chromosomal level...

Salt stress affects the growth, metabolism, yield, and quality of crops. To adapt to high-salt environments, plants form various regulatory mechanisms. Salt over sensitive (SOS) is the key gene of SOS signal transduction pathway. As a member of the SOS3 subfamily, the function of SOS3-3 under salt stress has not been reported. To verify the functio...

The Solanaceae family occupies a significant position, and the study of resistance genes within this family is extremely valuable. Therefore, our goal is to examine disease resistance genes based on the high-quality representative genomes of Solanaceae crops, and to develop corresponding Simple Sequence Repeat (SSR) molecular markers. Among nine re...

The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements in sequencing technologies. However, existing databases are limited by incomplete species representation, a lack of comprehensive comparative genomic tools and the absence o...

The auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA) family of genes are central components of the auxin signaling pathway and play essential roles in plant growth and development. Their large-scale analysis and evolutionary trajectory of origin are currently not known. Here, we identified the corresponding ARF and Aux/IAA famil...

With the rapid advancements in sequencing technology, an increasing number of genome sequences for medicinal plants have become available. In 2021, TCMPG was introduced as a comprehensive database dedicated to traditional Chinese medicine (TCM) plant genomes, capturing significant attention within the scientific community. To offer invaluable resou...

Flowering is one of the most important biological phenomena in the plant kingdom, which not only has important ecological significance, but also has substantial horticultural ornamental value. In this study, we undertook an exhaustive review of the advancements in our understanding of plant flowering genes. We delved into the identification and con...

With global warming and climate change, abiotic stresses often simultaneously occur. Combined salt and heat stress was a common phenomenon that was severe, particularly in arid/semi‐arid lands. We aimed to reveal the systematic responsive mechanisms of tomato genotypes with different salt/heat susceptibilities to combined salt and heat stress. Morp...

Waterlogging stress caused by concentrated and heavy rainfall has become an increasingly popular abiotic stress, especially for tomato production. The aim is to clarify the leaf physiological and biochemical responses as well as flower and fruit set of tomato plants at reproductive stage under waterlogging stress. Six tomato genotypes including 'MI...

The trihelix transcription factor (TTF) gene family is an important class of transcription factors that play key roles in regulating developmental processes and responding to various stresses. To date, no comprehensive analysis of the TTF gene family in large‐scale species has been performed. A cross‐genome exploration of its origin, copy number va...

Introduction Cytochrome P450 enzymes (P450s) are recognized as the most versatile catalysts worldwide, playing vital roles in numerous biological metabolism and biosynthesis processes across all kingdoms of life. Despite the vast number of P450 genes available in databases (over 300,000), only a small fraction of them (less than 0.2 %) have undergo...

XiangQingCai” (XQC, Brassica rapa ssp. chinensis) is an important Brassicaceae vegetable crop due to its strong volatile fragrance named. In this study, we report the high-quality chromosome-level genome sequence of XQC. The assemble genome length was determined as 466.11 Mb, with an N50 scaffold of 46.20 Mb. A total of 59.50% repetitive sequences...

Hypocotyl length is a critical determinant for the efficiency of mechanical harvesting in pakchoi production, but the knowledge on the molecular regulation of hypocotyl growth is very limited. Here, we report a spontaneous mutant of pakchoi, lhy7.1, and identified its characteristics. We found that it has an elongated hypocotyl phenotype compared t...

With global climate change, the frequency and intensity of waterlogging events are increasing due to frequent and heavy precipitation. Little is known however about the response of plants to repeated waterlogging stress events. The aim is to clarify physiological regulation mechanisms of tomato plants under repeated waterlogging stress, and whether...

Plant glycogen synthase kinase 3 (GSK3) family members, as a class of serine/threonine protein kinases, have been demonstrated to play essential roles in a wide range of biological processes in many plant species. Here is the first study to report on the GSK3 gene family in celery (Apium graveolens). A total of 11 GSK3 genes were identified, phylog...

Polygala tenuifolia is a perennial medicinal plant that has been widely used in traditional Chinese medicine for treating mental disease. However, the lack of genomic resources limits the insight into its evolutionary and biological characterization. In the present work, we reported the P. tenuifolia genome, the first genome assembly of the Polygal...

The rubber tree (Hevea brasiliensis) is grown in tropical regions and is the major source of natural rubber. Using traditional breeding approaches, the latex yield has increased by six‐fold in last century. However, the underlying genetic basis of rubber yield improvement is largely unknown. Here we present a high‐quality, chromosome‐level genome s...

Cabbage (Brassica oleracea L. var. capitata L.) is an important cruciferous vegetable, which is rich in dietary fiber, vitamins, beta-carotene and even good for cancer prevention. So, it is widely planted around the world. However, in the production of cabbage, the property of head-splitting not only reduces the appearance quality and commercial va...

With the advances in genomics and bioinformatics, particularly the extensive application of high-throughput sequencing technology, a large number of non-coding RNAs (ncRNAs) have been discovered, of which long ncRNAs (lncRNAs) refer to a class of transcripts that are more than 200 nucleotides in length. Accumulating evidence demonstrates that lncRN...

Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface— ‘The Vegetable Information Resources’ (TVIR, http://tvir.bio2db...

Celery (Apium graveolens L.), a plant from Apiaceae, is one of the most important vegetables and is grown worldwide. Carotenoids can capture light energy and transfer it to chlorophyll, which plays a central role in photosynthesis. Here, by performing transcriptomics and genomics analysis, we identified and conducted a comprehensive analysis of chl...

Background Brassinosteroids (BRs) are a group of essential steroid hormones involved in diverse developmental and physiological processes in plants. The Brassinazole-resistant 1 (BZR1) transcription factors are key components of BR signaling and integrate a wide range of internal and environmental signals to coordinate plant development, growth, an...

Ice plant (Mesembryanthemum crystallinum), a member of the Aizoaceae family, is a typical halophyte crop and a model plant for studying the mechanism of transition from C3 photosynthesis to crassulacean acid metabolism (CAM). Here, we report a high‐quality chromosome‐level ice plant genome sequence. This 98.05% genome sequence is anchored to nine c...

Cucurbitaceae is one of the most important plant families distributed worldwide. Transcription factors (TFs) regulate plant growth at the transcription level. Here, we performed a systematic analysis of 42 641 TFs from 63 families in 14 Cucurbitaceae and 10 non-cucurbit species. Whole-genome duplication (WGD) was the dominant event type in almost a...

Polyploids generated by the replication of a single genome (autopolyploid) or synthesis of two or more distinct genomes (allopolyploid) usually show significant advantages over their diploid progenitors in biological characteristics, including growth and development, nutrient accumulation, and plant resistance. Whereas, the impacts of genomic repli...

The Brassicaceae is an important plant family. We built a user-friendly, web-based, comparative, and functional genomic database, The Brassicaceae Genome Resource (TBGR, http://www.tbgr.org.cn), based on 82 released genomes from 27 Brassicaceae species. The TBGR database contains a large number of important functional genes, including 4,096 glucosi...

Varieties of various crops with high resilience are urgently needed to feed the increased population in climate change conditions. Human activities and climate change have led to frequent and strong weather fluctuation, which cause various abiotic stresses to crops. The understanding of crops’ responses to abiotic stresses in different aspects incl...

Background When researchers perform gene family analysis, they often analyze the structural characteristics of the gene, such as the distribution of introns and exons. At the same time, characteristic structural analysis of amino acid sequence is also essential, for example, motif and domain features. Researchers often integrate these analyses into...

Pepino (Solanum muricatum, 2n = 2x = 24), a member of the Solanaceae family, is an important globally grown fruit. Herein, we report high‐quality, chromosome‐level pepino genomes. The 91.67% genome sequence is anchored to 12 chromosomes, with a total length of 1.20 Gb and scaffold N50 of 87.03 Mb. More than half the genome comprises repetitive sequ...

With the aggravated abiotic stresses due to climate change and burgeoning population, a better understanding of crop responses to multiple stresses are needed to secure the crop production. The effects of individual climatic factor on crops were well documented, while the interaction of combined climatic factors received less attention. The frequen...

Heat shock transcription factor (Hsf) plays a critical role in regulating heat resistance. Here, 2950 Hsf family genes were identified from 111 horticultural and representative plants. More Hsf genes were detected in higher plants than lower plants. Based on all Hsf genes, we constructed a phylogenetic tree, which indicated that Hsf genes of each b...

Because of their great therapeutic and economic value, medicinal plants have attracted increasing scientific attention. With the rapid development of high-throughput sequencing technology, the genomes of many medicinal plants have been sequenced. Storing and analyzing the increasing volume of genomic data has become an urgent task. To solve this ch...

Heat stress caused by climate changes and global warming has become more frequent. Crop yield is usually quite sensitive to heat stress especially when it happens at reproductive stage. As evident by extensive yield loss in crops, the negative effects of heat stress on crops increased the risk of global food and nutrition security. In this chapter,...

Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poor...

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher...

As a reversible modification, N⁶-methyladenosine (m⁶A) plays key roles in series of biological processes. Although it has been found that m⁶A modification is regulated by writers, erasers and readers, their evolutionary processes are still not clearly and systematically described. In the present work, we identified 1592 m⁶A modification regulators...

Apiaceae is one of the most important families in Apiales and includes many economically important vegetables and medicinal plants. The TEOSINTE BRANCHED 1/CYCLOIDEA/PROLIFERATING CELL FACTOR 1/2 (TCP) gene family plays an important role in regulating plant growth and development, but it has not been widely studied in Apiaceae. In the present study...

Simple sequence repeats (SSRs) are popular and important molecular markers that exist widely in plants. Here, we conducted a comprehensive identification and comparative analysis of SSRs in 14 tree species. A total of 16, 298 SSRs were identified from 429, 449 genes, and primers were successfully designed for 99.44% of the identified SSRs. Our anal...

Large gene families are anticipated to show large-scale copy number changes from species to species due to relatively more freedom in selective pressure. In paleopolyploid plant species, recursive whole-genome duplication/triplication incurred considerable gene copy number increase and subsequent decrease due to genome instability, with a significa...

Ethiopian mustard (Brassica carinata) in the Brassicaceae family possesses many excellent agronomic traits. Here, the high-quality genome sequence of B. carinata is reported. Characterization revealed a genome anchored to 17 chromosomes with a total length of 1.087 Gb and an N50 scaffold length of 60 Mb. Repetitive sequences account for approximate...

The family Apiaceae includes many important vegetables and medicinal plants. Auxin response factors (ARFs) play critical roles in regulating plant growth and development. Here, we performed a comprehensive analysis of the ARF gene family in three Apiaceae species, celery, coriander, and carrot, and compared the results with the ARF gene family of l...

Coriander (Coriandrum sativum L.), also known as cilantro, is a globally important vegetable and spice crop. Its genome and that of carrot are models for studying the evolution of the Apiaceae family. Here, we developed the Coriander Genomics Database (CGDB, http://cgdb.bio2db.com/) to collect, store, and integrate the genomic, transcriptomic, meta...

Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high‐quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences...

Lycophytes and seed plants constitute the typical vascular plants. Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants. Here, genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events, with one occurring...

The aldo-keto reductase (AKR) superfamily plays a major role in oxidation-reduction in plants. D-galacturonic acid reductase (GalUR), an ascorbic acid (AsA) biosynthetic enzyme, belongs to this superfamily. However, the phylogenetic relationship and evolutionary history of the AKR gene family in plants has not yet been clarified. In this study, a t...

A genome-wide association study (GWAS) using 83 diverse non-heading Chinese cabbage (NHCC) accessions identified 42,526 high-quality single nucleotide polymorphism markers associated with turnip mosaic virus (TuMV) resistance. Seventeen associated loci were identified, along with the related genes that were differentially expressed between resistan...

Apiaceae is a major family from Apiales and includes many important vegetable and medicinal crops. Heat shock transcription factors (Hsf) play important roles in heat tolerance during plant development. Here, we conducted systematic analyses of the Hsf gene family in three Apiaceae species, including 17 Apium graveolens (celery), 32 Coriandrum sati...

Our aim was to understand how moderately increased light intensities influenced the response of chickpea to high temperature. Three chickpea genotypes (Acc#3, Acc#7 and Acc#8) were treated at control (26 °C and 300 μmol m⁻² s⁻¹ photosynthetic photon flux density/PPFD), high temperature (38 °C and 300 μmol m⁻² s⁻¹ PPFD), increased light intensity (2...

Background: Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and development of plants. Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics a...

Coriander (Coriandrum sativum L. 2n = 2x = 22), a plant from the Apiaceae family, also called cilantro or Chinese parsley, is a globally important crop used as vegetable, spice, fragrance, and traditional medicine. Here, we report a high-quality assembly and analysis of its genome sequence, anchored to 11 chromosomes, with total length of 2,118.68...

Background: UDP-glucuronate decarboxylase (UXS) is an enzyme in plants and participates in cell wall noncellulose. Previous research suggested that cotton GhUXS gene regulated the conversion of non-cellulosic polysaccharides and modulates their composition in plant cell walls, showing its possible cellular function determining the quality of cotton...

RNA modifications are involved in various kinds of cellular biological processes. Accumulated evidences have demonstrated that the functions of RNA modifications are determined by the effectors that can catalyze, recognize and remove RNA modifications. They are called ‘writers’, ‘readers’ and ‘erasers’. The identification of RNA modification effect...

Polyploidy has contributed to the divergence and domestication of plants; however, estimation of the relative roles that different types of polyploidy have played during evolution has been difficult. Unbalanced and balanced gene removal was previously related to allopolyploidies and autopolyploidies, respectively. Here, to infer the types of polypl...

As an essential post-transcriptional modification, N7-methylguanosine (m7G) regulates nearly every step of the life cycle of mRNA. Accurate identification of the m7G site in the transcriptome will provide insights into its biological functions and mechanisms. Although the m7G-methylated RNA immunoprecipitation sequencing (MeRIP-seq) method has been...

RNA N2-methylguanosine (m2G) is one kind of posttranscriptional modification and plays crucial roles in the control and stabilization of tRNA. However, our knowledge about the biological functions of m2G is still limited. The key step of revealing its new function is to recognize the m2G sites in the transcriptome. Since there is no effective metho...

Background After polyploidization, a genome may experience large-scale genome-repatterning, featuring wide-spread DNA rearrangement and loss, and often chromosome number reduction. Grasses share a common tetraploidization, after which the originally doubled chromosome numbers reduced to different chromosome numbers among them. A telomere-centric re...

Histone modifications are associated with alternative splicing. It has been suggested that histone modifications act in combinational patterns in gene expression regulation. However, how they interact with each other and what is their casual relationships in the process of RNA splicing remain unclear. In this study, the combinatorial patterns of 38...

Background: Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional doma...

Background: The BES1 gene family, an important class of plant-specific transcription factors, play key roles in the BR signal pathway in plants, regulating various development processes. Until now, there has been no comprehensive analysis of the BES1 gene family in Brassica napus, and a cross-genome exploration of their origin, copy number changes...

Turnip mosaic virus (TuMV) is a widely distributed pathogen that seriously affects the yield and quality of brassica crops. The SNARE genes in the host encode proteins that are very important for virus replication and movement. However, systematic and comprehensive analyses of these genes have not been reported for Chinese cabbage. In the present s...

Plants growing under high-density (HD) conditions experience increased competition for water, nutrients, and light, possibly leading to changes in size, biomass, morphology, and productivity. However, no research has focused on the relationship between whole-genome expression patterns and growth density. Here, we performed whole-genome RNA sequenci...