Zhiyuan Liu

Common bean (Phaseolus vulgaris L.) is an economically important grain legume for the human diet and sustainable agricultural development. Snap bean, a vegetable-type common bean cultivated for edible immature pods, serves as a crucial dietary source of essential vitamins, minerals and proteins. However, its evolutionary and domestication history remains poorly characterized. Here, we assembled and characterized the complete chloroplast genome of snap bean using PacBio HiFi sequencing technology. The chloroplast genome formed a single circular molecule of 150,248 bp, consisting of a pair of inverted repeat regions, a large single-copy region, and a small single-copy region. A total of 75 protein-coding genes, 37 tRNA genes, and 8 rRNA genes were annotated. Phylogenomics revealed that snap bean has the closest relationship with dry common bean, grouping with lima bean; Phaseolus is phylogenetically nearest to Vigna. Comparative plastid genomics identified variants in accD, rpoC2, matK, and other coding genes. Nucleotide diversity analysis detected several highly variable hotspot regions, including accD, trnY-psbD, ndhH, and ycf1-rps15, which are promising informative plastid markers for phylogeny and population genetics. These findings deepen our understanding of legume chloroplast evolution and lay genomic foundations for common bean phylogenetic research and genetic breeding improvement.

Fruit spine formation in spinach (Spinacia oleracea L.) affects seed processing and mechanized sowing, yet its molecular basis underlying this trait remains unclear. Therefore, we performed comparative transcriptome analysis of two contrasting genotypes, Sp35 (spiny) and Sp34 (spineless), at early morphogenesis and late developmental stages. RNA-seq analysis identified 3002 differentially expressed genes (DEGs) at the early developmental stage and 2737 DEGs at the later stage. Intersection analysis revealed that 1080 DEGs were differentially expressed in both stages, suggesting that these shared genes may play particularly important roles. Functional enrichment analysis of these 1080 shared DEGs revealed involvement in cell wall biogenesis, phenylpropanoid biosynthesis, and carbohydrate metabolism, highlighting roles for secondary cell wall formation and lignification in spine development. To identify the key regulatory gene, weighted gene co-expression network analysis (WGCNA) was conducted and found a significantly correlated gene module. In this co-expression gene module, a MYB transcription factor SOV2g002850 occupies a central position. Additionally, several MADS-box genes and WRKY regulatory genes were also identified in the co-expression network. Overall, this study provides a comprehensive transcriptomic framework for spinach spine development and identifies candidate genes for future functional validation and breeding.

Plant disease resistance is typically conferred by nucleotide-binding site leucine-rich repeats (NLR) proteins; however, the diversity of NLR genes in spinach has remained largely unexplored. We identified 2,549 NLR genes across 19 Spinacia assemblies of cultivated spinach and its two wild species, and constructed a comprehensive pan-NLRome, which was categorized into six subfamilies, and the most frequent NLR class was CC-NBARC-LRR. The pan-NLRome consists of 186 NLR families, comprising 38.7% core, 51.1% dispensable and 10.2% private families. By integrating pan-NLRome with k -mer-based genome-wide association studies (GWAS), we developed a novel pipeline for rapid identification of disease resistance genes. Using this approach, we directly pinpointed a candidate gene, Te17S24XX_Chr1_nlr42 , for the RPF1 locus, which confers resistance to spinach downy mildew pathogen races 1–7, 9, 11, 13, 15, 16, 18, and 20. In contrast, a single-genome-based method identified four candidate genes, which required further analysis confirm the final gene. The Spinacia pan-NLRome serves as an invaluable resource for exploring NLR gene evolution and plant disease resistance mechanisms. Our developed pipeline offers a reliable and efficient strategy for cloning resistance genes across multiple crops.

Spinach (Spinacia oleracea L.) is an important leafy vegetable but is vulnerable to viral infections that significantly affect its quality and yield. In this study, we identified virus-infected spinach exhibiting typical symptoms with yellowing, wrinkling, and mottling in Beijing. But conventional RT-PCR screening for twelve common plant viruses yielded negative results. Then, using transcriptome sequencing along with a de novo assembly approach, we obtained the complete viral genome, which consists of RNA1 (5916 nucleotides) and RNA2 (3576 nucleotides). BLASTN analysis against the NCBI viral genome database revealed high homology with broad bean wilt virus 2 (BBWV2), leading us to designate this isolate as BBWV2-SP (GenBank accession numbers PV102464 and PV102465). Phylogenetic analysis indicated that BBWV2-SP shares 96.69% nucleotide sequence identity with a Liaoning isolate from Chenopodium album MN786955 and clusters within the Chinese evolutionary lineage. We developed primers targeting the conserved region of the RNA2 coat protein, amplifying a 478-base-pair product. All symptomatic spinach samples tested positive, while asymptomatic controls remained negative, confirming the causal relationship between BBWV2-SP and the observed disease symptoms. This study provides the complete genome assembly of the spinach isolate BBWV2-SP and establishes a molecular detection protocol for BBWV2 in spinach. These findings offer essential technical support for field monitoring, epidemiological surveillance, and disease control strategies, while also enhancing our understanding of BBWV2′s genetic diversity and mechanisms of pathogenicity.

Background: Spinach (Spinacia oleracea L.) is an important leafy vegetable with dioecious and occasional monoecious plants. Monoecious lines are more suitable for hybrid production than dioecious lines due to their extended flowering period. However, genetic research on the sex determination of monoecism remains limited. Methods: In this study, RNA-seq analysis of monoecious and female spinach plants was performed at two distinct flowering stages. In total, we identified 4586 differentially expressed genes (DEGs), which were primarily involved in biological processes such as hormone signaling, cell wall biosynthesis, photosynthesis, and flower development, based on Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Results: Among these DEGs, 354 transcription factors, including 27 genes associated with the ABCDE gene, were discovered. Furthermore, a co-expression gene regulatory network was built, identifying nine key genes that play important roles in regulating sex differentiation between female and monoecious plants. Conclusions: Our findings provide crucial molecular insights into the mechanisms of monoecism in spinach and offer a scientific basis for future spinach breeding.

Spinach (Spinacia oleracea L.) is a dioecious, wind-pollinated, and important green leafy vegetable that is widely cultivated worldwide. The characteristics of spinach pollen remain unclear. Herein, we investigated the pollen microscopic morphology of nine spinach genotypes by scanning electron microscopy (SEM). Because pollen grains of spinach are isodiametric and spheroidal, the following data for the pollen properties were observed: the maximum diameter of the pollen (27.66–33.05 um), pore diameter max (1.26–2.57 um), the number of visible pores (30–44), the density of pore elements/100 μm² (4.33–11.00), and the density of spinule elements/10 μm² (4.00–5.33). These are useful characteristics in distinguishing the species. Furthermore, by applying the cluster analysis method, based on key components, nine varieties are categorized into two main classes. These results provide a useful reference for the classification and identification of different spinach varieties.

The common bean (Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties.

Spinach is a significant source of vitamins, minerals, and antioxidants. These nutrients make it delicious and beneficial for human health. However, the genetic mechanism underlying the accumulation of nutrients in spinach remains unclear. In this study, we analyzed the content of chlorophyll a, chlorophyll b, oxalate, nitrate, crude fiber, soluble sugars, manganese, copper, and iron in 62 different spinach accessions. Additionally, 3,356,182 high-quality, single-nucleotide polymorphisms were found using resequencing and used in a genome-wide association study. A total of 2077 loci were discovered that significantly correlated with the concentrations of the nutritional elements. Data mining identified key genes in these intervals for four traits: chlorophyll, oxalate, soluble sugar, and Fe. Our study provides insights into the genetic architecture of nutrient variation and facilitates spinach breeding for good nutrition.

The members of the myeloblastosis (MYB) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, such as circadian rhythm, metabolism, and flower development. However, the characterization of MYB genes across the genomes of spinach Spinacia oleracea L. has not been reported. Here, we identified 140 MYB genes in spinach and described their characteristics using bioinformatics approaches. Among the MYB genes, 54 were 1R-MYB, 80 were 2R-MYB, 5 were 3R-MYB, and 1 was 4R-MYB. Almost all MYB genes were located in the 0–30 Mb region of autosomes; however, the 20 MYB genes were enriched at both ends of the sex chromosome (chromosome 4). Based on phylogeny, conserved motifs, and the structure of genes, 2R-MYB exhibited higher conservation relative to 1R-MYB genes. Tandem duplication and collinearity of spinach MYB genes drive their evolution, enabling the functional diversification of spinach genes. Subcellular localization prediction indicated that spinach MYB genes were mainly located in the nucleus. Cis-acting element analysis confirmed that MYB genes were involved in various processes of spinach growth and development, such as circadian rhythm, cell differentiation, and reproduction through hormone synthesis. Furthermore, through the transcriptome data analysis of male and female flower organs at five different periods, ten candidate genes showed biased expression in spinach males, suggesting that these genes might be related to the development of spinach anthers. Collectively, this study provides useful information for further investigating the function of MYB TFs and novel insights into the regulation of sex determination in spinach.

Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting is relatively weak, with specific regulatory pathways and genes unclear. To clarify the regulatory characteristics and key genes related to bolting in spinach, we conducted a comparative transcriptome analysis. In this study, 18 samples from three periods of bolting-tolerant spinach material 12S3 and bolting-susceptible material 12S4 were analyzed using RNA-seq on, resulting in 10,693 differentially expressed genes (DEGs). Functional enrichment and co-expression trend analysis indicated that most DEGs were enriched in the photoperiod pathway, the hormone signaling pathway, and the cutin, suberin, and wax biosynthetic pathways. According to the weighted gene co-expression network analysis (WGCNA), SpFT (SOV4g003400), SOV4g040250, and SpGASA1 (SOV6g017600) were likely to regulate bolting through the gibberellin and photoperiod pathways, and SpELF4 (SOV1g028600) and SpPAT1 (SOV4g058860) caused differences in early and late bolting among different cultivars. These results provide important insights into the genetic control of bolting in spinach and will help elucidate the molecular mechanisms of bolting in leafy vegetables.