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Root–nodule symbiosis between leguminous plants and nitrogen-fixing bacteria (rhizobia) involves molecular communication between the two partners. Key components for the establishment of symbiosis are rhizobium-derived lipochitooligosaccharides (Nod factors; NFs) and their leguminous receptors (NFRs) that initiate nodule development and bacterial entry. Here we demonstrate that the soybean microsymbiont Bradyrhizobium elkanii uses the type III secretion system (T3SS), which is known for its delivery of virulence factors by pathogenic bacteria, to promote symbiosis. Intriguingly, wild-type B. elkanii , but not the T3SS-deficient mutant, was able to form nitrogen-fixing nodules on soybean nfr mutant En1282. Furthermore, even the NF-deficient B. elkanii mutant induced nodules unless T3SS genes were mutated. Transcriptional analysis revealed that expression of the soybean nodulation-specific genes ENOD40 and NIN was increased in the roots of En1282 inoculated with B. elkanii but not with its T3SS mutant, suggesting that T3SS activates host nodulation signaling by bypassing NF recognition. Root-hair curling and infection threads were not observed in the roots of En1282 inoculated with B. elkanii , indicating that T3SS is involved in crack entry or intercellular infection. These findings suggest that B. elkanii has adopted a pathogenic system for activating host symbiosis signaling to promote its infection.

Polygonatum cyrtonema Hua is valued both as a precious traditional Chinese medicinal herb and as a prime example of a plant that bridges medicinal and culinary applications. Renowned for its significant medicinal and edible qualities, this botanical exemplifies a unique convergence of therapeutic and nutritional benefits. However, the primary rhizome of Polygonatum cyrtonema Hua development is difficult to germinate into seedlings in the same year. The germination of primary rhizome buds of P. cyrtonema can be promoted by treatment with exogenous hormone 6-BA, but the related regulatory mechanism is not clear. In this study, we found that the cytokinin oxidase (CKX) plays a key role in the germination of primary rhizome buds of P. cyrtonema . PcCKX1,2,3 promoted the expression of dormancy positively regulated genes, and repressed the expression of dormancy negatively regulated genes, which in turn inhibited Arabidopsis seed germination, and PcCKX2 was the major gene. PcCKX1,2,3 promoted the expression of dormant positively regulated genes such as sweet potato IbZEP, IbNCED3, IbDOG1, IbABI5, IbCKX3 , and IbCKX7, which in turn delayed the sprouting of sweet potato rhizomes, and that PcCKX2 played a major role. We further screened three MYB transcription factors significantly associated with PcCKX1,2,3 . Yeast one-hybrid, Dual-LUC, and EMSA experiments showed that PcMYB4, PcKUA1, and PcCSA all bind to and repress the expression of elements of the PcCKX1,2,3 promoter. Heterologous transformation of Arabidopsis experiments showed that PcMYB4, PcKUA1 , and PcCSA repressed the expression of dormancy-associated genes such as DOG1 , NCED3 , ABI5 , CKX3 , and CKX7 , which, in turn, facilitated Arabidopsis seed germination. Taken together, we found that PcMYBs are involved in the transcriptional regulation of PcCKXs to promote the germination of primary rhizome buds of P. cyrtonema . The results of this study lay the foundation for analyzing the molecular mechanism of primary rhizome bud germination in P. cyrtonema .

Bamboo (Phyllostachys praecox) is one of the largest members of the grass family Poaceae, and is one of the most economically important crops in Asia. However, complete knowledge of bamboo development and its molecular mechanisms is still lacking. In the present study, the differences in anatomical structure among rhizome buds, rhizome shoots, and bamboo shoots were compared, and several genes related to the development of the bamboo rhizome bud were identified. The rice cross-species microarray hybridization showed a total of 318 up-regulated and 339 down-regulated genes, including those involved in regulation and signalling, metabolism, and stress, and also cell wall-related genes, in the bamboo rhizome buds versus the leaves. By referring to the functional dissection of the homologous genes from Arabidopsis and rice, the putative functions of the 52 up-regulated genes in the bamboo rhizome bud were described. Six genes related to the development of the bamboo rhizome bud were further cloned and sequenced. These show 66-90% nucleotide identity and 68-98% amino acid identity with the homologous rice genes. The expression patterns of these genes revealed significant differences in rhizome shoots, rhizome buds, bamboo shoots, leaves, and young florets. Furthermore, in situ hybridization showed that the PpRLK1 gene is expressed in the procambium and is closely related to meristem development of bamboo shoots. The PpHB1 gene is expressed at the tips of bamboo shoots and procambium, and is closely related to rhizome bud formation and procambial development. To our knowledge, this is the first report that uses rice cross-species hybridization to identify genes related to bamboo rhizome bud development, and thereby contributes to the further understanding of the molecular mechanism involved in bamboo rhizome bud development.

Summary Rhizomes are modified stems that grow underground and produce new individuals genetically identical to the mother plant. Recently, a breakthrough has been made in efforts to convert annual grains into perennial ones by utilizing wild rhizomatous species as donors, yet the developmental biology of this organ is rarely studied. Oryza longistaminata, a wild rice species featuring strong rhizomes, provides a valuable model for exploration of rhizome development. Here, we first assembled a double‐haplotype genome of O. longistaminata, which displays a 48‐fold improvement in contiguity compared to the previously published assembly. Furthermore, spatiotemporal transcriptomics was performed to obtain the expression profiles of different tissues in O. longistaminata rhizomes and tillers. Two spatially reciprocal cell clusters, the vascular bundle 2 cluster and the parenchyma 2 cluster, were determined to be the primary distinctions between the rhizomes and tillers. We also captured meristem initiation cells in the sunken area of parenchyma located at the base of internodes, which is the starting point for rhizome initiation. Trajectory analysis further indicated that the rhizome is regenerated through de novo generation. Collectively, these analyses revealed a spatiotemporal transcriptional transition underlying the rhizome initiation, providing a valuable resource for future perennial crop breeding.

Efficient artificial lighting is essential for optimizing plant growth and propagation in closed-type smart farms. This study aimed to evaluate the effects of light-emitting diode (LED) combinations using red (R), blue (B), and white (W) light on physiological responses and rhizome-based vegetative propagation in Dysophylla yatabeana , a poorly seed-propagable aquatic species. Plants were cultivated under five different spectral treatments and a natural light control. Key physiological indicators—including net photosynthetic rate (P n ), substomatal CO 2 partial pressure (C i ), transpiration rate (E), photo-synthetic quantum efficiency (Φ), and leaf-to-air temperature difference (ΔT)—were measured. Path analysis was conducted to clarify the direct and indirect relationships among these variables and growth traits such as shoot dry weight (SDW), rhizome dry weight (RDW), and number of rhizomes (RN). The addition of W significantly enhanced both SDW and RN, whereas high R: B ratios increased P n but suppressed RDW. Light quality was found to influence growth not only through direct spectral effects but also via complex physiological pathways regulating internal CO 2 dynamics and assimilate allocation. These results provide insight into light management strategies for controlled-environment agriculture, especially for species requiring vegetative propagation, and support the development of sustainable indoor cultivation systems using LED lighting.

Maintaining genetic fidelity in in vitro-regenerated plants derived from chimeric tissues presents a significant challenge during tissue culture experiments. Sansevieria trifasciata cv. Laurentii exhibits striking periclinal chimeric tissues along its leaves, which are compromised when propagating plants through leaf cuttings. In addition to establishing in vitro production of S. trifasciata cv. Laurentii, the regeneration efficiency of light exposed single-node rhizome explants was also evaluated. Among various types of rhizome explants, the single-node rhizome explant produced the highest mean number of shoots per explant (2.5) on MS medium supplemented with 3 mg L − 1 BA and 0.1 mg L − 1 NAA, which was approximately five times higher than that of other explants. Notably, all regenerated plants originating from nodal and terminal meristems were morphologically similar to their corresponding mother plants and retained their chimeric characteristics. In contrast, shoots derived from explants containing both nodal segments and terminal meristems (MN explants) exhibited some degree of morphological variation. Specifically, higher concentrations of BA (6 mg L − 1 ) were found to decrease the phenotypic stability of regenerated shoots by 50%. De novo rhizomes derived from light exposed single-node rhizome (NC explants) yielded the highest mean number of shoots (6 shoot per explant) on MS medium supplemented with 4 mg L − 1 NAA and either 0.5 or 0.35 mg L − 1 BA. Shoots from de novo rhizomes closely resembled the mother plants, while callus-derived shoots showed only 65% similarity. The presence of light-influenced elevated sugar levels in NC explants supports the hypothesis that the enhanced regeneration capacity in light-exposed single-node rhizome tissues is likely attributed to the upregulation of cytokinin synthesis-related genes and light-induced carbohydrate allocation, which alters hormonal homeostasis and triggers the mitotic activities necessary for de novo rhizome regeneration and shoot multiplication.

Background Caucasian clover ( Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. Result We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase ( BADH ) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. Conclusions This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.

Taro (Colocasia esculenta (L.) Schott) is the fifth largest rhizome crop, and it is widely distributed in tropical and subtropical areas in the world. Vegetative propagation with virus-infected corms can lead to cultivar degradation, yield decline, and quality deterioration. In this study, the shoot apical meristems excised from taro corms infected with dasheen mosaic virus, which belongs to the genus Potyvirus in the family Potyviridae, were cultured and treated with exogenous abscisic acid and high sucrose concentrations to induce micro-corm formation. Subsequently, candidate genes involved in micro-corm expansion were screened via transcriptome sequencing analysis. The results revealed that the shoot apical meristems could grow into adventitious shoots on the medium 1 mg/L 6-benzylaminopurine + 0.3 mg/L 1-naphthaleneacetic acid, and reverse transcription–polymerase chain reaction detection indicated that dasheen mosaic virus had been successfully eliminated from the test-tube plantlets. Moreover, 8% sucrose or 3% sucrose + 5 μM abscisic acid likewise induced taro corm formation, and genes related to cell division and the cell cycle, as well as starch and sucrose metabolism pathways, were significantly enriched during taro corm expansion. Furthermore, the cyclin-dependent kinases genes, cell cycle protein kinase subunit genes, and cyclin B2 genes, which are related to cell division and the cell cycle, were upregulated with abscisic acid treatment on the 3rd day. The sucrose synthase genes, β-amylase genes, glycogen branching enzyme genes, and soluble starch synthase genes, which are related to starch and sucrose metabolism, were upregulated on the 15th day, indicating that cell division largely occurs during taro corm formation, whereas carbohydrates are synthesized during taro corm expansion.

Background Rhizome is the storage underground stem of lotus ( Nelumbo nucifera ), which is enlarged before winter season and could be used for asexual propagation. In addition, the enlarged rhizome is a nutritional vegetable with abundant starch, proteins, and vitamins. Enlargement of lotus rhizome is not only significance for itself to survive from the cold winter, but also important for its economic value. Results To explore the mechanism underlying its enlargement, integrative analyses of morphology, physiology and proteomics were conducted on the rhizome at stolon, middle, and enlarged stages. Morphological observation and physiological analyses showed that rhizomes were gradually enlarged during this process, in which the starch accumulation was also initiated. Quantitative proteomic analysis on the rhizomes at these three stages identified 302 stage-specific proteins (SSPs) and 172 differently expressed proteins (DEPs), based on which GO and KEGG enrichment analyses were conducted. The results indicated that light and auxin signal might be transduced through secondary messenger Ca 2+ , and play important roles in lotus rhizome enlargement. Conclusion These results will provide new insights into understanding the mechanism of lotus rhizome enlargement. Meanwhile, some candidate genes might be useful for further studies on this process, as well as breeding of rhizome lotus.

Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O . longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O . longistaminata . The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus , Bacillus , and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter , YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae , which potentially benefits the host by facilitating CH 4 -dependent N 2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O . longistaminata in nutrient-poor environments for biofertilizer development in agriculture.