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Yellow horn ( Xanthoceras sorbifolia ) is an oil-rich woody plant cultivated for bio-energy production in China. Soil saline-alkalization is a prominent agricultural-related environmental problem limiting plant growth and productivity. In this study, we performed comparative physiological and transcriptomic analyses to examine the mechanisms of X . sorbifolia seedling responding to salt and alkaline-salt stress. With the exception of chlorophyll content, physiological experiments revealed significant increases in all assessed indices in response to salt and saline-alkali treatments. Notably, compared with salt stress, we observed more pronounced changes in electrolyte leakage (EL) and malondialdehyde (MDA) levels in response to saline-alkali stress, which may contribute to the greater toxicity of saline-alkali soils. In total, 3,087 and 2,715 genes were differentially expressed in response to salt and saline-alkali treatments, respectively, among which carbon metabolism, biosynthesis of amino acids, starch and sucrose metabolism, and reactive oxygen species signaling networks were extensively enriched, and transcription factor families of bHLH, C2H2, bZIP, NAC, and ERF were transcriptionally activated. Moreover, relative to salt stress, saline-alkali stress activated more significant upregulation of genes related to H + transport, indicating that regulation of intracellular pH may play an important role in coping with saline-alkali stress. These findings provide new insights for investigating the physiological changes and molecular mechanisms underlying the responses of X . sorbifolia to salt and saline-alkali stress.

Cardiospermum halicacabum L., a notable species of the genus Cardiospermum , is well-known for its culinary and medicinal properties. Nonetheless, a detailed description of the C. halicacabum chloroplast’s phylogeny and genes is still absent. We present the findings of an in-depth investigation of the chloroplast genome of C. halicacabum . The circular, 159,370 bp chloroplast genome of C. halicacabum has a 37.91% GC content. There are 134 genes in the circular genome, comprising 89 protein-coding genes, 37 tRNAs, and 8 rRNAs. There are 28 repeats of a simple sequence. A comparison of the chloroplast genomes of five related species reveals differences in the contraction and expansion of the reverse repeat region between C. halicacabum and other Sapindaceae. Our phylogenetic study reveals that C. halicacabum has a close connection with S. erecta . The chloroplast genome of C. halicacabum has been studied, which has helped us better understand the evolutionary links among Sapindaceae species.

Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production. However, little study explores the link between gene expression level and metabolite accumulation of X. sorbifolia in response to cold stress. Herein, we performed both transcriptomic and metabolomic analyses of X. sorbifolia seedlings to investigate the regulatory mechanism of resistance to low temperature (4 °C) based on physiological profile analyses. Cold stress resulted in a significant increase in the malondialdehyde content, electrolyte leakage and activity of antioxidant enzymes. A total of 1,527 common differentially expressed genes (DEGs) were identified, of which 895 were upregulated and 632 were downregulated. Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were strongly affected by cold stress. In addition, DEGs within the plant mitogen-activated protein kinase (MAPK) signaling pathway and TF families of ERF, WRKY, NAC, MYB, and bHLH were transcriptionally activated. Through metabolomic analysis, we found 51 significantly changed metabolites, particularly with the analysis of primary metabolites, such as sugars, amino acids, and organic acids. Moreover, there is an overlap between transcript and metabolite profiles. Association analysis between key genes and altered metabolites indicated that amino acid metabolism and sugar metabolism were enhanced. A large number of specific cold-responsive genes and metabolites highlight a comprehensive regulatory mechanism, which will contribute to a deeper understanding of the highly complex regulatory program under cold stress in X. sorbifolia.

GRAS family plays a critical role in plant growth and stress responses. In this study, we identified 47 GRAS (DlGRAS) genes in the longan genome and conducted a comprehensive bioinformatics analysis of these genes. RNA-seq analysis revealed that the expression of these DlGRAS genes differed during early SE and across various longan tissues. The quantitative real-time PCR (qRT-PCR) results indicated that the DlGRAS genes exhibited differential expression during the early SE of longan, with most of them showing high expression at the globular embryo (GE) stage. Under GA3 treatment, the transcript levels of DlGRAS12/15 decreased significantly. In contrast, exogenous ABA promoted the expression of DlGRAS6/10/23, indicating that DlGRAS genes are responsive to hormones. Compared with CaMV35S-driven GUS expression, the promoters of DlGRAS10/22 increased GUS expression, GA3 and ABA treatments enhanced promoter activity. DlGRAS10/22 were located in the nucleus. Overexpression of DlGRAS10/22 in longan SE significantly promoted the transcription levels of SE-related genes, including DlGID1, DlGA20ox2, DlLEC1, DlFUS3, DlABI3 and DlLEC2. Therefore, DlGRAS may be involved in the early morphogenesis of longan SE through the hormone signaling pathway.

Background Handeliodendron Rehder and Eurycorymbus Hand.-Mazz. are the monotypic genera in the Sapindaceae family. The phylogenetic relationship of these endangered species Handeliodendron bodinieri (Lévl.) Rehd. and Eurycorymbus cavaleriei (Lévl.) Rehd. et Hand.-Mazz. with other members of Sapindaceae s.l. is not well resolved. A previous study concluded that the genus Aesculus might be paraphyletic because Handeliodendron was nested within it based on small DNA fragments. Thus, their chloroplast genomic information and comparative genomic analysis with other Sapindaceae species are necessary and crucial to understand the circumscription and plastome evolution of this family. Results The chloroplast genome sizes of Handeliodendron bodinieri and Eurycorymbus cavaleriei are 151,271 and 158,690 bp, respectively. Results showed that a total of 114 unique genes were annotated in H. bodinieri and E. cavaleriei , and the ycf1 gene contained abundant SSRs in both genomes. Comparative analysis revealed that gene content, PCGs, and total GC content were remarkably similar or identical within 13 genera from Sapindaceae, and the chloroplast genome size of four genera was generally smaller within the family, including Acer , Dipteronia , Aesculus , and Handeliodendron . IR boundaries of the H. bodinieri showed a significant contraction, whereas it presented a notable expansion in E. cavaleriei cp genome. Ycf1 , ndhC-trnV-UAC , and rpl32-trnL-UAG-ccsA were remarkably divergent regions in the Sapindaceae species. Analysis of selection pressure showed that there are a few positively selected genes. Phylogenetic analysis based on different datasets, including whole chloroplast genome sequences, coding sequences, large single-copy, small single-copy, and inverted repeat regions, consistently demonstrated that H. bodinieri was sister to the clade consisting of Aesculus chinensis and A. wangii and strongly support Eurycorymbus cavaleriei as sister to Dodonaea viscosa . Conclusion This study revealed that the cp genome size of the Hippocastanoideae was generally smaller compared to the other subfamilies within Sapindaceae, and three highly divergent regions could be used as the specific DNA barcodes within Sapindaceae. Phylogenetic results strongly support that the subdivision of four subfamilies within Sapindaceae, and Handeliodendron is not nested within the genus Aesculus .

Fatty acid desaturases (FADs) play a pivotal role in the accumulation of oils in plant seeds. To elucidate the role of FADs in oil accumulation in the seeds of Xanthoceras sorbifolium , this study employed bioinformatics analysis methods to identify and analyze the FAD gene family. A total of 25 XsFAD genes were unevenly distributed across 11 chromosomes. Systematic phylogenetic analysis revealed that the XsFAD gene family is divided into three branches, with each branch exhibiting similar gene structures. The regulatory elements within the XsFAD gene promoter indicate that XsFAD genes are regulated by multiple factors. Quantitative real-time polymerase chain reaction (qRT-PCR) validation revealed a positive correlation between the expression levels of XsFAD genes and the oil content of X. sorbifolium . By conducting phenotypic measurements of the X. sorbifolium fruit and seeds, as well as quantitative analysis of the XsFAD gene expression, it has been preliminarily identified that the Liudong-5 variety may poseess the potential to be developed into a high-yield oil-producing variety, which may be related to the habitat of the X. sorbifolium germplasm and requires further investagation. In summary, this study provides a foundational understanding of the FAD gene family of X. sorbifolium , and the research outcomes will contribute to the theoretical basis for the selection of high-yielding oil varieties of X. sorbifolium in the Xinjiang region, as well as further genetic breeding and cultivation system studies.

Xanthoceras sorbifolia is a unique woody oilseed tree in China, and its leaves are rich in flavonoids, which are involved in plant growth, development and defense. However, the mining of flavonoid synthesis-related genes in Xanthoceras sorbifolia leaves is lacking. In this study, 226 leaves of Xanthoceras sorbifolia from eight provinces in the key distribution areas were measured for flavonoid content, and the differences in flavonoid content of Xanthoceras sorbifolia were analysed to screen out excellent seed sources and six excellent single plants with higher flavonoid content. Genome-wide association analysis (GWAS) was used to identify genes controlling the synthesis of flavonoids, and 62 significant Single nucleotide polymorphism (SNP) sites were identified, which were closely associated with 8 traits, and a total of 11 genes coding for proteins. We found that these genes mainly encode proteins such as WPP domain-associated protein (WAP) (Fragment), Protein pleiotropic regulatory locus 1 (PRL1) and Phosphomevalonate kinase, peroxisomal (PMK), etc. We found that these proteins may directly or indirectly affect the synthesis of flavonoids, which will provide a data base for molecular breeding and genetic improvement of Xanthoceras sorbifolia .

Background Lychee ( Litchi chinensis Sonn.), longan ( Dimocarpus longan Lour.), and rambutan ( Nephelium lappaceum L.) are popular tropical fruits in the family Sapindaceae, known for their succulent arils—specialized seed appendage with significant biological and commercial value. Despite their agricultural relevance, the molecular mechanisms underlying aril development in these species remain poorly understood. Results We conducted RNA-sequencing to profile transcriptomes during aril development, complemented by in-situ hybridization to validate the spatial expression of LcLBD1 . OrthoFinder identified species-specific and shared differentially expressed genes (DEGs), while functional enrichment analyses (GO, KEGG) and transcriptional network modeling elucidated regulatory pathways. After detailed analyses of transcriptomes, species-specific and shared DEGs were identified across lychee, longan, and rambutan using OrthoFinder. Members of the bHLH and MYB gene families were implicated in early aril development. Species-specific DEGs were primarily enriched in metabolic pathways. From shared DEGs, we identified ten transcription factors ( AGL8 , AP3 , SHP1 , WOX13 , LBD1 , LBD3, OBP1 , SPL2, SPL3, and SPL9 ) and three genes ( IAA8 , CSLD5 , and CYCD3;2 ) as key regulators. Interestingly, in-situ hybridization localized LcLBD1 expression to funicle and small aril cells, suggesting roles in cell differentiation and division. Conclusion We have identified ten transcription factors and three genes affecting aril development in lychee, longan, and rambutan, and validated the expression of LcLBD1 in funicle and aril cells. These results offer a new perspective on the molecular mechanism of aril development and lay the groundwork for future research into the functions and regulatory mechanisms of candidate genes.

Background Long non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan ( Dimocarpus longan ) somatic embryogenesis (SE) system is a good system for research on longan embryo development. Results In this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis -regulated target genes (5712 pairs) and 1605 trans -regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the “plant-pathogen interaction” and “plant hormone signaling” pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a). Conclusion Analyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE.

miRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan . We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8 , dlo-miR397a and DlLAC7 , dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.