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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.

Background and AimsPhysical dormancy (PY) occurs in seeds or fruits of 18 angiosperm families and is caused by a water-impermeable palisade cell layer(s) in seed or fruit coats. Prior to germination, the seed or fruit coat of species with PY must become permeable in order to imbibe water. Breaking of PY involves formation of a small opening(s) (water gap) in a morpho-anatomically specialized area in seeds or fruits known as the water-gap complex. Twelve different water-gap regions in seven families have previously been characterized. However, the water-gap regions had not been characterized in Cucurbitaceae; clade Cladrastis of Fabaceae; subfamilies Bombacoideae, Brownlowioideae and Bythnerioideae of Malvaceae; Nelumbonaceae; subfamily Sapindoideae of Sapindaceae; Rhamnaceae; or Surianaceae. The primary aims of this study were to identify and describe the water gaps of these taxa and to classify all the known water-gap regions based on their morpho-anatomical features.MethodsPhysical dormancy in 15 species was broken by exposing seeds or fruits to wet or dry heat under laboratory conditions. Water-gap regions of fruits and seeds were identified and characterized by use of microtome sectioning, light microscopy, scanning electron microscopy, dye tracking and blocking experiments.Key ResultsTen new water-gap regions were identified in seven different families, and two previously hypothesized regions were confirmed. Water-gap complexes consist of (1) an opening that forms after PY is broken; (2) a specialized structure that occludes the gap; and (3) associated specialized tissues. In some species, more than one opening is involved in the initial imbibition of water.ConclusionsBased on morpho-anatomical features, three basic water-gap complexes (Types-I, -II and -III) were identified in species with PY in 16 families. Depending on the number of openings involved in initial imbibition, the water-gap complexes were sub-divided into simple and compound. The proposed classification system enables understanding of the relationships between the water-gap complexes of taxonomically unrelated species with PY.

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.

Abstract The family Sapindaceae comprises species with different reproductive strategies and sexual systems; however, dioecy is rarer and has been little investigated in tree species. We analyzed the reproductive biology of Talisia esculenta (Cambess.) Radlk. to understand its sexual system and reproductive potential. For this purpose, we examined floral biology and the reproductive system in natural populations of T. esculenta. The species exhibits two sexual morphs: individuals with morphologically hermaphroditic but functionally pistillate flowers, characterized as female, and individuals with staminate flowers, characterized as male. The hermaphroditic flowers produce viable pollen but do not self-pollinate due to strong hercogamy and the permanent indehiscence of the anthers; therefore, they are functionally female. These characteristics classify T. esculenta as an allogamous and androdioecious species, specifically a functionally dioecious type. Natural and hand pollination between male and female individuals resulted in a higher percentage of fruit set with significantly superior quality compared to fruits from hand cross-pollination between female individuals. However, the fruit set rate in these crosses was only 25% of the floral investment. The species is an obligatory xenogamous and invests in a high floral display (75% of the flowers) to attract pollinators. This is a secondary sexual trait that favors pollination. Pollination tests indicate that local pollinators are effective, suggesting that other factors may influence the low natural fruit set rate. Genetic and phylogenetic studies are necessary to further understand androdioecy and the reproductive behavior of T. esculenta. Resumo A família Sapindaceae possui espécies com diferentes estratégias reprodutivas e sistemas sexuais, no entanto, a dioicia é mais rara e tem sido pouco investigada em espécies arbóreas. Analisamos a biologia reprodutiva de Talisia esculenta, com o objetivo de compreender o seu sistema sexual e potencial reprodutivo. Para isso, analisamos a biologia floral e o sistema reprodutivo em populações naturais de T. esculenta. A espécie tem dois morfos sexuais: indivíduos com flores morfologicamente hermafroditas, mas funcionalmente pistiladas, caracterizados como femininos e indivíduos com flores estaminadas, caracterizados como masculinos. As flores hermafroditas produzem pólen viável, mas não se autopolinizam devido à forte hercogamia e indeiscência permanente das anteras, portanto, são funcionalmente femininas. Essas características classificam T. esculenta como uma espécie alógama e androdioica, do tipo dioica funcional. A polinização natural e a manual entre indivíduos masculinos e femininos formou maior porcentagem de frutos com qualidade significativamente superior do que os frutos da polinização cruzada manual entre indivíduos femininos. Mesmo assim, a taxa de formação de frutos nesses cruzamentos foi de apenas 25% do investimento floral. A espécie é xenogâmica obrigatória e investe no elevado display floral (75% das flores) para atração de polinizadores. Essa é uma característica sexual secundária que favorece a polinização. Os testes de polinização indicam que os polinizadores locais são efetivos, sugerindo que outros fatores podem influenciar na baixa taxa de frutificação natural. Estudos genéticos e filogenéticos são necessários para compreender a androdioicia e o comportamento reprodutivo de T. esculenta.

Background and AimsPaleoclimatic data indicate that an abrupt climate change occurred at the Eocene–Oligocene (E–O) boundary affecting the distribution of tropical forests on Earth. The same period has seen the emergence of South-East (SE) Asia, caused by the collision of the Eurasian and Australian plates. How the combination of these climatic and geomorphological factors affected the spatio-temporal history of angiosperms is little known. This topic is investigated by using the worldwide sapindaceous clade as a case study.MethodsAnalyses of divergence time inference, diversification and biogeography (constrained by paleogeography) are applied to a combined plastid and nuclear DNA sequence data set. Biogeographical and diversification analyses are performed over a set of trees to take phylogenetic and dating uncertainty into account. Results are analysed in the context of past climatic fluctuations.Key ResultsAn increase in the number of dispersal events at the E–O boundary is recorded, which intensified during the Miocene. This pattern is associated with a higher rate in the emergence of new genera. These results are discussed in light of the geomorphological importance of SE Asia, which acted as a tropical bridge allowing multiple contacts between areas and additional speciation across landmasses derived from Laurasia and Gondwana.ConclusionsThis study demonstrates the importance of the combined effect of geomorphological (the emergence of most islands in SE Asia approx. 30 million years ago) and climatic (the dramatic E–O climate change that shifted the tropical belt and reduced sea levels) factors in shaping species distribution within the sapindaceous clade.

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.

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.

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.

Yellow horn (Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines. Gene ontology (GO) enrichment analysis revealed some critical GO terms related to oil accumulation, including acyl-[acyl-carrier-protein] desaturase activity, pyruvate kinase activity, acetyl-CoA carboxylase activity, and seed oil body biogenesis. The identified differentially expressed genes also included several transcription factors, such as, AP2-EREBP family members, B3 domain proteins and C2C2-Dof proteins. Several genes involved in fatty acid (FA) biosynthesis, glycolysis/gluconeogenesis, and pyruvate metabolism were also up-regulated in the high-oil line at different developmental stages. Our findings indicate that the higher oil accumulation in high-oil yellow horn could be mostly driven by increased FA biosynthesis and carbon supply, i.e. a source effect.

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.