Identification of Key Genes of Fruit Shape Variation in Jujube with Integrating Elliptic Fourier Descriptors and Transcriptome.

Jujube (Ziziphus jujuba) exhibits a rich diversity in fruit shape, with natural occurrences of gourd-like, flattened, and other special shapes. Despite the ongoing research into fruit shape, studies integrating elliptical Fourier descriptors (EFDs) with both Short Time-series Expression Miner (STEM) and weighted gene co-expression network analysis (WGCNA) for gene discovery remain scarce. In this study, six cultivars of jujube fruits with distinct shapes were selected, and samples were collected from the fruit set period to the white mature stage across five time points for shape analysis and transcriptome studies. By combining EFDs with WGCNA and STEM, the study aimed to identify the critical periods and key genes involved in the formation of jujube fruit shape. The findings indicated that the D25 (25 days after flowering) is crucial for the development of jujube fruit shape. Moreover, ZjAGL80, ZjABI3, and eight other genes have been implicated to regulate the shape development of jujubes at different periods of fruit development, through seed development and fruit development pathway. In this research, EFDs were employed to precisely delineate the shape of jujube fruits. This approach, in conjunction with transcriptome, enhanced the precision of gene identification, and offered an innovative methodology for fruit shape analysis. This integration facilitates the advancement of research into the morphological characteristics of plant fruits, underpinning the development of a refined framework for the genetic underpinnings of fruit shape variation.

Identification of High Tolerance to Jujube Witches' Broom in Indian Jujube (Ziziphus mauritiana Lam.) and Mining Differentially Expressed Genes Related to the Tolerance through Transcriptome Analysis.

The jujube witches' broom (JWB) disease is a severe threat to jujube trees, with only a few cultivars being genuinely tolerant or resistant to phytoplasma. The defense mechanism of jujube trees against phytoplasma is still unclear. In this study, we aimed to investigate the tolerance mechanism of Indian jujube 'Cuimi' to JWB and identify the key genes that contribute to JWB high tolerance. Based on the symptoms and phytoplasma concentrations after infection, we confirmed the high tolerance of 'Cuimi' to JWB. Comparative transcriptome analysis was subsequently performed between 'Cuimi' and 'Huping', a susceptible cultivar of Chinese jujube. Unique gene ontology (GO) terms were identified in 'Cuimi', such as protein ubiquitination, cell wall biogenesis, cell surface receptor signaling pathway, oxylipin biosynthetic process, and transcription factor activity. These terms may relate to the normal development and growth of 'Cuimi' under phytoplasma infection. We identified 194 differential expressed genes related to JWB high tolerance, involved in various processes, such as reactive oxygen species (ROS), Ca2+ sensors, protein kinases, transcription factors (TFs), lignin, and hormones. Calmodulin-like (CML) genes were significantly down-regulated in infected 'Cuimi'. We speculated that the CML gene may act as a negative regulatory factor related to JWB high tolerance. Additionally, the cinnamoyl-CoA reductase-like SNL6 gene was significantly up-regulated in infected 'Cuimi', which may cause lignin deposition, limit the growth of phytoplasma, and mediate immune response of 'Cuimi' to phytoplasma. Overall, this study provides insights into the contribution of key genes to the high tolerance of JWB in Indian jujube 'Cuimi'.

The Key Metabolic Network and Genes Regulating the Fresh Fruit Texture of Jujube (Ziziphus jujuba Mill.) Revealed via Metabolomic and Transcriptomic Analysis.

The texture of fresh jujube fruit is related to its popularity and commercial value. The metabolic networks and essential genes that regulate the texture of jujube (Ziziphus jujuba) fruit are still unknown. In this study, two jujube cultivars with significantly different textures were selected by a texture analyzer. The four developmental stages of the exocarp and mesocarp of jujube fruit were studied separately using metabolomic and transcriptomic analyses. Differentially accumulated metabolites were enriched in several critical pathways related to cell wall substance synthesis and metabolism. Transcriptome analysis confirmed this by finding enriched differential expression genes in these pathways. Combined analysis showed that 'Galactose metabolism' was the most overlapping pathway in two omics. Genes such as ß-Gal, MYB and DOF may affect fruit texture by regulating cell wall substances. Overall, this study provides an essential reference for the establishment of texture-related metabolic and gene networks of jujube fruit.

HPLC-MS/MS-based and transcriptome analysis reveal the effects of ABA and MeJA on jujube (Ziziphus jujuba Mill.) cracking.

Fruit cracking is a physiological disease that occurs during the development of jujube, abscisic acid (ABA) and jasmonic acid (JA) mainly regulate the cell wall metabolic pathway and induce fruit cracking. Here, we used high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to detect phytohormone-related metabolites at different developmental stages in cracking-susceptible (CS-15) and cracking-resistant (CR-04) individuals of full-sibling hybrid offspring. The fruit of 'Pingshunbenzao' jujube was treated with ABA and MeJA at the white-ripening stage, and the 48-h fruit cracking index was significantly increased compared to that of CK (water). Furthermore, RNA-seq of semi-red stage fruits identified several differentially expressed genes, related to the cell wall, such as SBT1.7 (Contig21.0.484), EXPA (Contig12.0.7) and QRT3 (newGene_1935), and transcription factors (TFs). These results reveal the relationship between the levels of different hormones and fruit cracking, identify genes associated with fruit cracking, and provide new insights to solve the problem of fruit cracking through hormonal regulation.

Genome-Wide Identification of Direct Targets of ZjVND7 Reveals the Putative Roles of Whole-Genome Duplication in Sour Jujube in Regulating Xylem Vessel Differentiation and Drought Tolerance.

The effects of whole-genome duplication span multiple levels. Previous study reported that the autotetraploid sour jujube exhibited superior drought tolerance than diploid. However, the difference in water transport system between diploids and autotetraploids and its mechanism remain unclear. Here, we found the number of xylem vessels and parenchyma cells in autotetraploid sour jujube increased to nearly twice that of diploid sour jujube, which may be closely related to the differences in xylem vessel differentiation-related ZjVND7 targets between the two ploidy types. Although the five enriched binding motifs are different, the most reliable motif in both diploid and autotetraploid sour jujube was CTTNAAG. Additionally, ZjVND7 targeted 236 and 321 genes in diploids and autotetraploids, respectively. More identified targeted genes of ZjVND7 were annotated to xylem development, secondary wall synthesis, cell death, cell division, and DNA endoreplication in autotetraploids than in diploids. SMR1 plays distinct roles in both proliferating and differentiated cells. Under drought stress, the binding signal of ZjVND7 to ZjSMR1 was stronger in autotetraploids than in diploids, and the fold-changes in the expression of ZjVND7 and ZjSMR1 were larger in the autotetraploids than in the diploids. These results suggested that the targeted regulation of ZjVND7 on ZjSMR1 may play valuable roles in autotetraploids in the response to drought stress. We hypothesized that the binding of ZjVND7 to ZjSMR1 might play a role in cell division and transdifferentiation from parenchyma cells to vessels in the xylem. This regulation could prolong the cell cycle and regulate endoreplication in response to drought stress and abscisic acid, which may be stronger in polyploids.

Comparative Transcriptomic Analyses of Different Jujube Cultivars Reveal the Co-Regulation of Multiple Pathways during Fruit Cracking.

Fruit cracking is a common physiological disorder in many fruit species. Jujube (Ziziphus jujuba Mill.) is an economically valuable fruit in which fruit cracking seriously affects fruit yield and quality and causes significant economic losses. To elucidate cracking-related molecular mechanisms, the cracking-susceptible cultivars 'Cuizaohong' and 'Jinsixiaozao' and the cracking-resistant cultivar 'Muzao' were selected, and comparative transcriptome analyses of cracking and non-cracking 'Cuizaohong' (CC and NC), cracking and non-cracking 'Jinsixiaozao' (CJ and NJ), and non-cracking 'Muzao' (NM) were conducted. A total of 131 differentially expressed genes (DEGs) were common to the CC vs. NC and CJ vs. NJ comparisons. To avoid passive processes after fruit cracking, we also mainly focused on the 225 gradually downregulated DEGs in the CJ, NJ, and NM samples. The functional annotation of the candidate DEGs revealed that 61 genes related to calcium, the cell wall, the cuticle structure, hormone metabolism, starch/sucrose metabolism, transcription factors, and water transport were highly expressed in cracking fruits. We propose that expression-level changes in these genes might increase the turgor pressure and weaken mechanical properties, ultimately leading to jujube fruit cracking. These results may serve as a rich genetic resource for future investigations on fruit cracking mechanisms in jujube and in other fruit species.

Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa.

BACKGROUND: Polyploid plants often exhibit enhanced stress tolerance. The underlying physiological and molecular bases of such mechanisms remain elusive. Here, we characterized the drought tolerance of autotetraploid sour jujube at phenotypic, physiological and molecular levels. RESULTS: The study findings showed that the autotetraploid sour jujube exhibited a superior drought tolerance and enhanced regrowth potential after dehydration in comparison with the diploid counterpart. Under drought stress, more differentially expressed genes (DEGs) were detected in autotetraploid sour jujube and the physiological responses gradually triggered important functions. Through GO enrichment analysis, many DEGs between the diploid and autotetraploid sour jujube after drought-stress exposure were annotated to the oxidation-reduction process, photosystem, DNA binding transcription factor activity and oxidoreductase activity. Six reactive oxygen species scavenging-related genes were specifically differentially expressed and the larger positive fold-changes of the DEGs involved in glutathione metabolism were detected in autotetraploid. Consistently, the lower O2- level and malonaldehyde (MDA) content and higher antioxidant enzymes activity were detected in the autotetraploid under drought-stress conditions. In addition, DEGs in the autotetraploid after stress exposure were significantly enriched in anthocyanin biosynthesis, DNA replication, photosynthesis and plant hormone, including auxin, abscisic acid and gibberellin signal-transduction pathways. Under osmotic stress conditions, genes associated with the synthesis and transport of osmotic regulators including anthocyanin biosynthesis genes were differentially expressed, and the soluble sugar, soluble protein and proline contents were significantly higher in the autotetraploid. The higher chlorophyll content and DEGs enriched in photosynthesis suggest that the photosynthetic system in the autotetraploid was enhanced compared with diploid during drought stress. Moreover, several genes encoding transcription factors (TFs) including GRAS, Bhlh, MYB, WRKY and NAC were induced specifically or to higher levels in the autotetraploid under drought-stress conditions, and hub genes, LOC107403632, LOC107422279, LOC107434947, LOC107412673 and LOC107432609, related to 18 up-regulated transcription factors in the autotetraploid compared with the diploid were identified. CONCLUSION: Taken together, multiple responses contribute to the enhanced drought tolerance of autotetraploid sour jujube. This study could provide an important basis for elucidating the mechanism of tolerance variation after the polyploidization of trees.

G protein γ subunit modulates expression of plant-biomass-degrading enzyme genes and mycelial-development-related genes in Penicillium oxalicum.

Heterotrimeric-G-protein-mediated signaling pathways modulate the expression of the essential genes in many fundamental cellular processes in fungi at the transcription level. However, these processes remain unclear in Penicillium oxalicum. In this study, we generated knockout and knockout-complemented strains of gng-1 (POX07071) encoding the Gγ protein and found that GNG-1 modulated the expression of genes encoding plant-biomass-degrading enzymes (PBDEs) and sporulation-related activators. Interestingly, GNG-1 affected expression of the cxrB that encodes a known transcription factor required for the expression of major cellulase and xylanase genes. Constitutive overexpression of cxrB in ∆gng-1 circumvented the dependence of PBDE production on GNG-1. Further evidence indicated that CxrB indirectly regulated the transcription levels of key amylase genes by controlling the expression of the regulatory gene amyR. These data extended the diversity of Gγ protein functions and provided new insight into the signal transduction and regulation of PBDE gene expression in filamentous fungi. KEY POINTS: • GNG-1 modulates the expression of PBDE genes and sporulation-related genes. • GNG-1 controls expression of the key regulatory gene cxrB. • Overexpression of cxrB circumvents dependence of PBDE production on GNG-1.

A mitogen-activated protein kinase PoxMK1 mediates regulation of the production of plant-biomass-degrading enzymes, vegetative growth, and pigment biosynthesis in Penicillium oxalicum.

Mitogen-activated protein kinase (MAPK) cascades are broadly conserved and play essential roles in multiple cellular processes, including fungal development, pathogenicity, and secondary metabolism. Their function, however, also exhibits species and strain specificity. Penicillium oxalicum secretes plant-biomass-degrading enzymes (PBDEs) that contribute to the carbon cycle in the natural environment and to utilization of lignocellulose in industrial processes. However, knowledge of the MAPK pathway in P. oxalicum has been relatively limited. In this study, comparative transcriptomic analysis of P. oxalicum, cultured on different carbon sources, found ten putative kinase genes with significantly modified transcriptional levels. Six of these putative kinase genes were knocked out in the parental strain ∆PoxKu70, and deletion of the gene, Fus3/Kss1-like PoxMK1 (POX00158), resulted in the largest reduction (91.1%) in filter paper cellulase production. Further tests revealed that the mutant ∆PoxMK1 lost 37.1 to 92.2% of PBDE production, under both submerged- and solid-state fermentation conditions, compared with ∆PoxKu70. In addition, the mutant ∆PoxMK1 had reduced vegetative growth and increased pigment biosynthesis. Comparative transcriptomic analysis showed that PoxMK1 deletion from P. oxalicum downregulated the expression of major PBDE genes and known regulatory genes such as PoxClrB and PoxCxrB, whereas the transcription of pigment biosynthesis-related genes was upregulated. Comparative phosphoproteomic analysis revealed that PoxMK1 deletion considerably modified phosphorylation of key transcription- and signal transduction-associated proteins, including transcription factors Mcm1 and Atf1, RNA polymerase II subunits Rpb1 and Rpb9, MAPK-associated Hog1 and Ste7, and cyclin-dependent kinase Kin28. These findings provide novel insights into understanding signal transduction and regulation of PBDE gene expression in fungi.Key points• PoxMK1 is involved in expression of PBDE- and pigment synthesis-related genes.• PoxMK1 is required for vegetative growth of P. oxalicum.• PoxMK1 is involved in phosphorylation of key TFs, kinases, and RNA polymerase II.

Probucol decreases homocysteine-stimulated CRP production in rat aortic smooth muscle cells via regulating HO-1/NADPH oxidase/ROS/p38 pathway.

The elevated homocysteine level is an independent risk factor for atherosclerosis, which is characterized as a chronic inflammatory disease associated with oxidative stress. We have confirmed that homocysteine can stimulate the production of C-reactive protein (CRP) in rat aortic smooth muscle cells (RASMCs). In the present study, we investigated the role of probucol in homocysteine-induced CRP expression in cultured RASMCs and high-methionine-diet-induced hyperhomocysteinemic rats. The results showed that probucol decreased homocysteine-induced CRP mRNA and protein expression in RASMCs in a concentration-dependent manner. In addition, the animal experiment showed that probucol not only inhibited CRP expression in the vessel wall but also reduced the circulating CRP level in hyperhomocysteinemic rats. Further investigations revealed that probucol markedly increased heme oxygenase-1 activity, suppressed nicotinamide adenine dinucleotide phosphate (NADPH) oxidase activity, diminished superoxide anion generation, and decreased p38 phosphorylation in RASMCs and hyperhomocysteinemic rat aorta. These data demonstrate that probucol can inhibit homocysteine-induced CRP generation by interfering with the NADPH oxidase/p38 signal pathway in RASMCs, which will provide new evidence for the anti-inflammatory and anti-atherosclerotic effects of probucol.

Genome-wide association studies of fruit quality traits in jujube germplasm collections using genotyping-by-sequencing.

Chinese jujube (Ziziphus jujuba Mill.) is an important fruit crop and harbors many highly diverse traits of potential economic importance. Fruit size, stone size, and fruit cracking have an important influence on the commercial value of jujube. This study is the first to conduct a genome-wide association study (GWAS) on 180 accessions of jujube and focuses on locating single-nucleotide polymorphisms (SNPs) associated with nine important fruit quality traits. Genotyping was performed using genotyping-by-sequencing and 4651 high-quality SNPs were identified. A genetic diversity analysis revealed the presence of three distinct groups, and rapid linkage disequilibrium decay was observed in this jujube population. Using a mixed linear model, a total of 45 significant SNP-trait associations were detected, among which 33 SNPs had associations with fruit size-related traits, nine were associated with stone size-related traits, and three with fruit cracking-related traits. In total, 21 candidate genes involved in cell expansion, abiotic stress responses, hormone signaling, and growth development were identified from the genome sequences of jujube. These results are useful as basic data for GWAS of other jujube traits, and these significant SNP loci and candidate genes should aid marker-assisted breeding and genomic selection of improved jujube cultivars.

Curcumin Suppresses Aldosterone-Induced CRP Generation in Rat Vascular Smooth Muscle Cells via Interfering with the ROS-ERK1/2 Signaling Pathway.

Aldosterone regulates the initiation and development of atherosclerosis which is identified as a chronic inflammatory disease by promoting the generation of C-reactive protein in vascular smooth muscle cells. Curcumin is the most active ingredient of turmeric with anti-inflammation and antioxidation effects. Here, the effect of curcumin on aldosterone-induced C-reactive protein generation in vascular smooth muscle and the molecular mechanisms involved were explored. Primary rat vascular smooth muscle cells and hyperaldosteronism model rats were used in this study. The amount of C-reactive protein, reactive oxygen species, and the signaling pathway-related molecules generated were estimated. We found that curcumin inhibited aldosterone-induced C-reactive protein generation in vascular smooth muscle cells by interfering with the reactive oxygen species-ERK1/2 signal pathway. The results provide new evidence for the potential anti-inflammatory and cardiovascular protective effects of curcumin.

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars.

BACKGROUND: Low temperature is a major factor influencing the growth and development of Chinese jujube (Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular mechanism, we conducted comparative transcriptome analysis between 'Dongzao' (low freezing tolerance cultivar) and 'Jinsixiaozao' (high freezing tolerance cultivar) using RNA-Seq. RESULTS: More than 20,000 genes were detected at chilling (4 °C) and freezing (- 10 °C, - 20 °C, - 30 °C and - 40 °C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca2+ signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors (WRKY, AP2/ERF, NAC and bZIP) participating in freezing stress were activated under different degrees of freezing stress. CONCLUSIONS: Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two Z. jujuba cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.

The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions.

BACKGROUND: Olive (Olea europaea L.) is an important oil and fruit crop worldwide, owning a rich germplasm with a large number of cultivars. Simple sequence repeats (SSRs) are excellent markers and have been used for the identification of olive cultivars. However, the limited number of SSR markers and the occurrence of confusion on the names of cultivars, as well as the possible appearance of clonal variation make it difficult to identify cultivars and interpret relationships among olive cultivars. METHOD: SSR markers were designed based on trinucleotide repeat sequences by screening the whole genome of olive, and the polymorphic SSR markers were developed that were applied to the identification of 53 olive accessions. The genetic characteristics and relationships of these olive accessions were evaluated based on the developed SSR markers. RESULTS: Twenty-one highly polymorphic genomic-SSR markers were developed, covering most chromosomes of olive. These SSR markers could well distinguish all 53 olive accessions, confirming their effectiveness. DNA fingerprints of the 53 olive accessions were constructed based on the 21 SSR markers. The dendrogram clearly divided the tested accessions into two main groups, which was also supported by the results of principal coordinate analysis. A total of 31 private alleles were detected in 15 olive accessions, which reflected the genetic diversity within 53 olive accessions to some extent. Six homonymy cases were also clarified by genetic analysis. These results suggest that the newly developed olive SSR markers are informative for the exploitation, preservation and breeding of olive.

Megasporogenesis, microsporogenesis, and female and male gametophyte development in Ziziphus jujuba Mill.

Jujube (Ziziphus jujuba Mill.) is an important fruit tree species in China. In this study, we studied the megasporogenesis, microsporogenesis, and female and male gametophyte development of two major jujube cultivars, "Dongzao" and "Mayazao," using the squash technique, improved paraffin section technology, and optical microscopy. Our investigation revealed that both "Dongzao" and "Mayazao" have bilocular ovaries, basal placenta, and anatropous, bitegmic, crassinucellate ovules. The tetrads formed by meiosis of megaspore mother cells are arranged in a straight line or a tetrahedron. Embryo sac development is of the Polygonum type. The flower buds contain five anthers, each having four pollen sacs. The anther wall, which is of the fundamental form, is composed of epidermis, endothecium, one or two middle layers, and glandular tapetum. Mature pollen grains are two-celled and three-colporate. Both "Dongzao" and "Mayazao" can form normal mature pollen grains. Our study, which has revealed the basic phenomena and progression of megasporogenesis, microsporogenesis, and female and male gametophyte development in jujube, has generated important data for further research on jujube cytology and reproductive biology. Finally, our explorations of the cytological mechanism of male sterility in "Dongzao" also have provided a cytological basis for crossbreeding.

TIPE1 promotes cervical cancer progression by repression of p53 acetylation and is associated with poor cervical cancer outcome.

Previous studies have shown that TIPE1 inhibits tumor proliferation and metastasis in certain cancers; however, increased expression of TIPE1 is observed in cervical cancer cell lines and tissues, indicating it might exert a distinctive role in cervical cancer. Cell and xenograft tumorigenicity assays showed that TIPE1 facilitates cervical cancer progression in this study. Further investigation demonstrated that TIPE1 binds to p53 and impairs its activity via inhibition of its acetylation. In addition, TIPE1 promoted cell proliferation and suppressed cisplatin susceptibility in a p53-dependent manner, indicating that TIPE1 facilitates cervical cancer progression primarily through the p53 pathway. TIPE1 expression in clinical samples also demonstrated that its upregulation predicts poor prognosis in patients with cervical cancer. Taken together, the results of this study showed that TIPE1 serves as an oncogene by restricting p53 activity in the development of cervical cancer, suggesting that TIPE1 will provide a new potential target for cervical cancer therapy and can be used as a biomarker to predict patient prognosis.

Genome-wide identification, characterization, and expression analysis of the expansin gene family in Chinese jujube (Ziziphus jujuba Mill.).

Main conclusion 30 expansin genes were identified in the jujube genome. Phylogenetic analysis classified expansins into 17 subgroups. Closely related expansins share a conserved gene structure. ZjEXPs had different expression patterns in different tissues. Plant-specific expansins were first discovered as pH-dependent cell-wall-loosening proteins involved in diverse physiological processes. No comprehensive analysis of the expansin gene family has yet been carried out at the whole genome level in Chinese jujube (Ziziphus jujuba Mill.). In this study, 30 expansin genes were identified in the jujube genome. These genes, which were distributed with varying densities across 10 of the 12 jujube chromosomes, could be divided into four subfamilies: 19 ZjEXPAs, 3 ZjEXPBs, 1 ZjEXLA, and 7 ZjEXLBs. Phylogenetic analysis of expansin genes in Arabidopsis, rice, apple, grape, and jujube classified these genes into 17 subgroups. Members of the same subfamily and subgroup shared conserved gene structure and motif compositions. Homology analysis identified 20 homologous gene pairs between jujube and Arabidopsis. Further analysis of ZjEXP gene promoter regions uncovered various growth, development and stress-responsive cis-acting elements. Expression analysis and transcript profiling revealed that ZjEXPs had different expression patterns in different tissues at various developmental stages. ZjEXPA4 and ZjEXPA6 were highly expressed in young fruits, ZjEXPA3 and ZjEXPA5 were significantly expressed in flowers, and ZjEXPA7 was specifically expressed in young leaves. The results of this study, the first systematic analysis of the jujube expansin gene family, can serve as a strong foundation for further elucidation of the physiological functions and biological roles of jujube expansin genes.

Reduced TIPE2 expression is inversely associated with proinflammatory cytokines and positively correlated with bone mineral density in patients with osteoporosis.

AIMS: The tumor necrosis factor (TNF)-alpha-induced protein 8-like 2 (TIPE2) participates in multiple inflammatory diseases. However, its underlying mechanism in osteoporosis has not been elucidated. The aim of current study is to preliminarily clarify the function of TIPE2 in the pathogenesis of osteoporosis. MAIN METHODS: TIPE2 expression in patients with osteoporosis was measured by Western blot and qRT-PCR methods. Proinflammatory cytokines including TNF-α, IL-1 and IL-6 were assessed via enzyme-linked immunosorbent assay. Serum fasting PINP and ß-CTX were measured by the chemiluminescence method. Simple logistic regression analysis was performed for the odds ratio (OR) for TIPE2. KEY FINDINGS: TIPE2 expression in patients with osteoporosis was dramatically decreased and negatively correlated with proinflammatory cytokines. Furthermore, TIPE2 level was negatively correlated with fasting ß-CTX, but not PINP, indicating that TIPE2 participates in the pathogenesis of osteoporosis dominantly by supression of bone resorption. Interestingly, TIPE2 expression level was positively correlated with bone mineral density (BMD), and its expression level can predict the risk of bone fracture using the simple logistic regression assay. SIGNIFICANCE: Our findings clarify that TIPE2 alleviates the pathogenesis of osteoporosis by suppressing the inflammatory status and the ability of TIPE2 for predicts bone fracture further demonstrated that TIPE2 might serve as a novel diagnostic marker and a therapeutic target for osteoporosis.

De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae).

Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059⁻0.116, gene flow = 1.904⁻3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.

Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing.

Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.