The Role of miRNA and Long Noncoding RNA in Cholestatic Liver Diseases.

Cholestatic liver diseases encompass a range of organic damages, metabolic disorders, and dysfunctions within the hepatobiliary system, arising from various pathogenic causes. These factors contribute to disruptions in bile production, secretion, and excretion. Cholestatic liver diseases can be classified into intrahepatic and extrahepatic cholestasis, according to the location of occurrence. The etiology of cholestatic liver diseases is complex, and includes drugs, poisons, viruses, parasites, bacteria, autoimmune responses, tumors, and genetic metabolism. The pathogenesis of cholelstatic liver disease is not completely clarified, and effective therapy is lacking. Clarifying its mechanism to find more effective therapeutic targets and drugs is an unmet need. Increasing evidence demonstrates that miRNA and long noncoding RNA are involved in the progression of cholestatic liver diseases. This review provides a comprehensive summary of the research progress on the roles of miRNA and long noncoding RNA in cholestatic liver diseases. The aim of the review is to enhance the understanding of their potential diagnostic, therapeutic, and prognostic value for patients with cholestasis.

Morphological, anatomical, and transcriptomics analysis reveals the regulatory mechanisms of cassava plant height development.

BACKGROUND: Cassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated. RESULTS: In this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars. CONCLUSIONS: Our findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.

Assembly and comparative analysis of the complete mitochondrial and chloroplast genome of Cyperus stoloniferus (Cyperaceae), a coastal plant possessing saline-alkali tolerance.

BACKGROUND: Cyperus stoloniferus is an important species in coastal ecosystems and possesses economic and ecological value. To elucidate the structural characteristics, variation, and evolution of the organelle genome of C. stoloniferus, we sequenced, assembled, and compared its mitochondrial and chloroplast genomes. RESULTS: We assembled the mitochondrial and chloroplast genomes of C. stoloniferus. The total length of the mitochondrial genome (mtDNA) was 927,413 bp, with a GC content of 40.59%. It consists of two circular DNAs, including 37 protein-coding genes (PCGs), 22 tRNAs, and five rRNAs. The length of the chloroplast genome (cpDNA) was 186,204 bp, containing 93 PCGs, 40 tRNAs, and 8 rRNAs. The mtDNA and cpDNA contained 81 and 129 tandem repeats, respectively, and 346 and 1,170 dispersed repeats, respectively, both of which have 270 simple sequence repeats. The third high-frequency codon (RSCU > 1) in the organellar genome tended to end at A or U, whereas the low-frequency codon (RSCU < 1) tended to end at G or C. The RNA editing sites of the PCGs were relatively few, with only 9 and 23 sites in the mtDNA and cpDNA, respectively. A total of 28 mitochondrial plastid DNAs (MTPTs) in the mtDNA were derived from cpDNA, including three complete trnT-GGU, trnH-GUG, and trnS-GCU. Phylogeny and collinearity indicated that the relationship between C. stoloniferus and C. rotundus are closest. The mitochondrial rns gene exhibited the greatest nucleotide variability, whereas the chloroplast gene with the greatest nucleotide variability was infA. Most PCGs in the organellar genome are negatively selected and highly evolutionarily conserved. Only six mitochondrial genes and two chloroplast genes exhibited Ka/Ks > 1; in particular, atp9, atp6, and rps7 may have undergone potential positive selection. CONCLUSION: We assembled and validated the mtDNA of C. stoloniferus, which contains a 15,034 bp reverse complementary sequence. The organelle genome sequence of C. stoloniferus provides valuable genomic resources for species identification, evolution, and comparative genomic research in Cyperaceae.

Mutator-like transposable element 9A interacts with metacaspase 1 and modulates the incidence of Al-induced programmed cell death in peanut.

The toxicity of aluminum (Al) in acidic soil inhibits plant root development and reduces crop yields. In the plant response to Al toxicity, the initiation of programmed cell death (PCD) appears to be an important mechanism for the elimination of Al-damaged cells to ensure plant survival. In a previous study, the type I metacaspase AhMC1 was found to regulate the Al stress response and to be essential for Al-induced PCD. However, the mechanism by which AhMC1 is altered in the peanut response to Al stress remained unclear. Here, we show that a nuclear protein, mutator-like transposable element 9A (AhMULE9A), directly interacts with AhMC1 in vitro and in vivo. This interaction occurs in the nucleus in peanut and is weakened during Al stress. Furthermore, a conserved C2HC zinc finger domain of AhMULE9A (residues 735-751) was shown to be required for its interaction with AhMC1. Overexpression of AhMULE9A in Arabidopsis and peanut strongly inhibited root growth with a loss of root cell viability under Al treatment. Conversely, knock down of AhMULE9A in peanut significantly reduced Al uptake and Al inhibition of root growth, and alleviated the occurrence of typical hallmarks of Al-induced PCD. These findings provide novel insight into the regulation of Al-induced PCD.

De Novo Assembly and Comparative Analysis of Mitochondrial Genomes of Two Pueraria montana Varieties.

Pueraria montana is a species with important medicinal value and a complex genetic background. In this study, we sequenced and assembled the mitochondrial (mt) genomes of two varieties of P. montana. The mt genome lengths of P. montana var. thomsonii and P. montana var. montana were 457,390 bp and 456,731 bp, respectively. Both P. montana mitogenomes showed a multi-branched structure consisting of two circular molecules, with 56 genes annotated, comprising 33 protein-coding genes, 18 tRNA genes (trnC-GCA and trnM-CAU are multi-copy genes), and 3 rRNA genes. Then, 207 pairs of long repeats and 96 simple sequence repeats (SSRs) were detected in the mt genomes of P. montana, and 484 potential RNA-editing sites were found across the 33 mitochondrial protein-coding genes of each variety. Additionally, a syntenic sequence analysis showed a high collinearity between the two mt genomes. This work is the first to analyze the mt genomes of P. montana. It can provide information that can be used to analyze the structure of mt genomes of higher plants and provide a foundation for future comparative genomic studies and evolutionary biology research in related species.

Up-regulation of the human-specific CHRFAM7A gene protects against renal fibrosis in mice with obstructive nephropathy.

Renal fibrosis is a major factor in the progression of chronic kidney diseases. Obstructive nephropathy is a common cause of renal fibrosis, which is also accompanied by inflammation. To explore the effect of human-specific CHRFAM7A expression, an inflammation-related gene, on renal fibrosis during obstructive nephropathy, we studied CHRFAM7A transgenic mice and wild type mice that underwent unilateral ureteral obstruction (UUO) injury. Transgenic overexpression of CHRFAM7A gene inhibited UUO-induced renal fibrosis, which was demonstrated by decreased fibrotic gene expression and collagen deposition. Furthermore, kidneys from transgenic mice had reduced TGF-ß1 and Smad2/3 expression following UUO compared with those from wild type mice with UUO. In addition, the overexpression of CHRFAM7A decreased release of inflammatory cytokines in the kidneys of UUO-injured mice. In vitro, the overexpression of CHRFAM7A inhibited TGF-ß1-induced increase in expression of fibrosis-related genes in human renal tubular epithelial cells (HK-2 cells). Additionally, up-regulated expression of CHRFAM7A in HK-2 cells decreased TGF-ß1-induced epithelial-mesenchymal transition (EMT) and inhibited activation f TGF-ß1/Smad2/3 signalling pathways. Collectively, our findings demonstrate that overexpression of the human-specific CHRFAM7A gene can reduce UUO-induced renal fibrosis by inhibiting TGF-ß1/Smad2/3 signalling pathway to reduce inflammatory reactions and EMT of renal tubular epithelial cells.

Molecular Cloning, Expression Analysis, and Functional Analysis of Nine IbSWEETs in Ipomoea batatas (L.) Lam.

Sugar Will Eventually be Exported Transporter (SWEET) genes play an important regulatory role in plants' growth and development, stress response, and sugar metabolism, but there are few reports on the role of SWEET proteins in sweet potato. In this study, nine IbSWEET genes were obtained via PCR amplification from the cDNA of sweet potato. Phylogenetic analysis showed that nine IbSWEETs separately belong to four clades (Clade I~IV) and contain two MtN3/saliva domains or PQ-loop superfamily and six~seven transmembrane domains. Protein interaction prediction showed that seven SWEETs interact with other proteins, and SWEETs interact with each other (SWEET1 and SWEET12; SWEET2 and SWEET17) to form heterodimers. qRT-PCR analysis showed that IbSWEETs were tissue-specific, and IbSWEET1b was highly expressed during root growth and development. In addition to high expression in leaves, IbSWEET15 was also highly expressed during root expansion, and IbSWEET7, 10a, 10b, and 12 showed higher expression in the leaves. The expression of SWEETs showed a significant positive/negative correlation with the content of soluble sugar and starch in storage roots. Under abiotic stress treatment, IbSWEET7 showed a strong response to PEG treatment, while IbSWEET10a, 10b, and 12 responded significantly to 4 °C treatment and, also, at 1 h after ABA, to NaCl treatment. A yeast mutant complementation assay showed that IbSWEET7 had fructose, mannose, and glucose transport activity; IbSWEET15 had glucose transport activity and weaker sucrose transport activity; and all nine IbSWEETs could transport 2-deoxyglucose. These results provide a basis for further elucidating the functions of SWEET genes and promoting molecular breeding in sweet potato.

Transcriptomic analysis of tuberous root in two sweet potato varieties reveals the important genes and regulatory pathways in tuberous root development.

BACKGROUND: Tuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is unclear. RESULTS: In this study, the transcriptome of fibrous roots (R0) and tuberous roots in three developmental stages (Rl, R2, R3) were analyzed in two sweet potato varieties, GJS-8 and XGH. A total of 22,914 and 24,446 differentially expressed genes (DEGs) were identified in GJS-8 and XGH respectively, 15,920 differential genes were shared by GJS-8 and XGH. KEGG pathway enrichment analysis showed that the DEGs shared by GJS-8 and XGH were mainly involved in "plant hormone signal transduction" "starch and sucrose metabolism" and "MAPK signal transduction". Trihelix transcription factor (Tai6.25300) was found to be closely related to tuberous root enlargement by the comprehensive analysis of these DEGs and weighted gene co-expression network analysis (WGCNA). CONCLUSION: A hypothetical model of genetic regulatory network for tuberous root development of sweet potato is proposed, which emphasizes that some specific signal transduction pathways like "plant hormone signal transduction" "Ca2+signal" "MAPK signal transduction" and metabolic processes including "starch and sucrose metabolism" and "cell cycle and cell wall metabolism" are related to tuberous root development in sweet potato. These results provide new insights into the molecular mechanism of tuberous root development in sweet potato.

Genome-wide identification, evolutionary and expression analyses of LEA gene family in peanut (Arachis hypogaea L.).

BACKGROUND: Late embryogenesis abundant (LEA) proteins are a group of highly hydrophilic glycine-rich proteins, which accumulate in the late stage of seed maturation and are associated with many abiotic stresses. However, few peanut LEA genes had been reported, and the research on the number, location, structure, molecular phylogeny and expression of AhLEAs was very limited. RESULTS: In this study, 126 LEA genes were identified in the peanut genome through genome-wide analysis and were further divided into eight groups. Sequence analysis showed that most of the AhLEAs (85.7%) had no or only one intron. LEA genes were randomly distributed on 20 chromosomes. Compared with tandem duplication, segmental duplication played a more critical role in AhLEAs amplication, and 93 segmental duplication AhLEAs and 5 pairs of tandem duplication genes were identified. Synteny analysis showed that some AhLEAs genes come from a common ancestor, and genome rearrangement and translocation occurred among these genomes. Almost all promoters of LEAs contain ABRE, MYB recognition sites, MYC recognition sites, and ERE cis-acting elements, suggesting that the LEA genes were involved in stress response. Gene transcription analyses revealed that most of the LEAs were expressed in the late stages of peanut embryonic development. LEA3 (AH16G06810.1, AH06G03960.1), and Dehydrin (AH07G18700.1, AH17G19710.1) were highly expressed in roots, stems, leaves and flowers. Moreover, 100 AhLEAs were involved in response to drought, low-temperature, or Al stresses. Some LEAs that were regulated by different abiotic stresses were also regulated by hormones including ABA, brassinolide, ethylene and salicylic acid. Interestingly, AhLEAs that were up-regulated by ethylene and salicylic acid showed obvious subfamily preferences. Furthermore, three AhLEA genes, AhLEA1, AhLEA3-1, and AhLEA3-3, which were up-regulated by drought, low-temperature, or Al stresses was proved to enhance cold and Al tolerance in yeast, and AhLEA3-1 enhanced the drought tolerance in yeast. CONCLUSIONS: AhLEAs are involved in abiotic stress response, and segmental duplication plays an important role in the evolution and amplification of AhLEAs. The genome-wide identification, classification, evolutionary and transcription analyses of the AhLEA gene family provide a foundation for further exploring the LEA genes' function in response to abiotic stress in peanuts.

First Report of Stem and Leaf Blight Disease on Mesona chinensis Caused by Rhizoctonia solani in China.

Mesona chinensis is an important medicinal and edible plant resource distributed in eight provinces in southern China. In December 2021, an unknown stem and leaf blight disease was found in M. chinensis cultivation areas in Longzhou County, Guangxi, China. Sixty days after transplanting, the incidence of this disease was 10%. Leaf spots mostly appeared from the leaf edge, were irregular, brown to dark brown, causing more than half of the leaf or the whole leaf to die. The infected stem first showed dark brown spots, then constricted slightly, became necrotic and rotted with the expansion of the spots, resulting in the death of the whole plant. Loose cobweb-like mycelia, which resembled Rhizoctonia, could be seen on the diseased tissues in conditions of high humidity. To identify the pathogen, diseased stems and leaves with typical symptoms from Longzhou County were collected and surface-sterilized with 75% ethanol for 30 s. Small fragments (5×5 mm) at the junction of diseased and healthy tissues were disinfected with 1% NaClO for 1min, washed with sterile water three times, transferred to potato dextrose agar (PDA), and incubated at 28°C for 3 days. Mycelial tips were removed, and six isolates (No. R1-R6) were obtained. The colonies were initially gray white and later light brown. Many nearly round to irregular sclerotia appeared after 7 days of culture. The sclerotia turned from light brown to deep brown and were 1 to 5 mm in diameter. The mycelium branched at a 90° angle, with septa near the branches and a constriction of the mycelium at the base of the branch. These morphological characteristics were consistent with Rhizoctonia. For molecular identification, genomic DNA of the six isolates was obtained using an extraction kit (Biocolor, Shanghai, China), and primers ITS4/ITS5 were used to amplify the internal transcribed spacers (ITS) and 5.8S rRNA (White et al. 1990). A 750 bp DNA fragment was obtained and the sequences were deposited in GenBank (OM095383-OM095388). All isolates had ≥ 99% identity with anastomosis group AG1-1B (HG934429 and HQ185364) of R. solani. A phylogenetic tree showed that the isolates and those from anastomosis group AG1-1B clustered into one branch. To satisfy Koch's postulates, the isolates from diseased leaf (No. R1, R2, and R3) and diseased stem (No. R4, R5, and R6) were inoculated on leaves and stems of 45-day-old M. chinensis plants. Five leaves and stems were inoculated with mycelial plugs of each isolate without wounding and another five leaves and stems were inoculated with mycelial plugs of each isolate after pinprick wounding. Control wounded leaves and stems were inoculated with sterile PDA discs. To maintain high humidity, the plants were incubated at 28°C and covered with transparent plastic covers. Diseased spots first appeared 24 h after inoculation. Three days post-inoculation, all inoculated leaves and stems showed symptoms like those observed in the field, whereas controls were asymptomatic. The pathogen was re-isolated from the diseased inoculated tissues using the method described above, and isolated fungi had the morphological characteristics of R. solani. Thus, the pathogen causing stem and leaf blight disease of M. chinensis was determined to be R. solani. The host range of R. solani is wide, and anastomosis group AG1-1B has been reported to infect plants such as rice, bean, fig, cabbage, and lettuce (Sneh et al. 1991). To our knowledge, this is the first report of R. solani causing a stem and leaf blight on M. chinensis, and provides a basis for diagnosis and control of the disease.

Comparative Transcriptome Analysis Provides Insights into the Resistance in Pueraria [Pueraria lobata (Willd.) Ohwi] in Response to Pseudo-Rust Disease.

Pueraria lobata is an important medicinal and edible homologous plant that is widely cultivated in Asian countries. However, its production and quality are seriously threatened by its susceptibility to pseudo-rust disease. The underlying molecular mechanisms are poorly known, particularly from a transcriptional perspective. Pseudo-rust disease is a major disease in pueraria, primarily caused by Synchytrium puerariae Miy (SpM). In this study, transcriptomic profiles were analyzed and compared between two pueraria varieties: the disease-resistant variety (GUIGE18) and the susceptible variety (GUIGE8). The results suggest that the number of DEGs in GUIGE18 is always more than in GUIGE8 at each of the three time points after SpM infection, indicating that their responses to SpM infection may be different, and that the active response of GUIGE18 to SpM infection may occur earlier than that of GUIGE8. A total of 7044 differentially expressed genes (DEGs) were identified, and 406 co-expressed DEGs were screened out. Transcription factor analysis among the DEGs revealed that the bHLH, WRKY, ERF, and MYB families may play an important role in the interaction between pueraria and pathogens. A GO and KEGG enrichment analysis of these DEGs showed that they were mainly involved in the following pathways: metabolic, defense response, plant hormone signal transduction, MAPK signaling pathway-plant, plant pathogen interaction, flavonoid biosynthesis, phenylpropanoid biosynthesis, and secondary metabolite biosynthesis. The CPK, CESA, PME, and CYP gene families may play important roles in the early stages after SpM infection. The DEGs that encode antioxidase (CAT, XDH, and SOD) were much more up-regulated. Defense enzyme activity, endogenous hormones, and flavonoid content changed significantly in the two varieties at the three infection stages. Finally, we speculated on the regulatory pathways of pueraria pseudo-rust and found that an oxidation-reduction process, flavonoid biosynthesis, and ABA signaling genes may be associated with the response to SpM infection in pueraria. These results expand the understanding of pueraria resistance and physiological regulations by multiple pathways.

Regulatory mechanism of GA3 on tuber growth by DELLA-dependent pathway in yam (Dioscorea opposita).

KEY MESSAGE: Endogenous and exogenous GA3 responses to DoEXP and DoXTH depend on the DoGA20ox1, DoGA3ox1, DoGA2ox3, DoGA2ox4, DoGID1a, and DoDELLA1 to regulate yam tuber growth. Yam tuber undergoes significant alteration in morphogenesis and functions during growth, and gibberellins (GA) are considered potentially important regulators of tuber growth. However, it is little known about the regulation of GA metabolism and GA signaling components genes in tuber growth of yam. In this study, the cloning and expressions of GA3 level, GA metabolism and signaling genes, and cell wall genes in tuber growth in response to GA3 and GA biosynthesis inhibitor paclobutrazol (PP333) treatments were studied. The contents of GA3 accumulated at the tuber growth, with the highest levels in the early expansion stage. DoGA20ox1, DoGA3ox1, and four DoGA2ox genes were significantly abundant in the early expansion stage of tuber and gradually declined along with tuber growth. Three DoGID1 and three DoDELLA genes were showed different expression patterns in the early expansion stage of tuber and gradually declined along with tuber growth. Five DoEXP and three DoXTH genes expression levels were higher in the early expansion stage than in other stages. Exogenous GA3 increased endogenous GA3 levels, whereas the expression levels of DoGA20ox1, DoGA3ox1, DoGID1a, and DoDELLA1 were down-regulated in the early expansion stage of tuber by GA3 treatment, DoGA2ox3 and DoGA2ox4 were up-regulated. PP333 application exhibited opposite consequences. Thus, a mechanism of GA3 regulating yam tuber growth by DELLA-dependent pathway is established.

Genome-wide identification and evolutionary analysis of RLKs involved in the response to aluminium stress in peanut.

BACKGROUND: As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinases play important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogeny, and expression of RLKs in peanut, and no comprehensive analysis of RLKs in the Al stress response in peanuts have been reported. RESULTS: A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLecRLKs were further divided into 24 and 35 subfamilies, respectively. The AhRLKs were randomly distributed across all 20 chromosomes in the peanut. Among these AhRLKs, 9.53% and 61.78% originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 96.97% (96/99) of tandem duplication gene pairs and 98.78% (646/654) of segmental duplication gene pairs were less than 1. Among the tested tandem duplication clusters, there were 28 gene conversion events. Moreover, all total of 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of the Al-responsive AhRLKs that clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analysed, and tissue-specifically expressed genes, including 14 root-specific Al-responsive AhRLKs were found. In addition, all 90 Al-responsive AhRLKs which were distributed unevenly in the subfamilies of AhRLKs, showed different expression patterns between the two peanut varieties (Al-sensitive and Al-tolerant) under Al stress. CONCLUSIONS: In this study, we analysed the RLK gene family in the peanut genome. Segmental duplication events were the main driving force for AhRLK evolution, and most AhRLKs subject to purifying selection. A total of 90 genes were identified as Al-responsive AhRLKs, and the classification, conserved motifs, structures, tissue expression patterns and predicted functions of Al-responsive AhRLKs were further analysed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs and Al-responsive AhRLKs.

Interface Engineering Ti3 C2 MXene/Silicon Self-Powered Photodetectors with High Responsivity and Detectivity for Weak Light Applications.

Interfacial engineering and heterostructures designing are two efficient routes to improve photoelectric characteristics of a photodetector. Herein, a Ti3 C2 MXene/Si heterojunction photodetector with ultrahigh specific detectivity (2.03 × 1013 Jones) and remarkable responsivity (402 mA W-1 ) at zero external bias without decline as with increasing the light power is reported. This is achieved by chemically regrown interfacial SiOx layer and the control of Ti3 C2 MXene thickness to suppress the dark noise current and improve the photoresponse. The photodetector demonstrates a high light on/off ratio of over 106 , an outstanding peak external quantum efficiency (EQE) of 60.3%, while it maintains an ultralow dark current at 0 V bias. Moreover, the device holds high performance with EQE of over 55% even after encapsulated with silicone, trying to resolve the air stability issue of Ti3 C2 MXene. Such a photodetector with high detectivity, high responsivity, and self-powered capability is particularly applicable to detect weak light signal, which presents high potential for imaging, communication and sensing applications.

Sugarcane/peanut intercropping system improves the soil quality and increases the abundance of beneficial microbes.

Sugarcane/peanut intercropping is a highly efficient planting pattern in South China. However, the effects of sugarcane/peanut intercropping on soil quality need to be clarified. This study characterized the soil microbial community and the soil quality in sugarcane/peanut intercropping systems by the Illumina MiSeq platform. The results showed that the intercropping sugarcane (IS) system significantly increased the total N (TN), available N (AN), available P (AP), pH value, and acid phosphatase activity (ACP), but it had little effect on the total P (TP), total K (TK), available K (AK), organic matter (OM), urease activity, protease activity, catalase activity, and sucrase activity, compared with those in monocropping sugarcane (MS) and monocropping peanut (MP) systems. Both intercropping peanut (IP) and IS soils contained more bacteria and fungi than soils in the MP and MS fields, and the microbes identified were mainly Chloroflexi and Acidobacteria, respectively. Intercropping significantly increased the number of unique microbes in IS soils (68 genera), compared with the numbers in the IP (14), MS (17), and MP (16) systems. The redundancy analysis revealed that the abundances of culturable Acidobacteriaceae subgroup 1, nonculturable DA111, and culturable Acidobacteria were positively correlated with the measured soil quality in the intercropping system. Furthermore, the sugarcane/peanut intercropping significantly increased the economic benefit by 87.84% and 36.38%, as compared with that of the MP and MS, respectively. These results suggest that peanut and sugarcane intercropping increases the available N and P content by increasing the abundance of rhizospheric microbes, especially Acidobacteriaceae subgroup 1, DA111, and Acidobacteria.

Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut.

Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response.

Integrated mRNA and miRNA transcriptome analysis reveals a regulatory network for tuber expansion in Chinese yam (Dioscorea opposita).

BACKGROUND: Yam tuber is a storage organ, derived from the modified stem. Tuber expansion is a complex process, and depends on the expressions of genes that can be influenced by environmental and endogenous factors. However, little is known about the regulatory mechanism of tuber expansion. In order to identify the genes and miRNAs involved in tuber expansion, we examined the mRNAs and small RNAs in Dioscorea opposita (Chinese yam) cv. Guihuai 16 tuber during its initiation and expansion stages. RESULTS: A total of 14,238 differentially expressed genes in yam tuber at its expansion stage were identified by using RNA sequencing technology. Among them, 5723 genes were up-regulated, and 8515 genes were down-regulated. Functional analysis revealed the coordination of tuber plant involved in processes of cell events, metabolism, biosynthesis, and signal transduction pathways at transcriptional level, suggesting that these differentially expressed genes are somehow involved in response to tuber expansion, including CDPK, CaM, CDL, SAUR, DELLA, SuSy, and expansin. In addition, 541 transcription factor genes showed differential expression during the expansion stage at transcriptional level. MADS, bHLH, and GRAS were involved in cell differentiation, division, and expansion, which may relate to tuber expansion. Noteworthy, data analysis revealed that 22 known tuber miRNAs belong to 10 miRNA families, and 50 novel miRNAs were identified. The integrated analysis of miRNA-mRNA showed that 4 known miRNAs and 11 genes formed 14 miRNA-target mRNA pairs were co-expressed in expansion stage. miRNA160, miRNA396, miRNA535 and miRNA5021 may be involved in complex network to regulate cell division and differentiation in yam during its expansion stage. CONCLUSION: The mRNA and miRNA datasets presented here identified a subset of candidate genes and miRNAs that are putatively associated with tuber expansion in yam, a hypothetical model of genetic regulatory network associated with tuber expansion in yam was put forward, which may provide a foundation for molecular regulatory mechanism researching on tuber expansion in Dioscorea species.

Cassava/peanut intercropping improves soil quality via rhizospheric microbes increased available nitrogen contents.

BACKGROUND: Intercropping, an essential cultivation pattern in modern agricultural systems, increases crop yields and soil quality. Cassava and peanut intercropping systems exhibit advantages in solar utilization and cadmium absorption, etc. However, the inner mechanisms need to be elucidated. In this study, Illumina MiSeq platform was used to reveal the rhizospheric microbes and soil quality in cassava/peanut intercropping systems, and the results provided a reference for the application of this method in studying other intercropping systems. RESULTS: Both intercropping cassava/peanut (IP) and intercropping peanut/cassava (IC) systems significantly increased available N, available K, pH value, and urease activity, comparing with that in monocropping cassava (MC) and monocropping peanut (MP) system. However, there were few effects on the total N, total P, total K, available P, organic matter, protease activity, catalase activity, sucrase activity, and acid phosphatase activity. Both IP and MP soils contained more bacteria and fungi than those in the IC and MC soils, which were mainly made of Proteobacteria and Actinobacteria. Intercropping remarkably increased the number of Nitrospirae in IP and IC soils comparing those in MC and MP soils. Redundancy analysis (RDA) revealed that the abundances of DA101, Pilimelia, and Ramlibacter were positively correlated to the soil quality. These results suggest that intercropping enhances the available nitrogen content of soil through increasing the quantity of rhizospheric microbes, especially that of DA101 and Pilimelia. CONCLUSIONS: The cassava/peanut intercropping system improves soil quality through increasing the available nitrogen content and abundance of DA101, Pilimelia, and Ramlibacter in the soil.

Crosstalk between melatonin and nitric oxide in plant development and stress responses.

Melatonin is widely involved in plant growth and stress responses as a master regulator. Melatonin treatment alters the levels of endogenous nitric oxide (NO) and NO affects endogenous melatonin content. Melatonin and NO may induce various plant physiological behavior through interaction mechanism. However, the interactions between melatonin and NO in plants are largely unknown. The review presented the metabolism of endogenous melatonin and NO and their relationship in plants. The interactions between melatonin and NO in plant growth and development and responses to environmental stress were summarized. The molecular mechanisms of interaction between melatonin and NO in plants were also proposed.

Genome-wide analysis of the MATE gene family in potato.

The multidrug and toxic compound extrusion (MATE) protein family is a newly discovered family of secondary transporters that extrude metabolic waste and a variety of antibiotics out of the cell using an electrochemical gradient of H+ or Na+ across the membrane. The main function of MATE gene family is to participate in the process of plant detoxification and morphogenesis. The genome-wide analysis of the MATE genes in potato genome was conducted. At least 48 genes were initially identified and classified into six subfamilies. The chromosomal localization of MATE gene family showed that they could be distributed on 11 chromosomes except chromosome 9. The number of amino acids is 145-616, the molecular weight of proteins is 15.96-66.13 KD, the isoelectric point is 4.97-9.17, and they were located on the endoplasmic reticulum with having 4-13 transmembrane segments. They contain only two parts of the exons and UTR without introns. Some members of the first subfamily of potato MATE gene family are clustered with At2g04070 and they may be related to the transport of toxic compounds such as alkaloids and heavy metal. The function of the members of the second subfamily may be similar to that of At3g23560, which is related to tetramethylammonium transport. Some members of the third subfamily are clustered with At3g59030 and they may be involved in the transport of flavonoids. The fifth subfamily may be related to the transport of iron ions. The function of the sixth subfamily may be similar to that of At4g39030, which is related to salicylic acid transport. There are three kinds of conserved motifs in potato MATE genes, including the motif 1, motif 2, and motif 3. Each motif has 50 amino acids. The number of each motif is different in the gene sequence, of which 45 MATE genes contain at least a motif, but there is no motif in ST0015301, ST0045283, and ST0082336. These results provide a reference for further research on the function of potato MATE genes.