MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.
Nitrogen is a critical nutrient vital for crop growth. However, our current understanding of nitrogen use efficiency (NUE) under drought remains inadequate. To delve into the molecular mechanisms underlying NUE under drought, a transcriptome and physiological co-expression analysis was performed in rice, which is particularly sensitive to drought. We conducted a pot experiment using rice grown under normal irrigation, mild drought stress, and severe drought stress. Compared to the normal treatment, drought stress led to a significant reduction in NUE across growth stages, with decreases ranging from 2.18% to 31.67%. Totals of 4,424 and 2,452 genes were identified as NUE-related DEGs that showed differential expressions (DEGs) and significantly correlated with NUE (NUE-related) under drought in the vegetative and reproductive stages, respectively. Interestingly, five genes involved in nitrogen metabolism were found in the overlapped genes of these two sets. Furthermore, the two sets of NUE-related DEGs were enriched in glyoxylate and dicarboxylate metabolism, as well as carbon fixation in photosynthetic organisms. Several genes in these two pathways were identified as hub genes in the two sets of NUE-related DEGs. This study offers new insights into the molecular mechanism of rice NUE under drought in agricultural practices and provides potential genes for breeding drought-resistant crops with high NUE.
Abstract miR156 play important roles in regulation of plant growth and development, secondary metabolite synthesis and other biological processes by targeting the SQUAMOSA promoter binding protein-like (SPL) family. Our previous sequencing data analysis suggested that Csn-miR156d may regulate flowering and anthocyanin accumulation by cleavage and degradation of the expression of the SPL in tea plant, but it remains to be elucidated. In this study, 5′RLM-RACE experiment, tobacco transient transformation, qRT-PCR and antisense oligonucleotide (asODN) were used to verify that CsSPL1 is the target gene of Csn-miR156d. Stable transformation of Arabidopsis revealed that Csn-miR156d could delay flowering by negatively regulating the transcript levels of FT, AP1, FUL and SOC1, while overexpression of CsSPL1 showed an opposite effect. Additionally, overexpression of Csn-miR156d in Arabidopsis could enhance the transcription of the anthocyanin biosynthesis-related structural genes DFR, ANS, F3H, UGT78D2 and LDOX, as well as regulatory genes PAP1, MYB113, GL3, MYB11 and MYB12, leading to anthocyanin accumulation. Moreover, asODN experiment revealed that Csn-miR156d could increase the anthocyanin content in tea plant. These results suggest that Csn-miR156d regulates flowering and anthocyanin accumulation in tea plant by suppressing the expression of CsSPL1. Our study provides new insights into the development and anthocyanin accumulation in tea plant and lays a theoretical foundation for further research on the molecular mechanism of miRNAs in regulating tea plant growth and secondary metabolism.
To establish a quality classification standard for Aucklandia lappa.Seed purity, 1 000-grain weight, germination rate, water content of 37 seed samples from different areas were measured, and seed external characters were observed. The cluster analysis was applied for establishment of the primary quality classification standard of A. lappa seed.The seed quality grading of A. lappa was described as three grades. The seed quality of each grade should reach following requirements: for first grade seeds, seed germination rate > or = 85%, purity > or = 99%, 1 000-grain weight > or = 26.0 g, water content < or = 8.8%; for second grade seeds, seed germination rate > or = 70%, purity > or = 98%, 1 000-grain weight > or = 23.8 g, water content < or = 10%; for third grade seeds, seed germination rate > or = 50%, purity > or = 96%, 1 000-grain weight > or = 23.0 g, water content < or = 11%.This quality classification standard of A. lappa can be used as the quality control standard of A. lappa.
Plant Trihelix transcription factors, specifically bind to GT elements and play important roles in plant physiology and development. Wheat is a main cereal crop. Brachypodium distachyon is a close relative of wheat and has been described as a new model species for studying of grass functional genomics. Presently, little is known about wheat and B. distachyon Trihelix genes. In 51 species, 2387 Trihelix genes were identified, including 80 wheat Trihelix genes and 27 B. distachyon Trihelix genes. Consistent with the results of previous studies, these genes were classified into five subfamilies: GT-1, GT-2, SIP1, GTγ, and SH4. Members of the same subfamily shared similar gene structures and common motifs. Most TaGT and BdGT genes contained many kinds of cis-elements, such as development-, stress-, and phytohormone-related cis-acting elements. Additionally, 21 randomly selected TaGT genes were mainly expressed in the roots and flowers, while the expression of 19 selected BdGT genes was constitutive. These results indicate that the roles of Trihelix genes in wheat and B. distachyon might have diversified during the evolutionary process. The expression of the most selected TaGT and BdGT genes was down-regulated when exposed to low temperatures, NaCl, ABA, and PEG, implying that TaGT and BdGT genes negatively respond to abiotic stress. On the contrary, the expression of some genes was up-regulated under heat stress. Trihelix genes exist extensively in plants and have many functions. During the evolutionary process, this gene family expanded and their functions diversified. As a result, the expression pattern and functions of members of the same family might be different. This study lays a foundation for further functional analyses of TaGT and BdGT genes.
Histone methylation plays an important regulatory role in the drought response of many plants, but its regulatory mechanism in the drought response of the tea plant remains poorly understood. Here, drought stress was shown to induce lower relative water content and significantly downregulate the methylations of histone H3K4 in the tea plant. Based on our previous analysis of the SET Domain Group (SDG) gene family, the full-length coding sequence (CDS) of CsSDG36 was cloned from the tea cultivar ‘Fuding Dabaicha’. Bioinformatics analysis showed that the open reading frame (ORF) of the CsSDG36 gene was 3138 bp, encoding 1045 amino acids and containing the conserved structural domains of PWWP, PHD, SET and PostSET. The CsSDG36 protein showed a close relationship to AtATX4 of the TRX subfamily, with a molecular weight of 118,249.89 Da, and a theoretical isoelectric point of 8.87, belonging to a hydrophilic protein without a transmembrane domain, probably located on the nucleus. The expression of CsSDG36 was not detected in the wild type, while it was clearly detected in the over-expression lines of Arabidopsis. Compared with the wild type, the over-expression lines exhibited lower hyperosmotic resistance by accelerating plant water loss, increasing reactive oxygen species (ROS) pressure, and increasing leaf stomatal density. RNA-seq analysis suggested that the CsSDG36 overexpression caused the differential expression of genes related to chromatin assembly, microtubule assembly, and leaf stomatal development pathways. qRT-PCR analysis revealed the significant down-regulation of stomatal development-related genes (BASL, SBT1.2(SDD1), EPF2, TCX3, CHAL, TMM, SPCH, ERL1, and EPFL9) in the overexpression lines. This study provides a novel sight on the function of histone methyltransferase CsSDG36 under drought stress.
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