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Ethylene plays a pivotal role in plant stress resistance and 1-aminocyclopropane-1-carboxylic acid synthase (ACS) is the rate-limiting enzyme in ethylene biosynthesis. Upland cotton (Gossypium hirsutum L.) is the most important natural fiber crop, but the function of ACS in response to abiotic stress has rarely been reported in this plant. We identified 18 GaACS, 18 GrACS, and 35 GhACS genes in Gossypiumarboreum, Gossypium raimondii and Gossypiumhirsutum, respectively, that were classified as types I, II, III, or IV. Collinearity analysis showed that the GhACS genes were expanded from diploid cotton by the whole-genome-duplication. Multiple alignments showed that the C-terminals of the GhACS proteins were conserved, whereas the N-terminals of GhACS10 and GhACS12 were different from the N-terminals of AtACS10 and AtACS12, probably diverging during evolution. Most type II ACS genes were hardly expressed, whereas GhACS10/GhACS12 were expressed in many tissues and in response to abiotic stress; for example, they were highly and hardly expressed at the early stages of cold and heat exposure, respectively. The GhACS genes showed different expression profiles in response to cold, heat, drought, and salt stress by quantitative PCR analysis, which indicate the potential roles of them when encountering the various adverse conditions, and provide insights into GhACS functions in cotton’s adaptation to abiotic stress.

FKBP10, a member of the FK506-binding protein (FKBP) family, has been implicated in cancer development, although its prognostic function remains controversial. In this study, we analyzed the expression of FKBP10 in tumor tissues using online databases (TCGA) as well as our CRC cohort, and investigated the relationship between its subcellular expression pattern and patient outcomes. Cox regression analysis was used to determine the associations between different subcellular expression patterns of FKBP10 and clinical features of patients. We also discussed the expression level of FKBP10 based on different subcellular expression patterns. Our results showed that FKBP10 was significantly elevated in CRC tissues and exhibited three different subcellular expression patterns which were defined as ‘FKBP10-C’ (concentrated), ‘FKBP10-T’ (transitional) and ‘FKBP10-D’ (dispersive). The FKBP10-D expression pattern was only found in tumor tissues and was associated with unfavorable disease-free survival in CRC patients. High expression levels of FKBP10-C predicted an unfavorable prognosis of recurrence of CRC, while FKBP10-D did not. Our findings suggest that the subcellular expression patterns and expression level of FKBP10 play crucial prognostic roles in CRC, which revealed that FKBP10 may be a viable prognostic and therapeutic target for the diagnosis and treatment of CRC.

The red-necked longicorn beetle, Aromia bungii (Faldermann) (Coleoptera: Cerambycidae), is a major destructive, wood-boring pest, which is widespread throughout the world. The sex pheromone of A. bungii was reported earlier; however, the chemosensory mechanism of the beetle remains almost unknown. In this study, 45 AbunORs, 6 AbunGRs and 2 AbunIRs were identified among 42,197 unigenes derived from the antennal transcriptome bioinformatic analysis of A. bungii adults. The sequence of putative Orco (AbunOR25) found in this study is highly conserved with the known Orcos from other Coleoptera species, and these Orco genes might be potentially used as target genes for the future development of novel and effective control strategies. Tissue expression analysis showed that 29 AbunOR genes were highly expressed in antennae, especially in the antennae of females, which was consistent with the idea that females might express more pheromone receptors for sensing pheromones, especially the sex pheromones produced by males. AbunOR5, 29, 31 and 37 were clustered with the pheromone receptors of the cerambycid Megacyllene caryae, suggesting that they might be putative pheromone receptors of A. bungii. All six AbunGRs were highly expressed in the mouthparts, indicating that these GRs may be involved in the taste perception process. Both AbunIRs were shown to be female-mouthparts-biased, suggesting that they might also be related to the tasting processes. Our study provides some basic information towards a deeper understanding of the chemosensing mechanism of A. bungii at a molecular level.

Alternanthera philoxeroides is a notorious invasive weed worldwide, but it still lacks a genome information currently. In this study, we collected 4 groups of A. philoxeroides Illumina RNA-seq data (62.5 Gb) and performed a comprehensive de novo assembling. Totally, 421,372 unigenes were obtained with a total length of 230,842,460 bp, with 43,430 (10.31%) unigenes longer than 1000 bp. Then 119,222 (28.3%) unigenes were functional annotated and 235,885 (56.0%) were grouped into reliable lncRNAs reservoir. Besides, 534 tRNA and 234 rRNAs were identified in assembly sequences. Additionally, 131,624 microsatellites were characterized in 106,761 sequences. Then SSR primers were developed for the amplification of 40,752 microsatellites in 36,329 sequences. The miRNAs are key post-transcriptional regulators, about 86 candidate miRNA sequences were detected from A. philoxeroides assembly, and miRNA target genes prediction revealed possible functions of them in growth and development as well as stress responding processes. These results provide a vital basis for sequence-based studies of A. philoxeroides in the future, especially gene function analysis.

Moths can biosynthesize sex pheromones in the female sex pheromone glands (PGs) and can distinguish species-specific sex pheromones using their antennae. However, the biosynthesis and transportation mechanism for Type II sex pheromone components has rarely been documented in moths. In this study, we constructed a massive PG transcriptome database (14.72 Gb) from a moth species, Ectropis grisescens, which uses type II sex pheromones and is a major tea pest in China. We further identified putative sex pheromone biosynthesis and transportation-related unigenes: 111 cytochrome P450 monooxygenases (CYPs), 25 odorant-binding proteins (OBPs), and 20 chemosensory proteins (CSPs). Tissue expression and phylogenetic tree analyses showed that one CYP (EgriCYP341-fragment3), one OBP (EgriOBP4), and one CSP (EgriCSP10) gene displayed an enriched expression in the PGs, and that EgriOBP2, 3, and 25 are clustered in the moth pheromone-binding protein clade. We considered these our candidate genes. Our results yielded large-scale PG sequence information for further functional studies.

Background WRKY proteins comprise a large family of transcription factors that play important roles in many aspects of physiological processes and adaption to environment. However, little information was available about the WRKY genes in pineapple ( Ananas comosus ), an important tropical fruits. The recent release of the whole-genome sequence of pineapple allowed us to perform a genome-wide investigation into the organization and expression profiling of pineapple WRKY genes. Results In the present study, 54 pineapple WRKY (AcWRKY) genes were identified and renamed on the basis of their respective chromosome distribution. According to their structural and phylogenetic features, the 54 AcWRKYs were further classified into three main groups with several subgroups. The segmental duplication events played a major role in the expansion of pineapple WRKY gene family. Synteny analysis and phylogenetic comparison of group III WRKY genes provided deep insight into the evolutionary characteristics of pineapple WRKY genes. Expression profiles derived from transcriptome data and real-time quantitative PCR analysis exhibited distinct expression patterns of AcWRKY genes in various tissues and in response to different abiotic stress and hormonal treatments. Conclusions Fifty four WRKY genes were identified in pineapple and the structure of their encoded proteins, their evolutionary characteristics and expression patterns were examined in this study. This systematic analysis provided a foundation for further functional characterization of WRKY genes with an aim of pineapple crop improvement.

Chamaemelum nobile is a traditional Chinese herbal medicine, whose secondary metabolites used in the pharmacology of Chinese medicine. Among them, the flavonoids have great research value. Flavanone 3-hydroxylase (F3H) is one of the core enzymes in the early steps of flavonoid biosynthesis. This study aimed to elucidate the structures, functions, and expression levels of F3H families from C. nobile. Four members of the F3H family were screened from C. nobile transcriptome data and performed bioinformatics analysis. Results showed that CnF3H1~4 had a high similarity with the other F3H plants, and all genes contained two conserved isopenicillin N synthase-like and oxoglutarate/iron-dependent dioxygenase domains. Further analysis revealed that the four CnF3H proteins contained some differences in binding sites. The results of secondary and 3-D structures displayed that the composition and proportion of the four CnF3H secondary structures were basically the same, and their 3D structures were consistent with the secondary structures. The phylogenetic tree displayed that CnF3H2, CnF3H3, and CnF3H4 were grouped with Asteraceae. The expression patterns of CnF3Hs in the roots, stems, leaves, and flowers of C. nobile were evaluated using the value of RPKM. The results indicated that CnF3Hs had significant difference in the expression of different tissues. Especially, CnF3H1~3 and CnF3H4 had the highest expression levels in the flowers and roots, respectively. Hence, CnF3Hs played a significant role in the flavonoid metabolism.

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.

The C2H2 zinc finger protein (C2H2-ZFP) is a large transcription factor (TF) in plants, widely distributed across plants and playing crucial roles in growth, development, and responses to abiotic stress. However, most studies on the C2H2-ZFP gene family have mainly focused on model plants. In this study, we systematically identified the C2H2-ZFP gene family members in Populus euphratica , a tree species with high tolerance to salt and alkali stress, by analyzing gene localizations, conserved motifs, gene structures, and phylogenetic relationships. A total of 67 members of the P. euphratica C2H2-ZFP gene family were identified and were divided into five subfamilies. Promoter analysis revealed numerous cis-acting elements related to development, hormones, and abiotic stress. Both tandem and segmental duplications were identified as the main driving forces behind the expansion of the PeZFP gene family. Expression profiling showed that most PeZFPs exhibit tissue-specific expression patterns and respond to salt stress. Among them, PeZFP38 was strongly induced by salt stress in roots, stems, and leaves, with expression levels increased by 4.3–10.2-fold, 6–10.4-fold, and 28–63.7-fold, respectively. Subcellular localization demonstrated that PeZFP38 is a nuclear protein. Functional assays showed that transient overexpression of PeZFP38 in poplar leaves enhanced salt tolerance, and stable overexpression of PeZFP38 in Arabidopsis thaliana increased biomass (~68% fresh weight), enhanced antioxidant enzyme activities (e.g., SOD activity reached 1.7-fold that of WT), and reduced oxidative damage (~30% MDA decrease). These results suggest that PeZFP38 may play a role in enhancing salt tolerance by integrating ABA signaling with ROS scavenging systems. Collectively, this study systematically deciphers the evolutionary relationships and expression patterns of the C2H2-ZFP family in P. euphratica . For the first time, it functionally identifies the positive regulatory role of PeZFP38 in salt stress response. These findings provide novel genetic resources and a theoretical basis for understanding stress resistance mechanisms and genetic improvement in forest trees.

Background GRAS is a family of plant-specific transcription factors (TFs) that play a vital role in plant growth and development and response to adversity stress. However, systematic studies of the GRAS TF family in kiwifruit have not been reported. Results In this study, we used a bioinformatics approach to identify eighty-six AcGRAS TFs located on twenty-six chromosomes and phylogenetic analysis classified them into ten subfamilies. It was found that the gene structure is relatively conserved for these genes and that fragmental duplication is the prime force for the evolution of AcGRAS genes. However, the promoter region of the AcGRAS genes mainly contains cis-acting elements related to hormones and environmental stresses, similar to the results of GO and KEGG enrichment analysis, suggesting that hormone signaling pathways of the AcGRAS family play a vital role in regulating plant growth and development and adversity stress. Protein interaction network analysis showed that the AcGRAS51 protein is a relational protein linking DELLA, SCR, and SHR subfamily proteins. The results demonstrated that 81 genes were expressed in kiwifruit AcGRAS under salt stress, including 17 differentially expressed genes, 13 upregulated, and four downregulated. This indicates that the upregulated AcGRAS55 , AcGRAS69 , AcGRAS86 and other GRAS genes can reduce the salt damage caused by kiwifruit plants by positively regulating salt stress, thus improving the salt tolerance of the plants. Conclusions These results provide a theoretical basis for future exploration of the characteristics and functions of more AcGRAS genes. This study provides a basis for further research on kiwifruit breeding for resistance to salt stress. RT-qPCR analysis showed that the expression of 3 AcGRAS genes was elevated under salt stress, indicating that AcGRAS exhibited a specific expression pattern under salt stress conditions.