Transcriptome-wide Identification Research Articles

Transcriptome-wide identification of the Hsp70 gene family in Pugionium cornutum and functional analysis of PcHsp70-5 under drought stress.

The PcHsp70-5 enhances drought stress tolerance in transgenic Arabidopsis thaliana by upregulating stress tolerance genes and antioxidant enzyme activities. Heat shock proteins (HSPs) constitute a class of evolutionarily conserved proteins synthesized by organisms in response to various adverse environmental stimuli such as elevated temperatures, drought, hormonal fluctuations, high salt concentrations, and mechanical stress. However, research on HSPs has predominantly focused on model plants and crops, whereas their functions in desert plants have not been well investigated. This study analyzed the transcriptome of Pugionium cornutum and identified the complete ORFs of 25 genes of the PcHsp70 family genes. Their expression levels under drought stress were investigated using existing RNA-seq data. PcHsp70-5 genes exhibited high expression levels in both roots and leaves under drought stress. Consequently, the PcHsp70-5 genes were cloned and transformed into Arabidopsis thaliana for further analysis of their roles in drought stress response. Real-time fluorescence quantitative PCR (qRT-PCR) analysis demonstrated that both, drought stress and ABA, induced PcHsp70-5 expression. Under drought conditions, transgenic Arabidopsis plants exhibited markedly enhanced growth compared to wild-type plants, as evidenced by improved survival rates, root length, fresh weight, chlorophyll content, and reduced levels of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in leaves, indicating that PcHsp70-5 overexpression mitigated growth inhibition and oxidative damage induced by drought stress. Subsequent research revealed that PcHsp70-5 overexpression significantly augmented the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and increased the proline content in transgenic Arabidopsis under drought conditions, alongside a significant increase in the expression levels of genes related to stress tolerance. This suggests that PcHsp70-5 enhances drought stress tolerance in transgenic Arabidopsis by upregulating stress tolerance genes and antioxidant enzyme activities.

Transcriptome-Wide Identification of Dark- and Salt-Induced Senescence-Related NAC Gene Family Members in Alfalfa.

Leaves are a key forage part for livestock, and the aging of leaves affects forage biomass and quality. Preventing or delaying premature leaf senescence leads to an increase in pasture biomass accumulation and an improvement in alfalfa quality. NAC transcription factors have been reported to affect plant growth and abiotic stress responses. In this study, 48 NAC genes potentially associated with leaf senescence were identified in alfalfa under dark or salt stress conditions. A phylogenetic analysis divided MsNACs into six subgroups based on similar gene structure and conserved motif. These MsNACs were unevenly distributed in 26 alfalfa chromosomes. The results of the collinearity analysis show that all of the MsNACs were involved in gene duplication. Some cis-acting elements related to hormones and stress were screened in the 2-kb promoter regions of MsNACs. Nine of the MsNAC genes were subjected to qRT-PCR to quantify their expression and Agrobacterium-mediated transient expression to verify their functions. The results indicate that Ms.gene031485, Ms.gene032313, Ms.gene08494, and Ms.gene77666 might be key NAC genes involved in alfalfa leaf senescence. Our findings extend the understanding of the regulatory function of MsNACs in leaf senescence.

Transcriptome-Wide Identification of m6A Writers, Erasers and Readers and Their Expression Profiles under Various Biotic and Abiotic Stresses in Pinus massoniana Lamb.

N6-methyladenosine (m6A) RNA modification is the most prevalent form of RNA methylation and plays a crucial role in plant development. However, our understanding of m6A modification in Masson pine (Pinus massoniana Lamb.) remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in Masson pine was performed, and 22 m6A regulatory genes were identified in total, including 7 m6A writers, 7 m6A erases, and 8 readers. Phylogenetic analysis revealed that all m6A regulators involved in Masson pine could be classified into three distinct groups based on their domains and motifs. The tissue expression analysis revealed that the m6A regulatory gene may exert a significant influence on the development of reproductive organs and leaves in Masson pine. Moreover, the results from stress and hormone expression analysis indicated that the m6A regulatory gene in Masson pine might be involved in drought stress response, ABA-signaling-pathway activation, as well as resistance to Monochamus alternatus. This study provided valuable and anticipated insights into the regulatory genes of m6A modification and their potential epigenetic regulatory mechanisms in Masson pine.

Systematic identification and validation of the reference genes from 447 transcriptome datasets of moso bamboo (Phyllostachys edulis)

Bamboo was one of the first plants to be cultivated in China and is widely used in industry and daily life. The study of gene function has become an important part of bamboo breeding, whereas quantitative real-time PCR (qRT-PCR) is a powerful tool for gene expression analysis. The accuracy of qRT-PCR results largely depends on suitable reference genes. In this study, a transcriptome-wide identification of reference genes was conducted based on 447 transcriptome datasets, comprising 200 tissue samples, 107 treated samples, and 140 samples from various moso bamboo (Phyllostachys edulis) forms. A total of 3444, 1013, and 3962 stably expressed genes were identified from these three groups, respectively. Functional enrichment analysis revealed significant enrichment of these genes in pathways, including the spliceosome, proteasome, and oxidative phosphorylation. Eight candidate genes (ADPRE, GAPDH, TRX, TUBA, NRP, MBF, UNK, and CAM1), were selected for qRT-PCR validation using 112 samples. To assess their stability, five statistical methods (geNorm, NormFinder, BestKeeper, Delta-Ct, and RefFinder) were employed. The most suitable reference genes were ADPRE and GAPDH for different tissues, GAPDH and CAM1 for different treatments, and GAPDH and TRX for various moso bamboo forms. Overall, ADPRE and GAPDH were the most stable reference genes across all conditions, while TUBA and TRX were the least stable reference genes. In addition, a significant negative correlation was found between the Ct values of RT-qPCR and the log2TPM values from the transcriptome data (Ct = −1.534x + 37.221), providing a potential method for estimating gene expression levels. The identified reference genes, particularly ADPRE and GAPDH, provide a robust set of references for gene expression studies in moso bamboo.

Transcriptome-wide identification of ARF gene family in medicinal plant Polygonatum kingianum and expression analysis ofPkARF members in different tissues.

Polygonatum kingianum holds significant importance in Traditional Chinese Medicine due to its medicinal properties, characterized by its diverse chemical constituents including polysaccharides, terpenoids, flavonoids, phenols, and phenylpropanoids. The Auxin Response Factor (ARF) is a pivotal transcription factor known for its regulatory role in both primary and secondary metabolite synthesis. However, our understanding of the ARF gene family in P. kingianum remains limited. We employed RNA-Seq to sequence three distinct tissues (leaf, root, and stem) of P. kingianum. The analysis revealed a total of 31,558 differentially expressed genes (DEGs), with 43 species of transcription factors annotated among them. Analyses via gene ontology and the Kyoto Encyclopedia of Genes and Genomes demonstrated that these DEGs were predominantly enriched in metabolic pathways and secondary metabolite biosynthesis. The proposed temporal expression analysis categorized the DEGs into nine clusters, suggesting the same expression trends that may be coordinated in multiple biological processes across the three tissues. Additionally, we conducted screening and expression pattern analysis of the ARF gene family, identifying 12 significantly expressed PkARF genes in P. kingianum roots. This discovery lays the groundwork for investigations into the role of PkARF genes in root growth, development, and secondary metabolism regulation. The obtained data and insights serve as a focal point for further research studies, centred on genetic manipulation of growth and secondary metabolism in P. kingianum. Furthermore, these findings contribute to the understanding of functional genomics in P. kingianum, offering valuable genetic resources.

Transcriptome-wide identification of microRNAs regulating plant immunity in Gossypium arboreum L.

Transcriptome-wide identification of microRNAs regulating plant immunity in Gossypium arboreum L.

A transcriptome-wide identification of ATP-binding cassette (ABC) transporters revealed participation of ABCB subfamily in abiotic stress management of Glycyrrhiza glabra L

Transcriptome-wide survey divulged a total of 181 ABC transporters in G. glabra which were phylogenetically classified into six subfamilies. Protein–Protein interactions revealed nine putative GgABCBs (-B6, -B14, -B15, -B25, -B26, -B31, -B40, -B42 &-B44) corresponding to five AtABCs orthologs (-B1, -B4, -B11, -B19, &-B21). Significant transcript accumulation of ABCB6 (31.8 folds), -B14 (147.5 folds), -B15 (17 folds), -B25 (19.7 folds), -B26 (18.31 folds), -B31 (61.89 folds), -B40 (1273 folds) and -B42 (51 folds) was observed under the influence of auxin. Auxin transport-specific inhibitor, N-1-naphthylphthalamic acid, showed its effectiveness only at higher (10 µM) concentration where it down regulated the expression of ABCBs, PINs (PIN FORMED) and TWD1 (TWISTED DWARF 1) genes in shoot tissues, while their expression was seen to enhance in the root tissues. Further, qRT-PCR analysis under various growth conditions (in-vitro, field and growth chamber), and subjected to abiotic stresses revealed differential expression implicating role of ABCBs in stress management. Seven of the nine genes were shown to be involved in the stress physiology of the plant. GgABCB6, 15, 25 and ABCB31 were induced in multiple stresses, while GgABCB26, 40 & 42 were exclusively triggered under drought stress. No study pertaining to the ABC transporters from G. glabra is available till date. The present investigation will give an insight to auxin transportation which has been found to be associated with plant growth architecture; the knowledge will help to understand the association between auxin transportation and plant responses under the influence of various conditions.

Transcriptome-Wide Identification and Integrated Analysis of a UGT Gene Involved in Ginsenoside Ro Biosynthesis in Panax ginseng.

Panax ginseng as a traditional medicinal plant with a long history of medicinal use. Ginsenoside Ro is the only oleanane-type ginsenoside in ginseng, and has various pharmacological activities, including anti-inflammatory, detoxification, and antithrombotic activities. UDP-dependent glycosyltransferase (UGT) plays a key role in the synthesis of ginsenoside, and the excavation of UGT genes involved in the biosynthesis of ginsenoside Ro has great significance in enriching ginsenoside genetic resources and further revealing the synthesis mechanism of ginsenoside. In this work, ginsenoside-Ro-synthesis-related genes were mined using the P. ginseng reference-free transcriptome database. Fourteen hub transcripts were identified by differential expression analysis and weighted gene co-expression network analysis. Phylogenetic and synteny block analyses of PgUGAT252645, a UGT transcript among the hub transcripts, showed that PgUGAT252645 belonged to the UGT73 subfamily and was relatively conserved in ginseng plants. Functional analysis showed that PgUGAT252645 encodes a glucuronosyltransferase that catalyzes the glucuronide modification of the C3 position of oleanolic acid using uridine diphosphate glucuronide as the substrate. Furthermore, the mutation at 622 bp of its open reading frame resulted in amino acid substitutions that may significantly affect the catalytic activity of the enzyme, and, as a consequence, affect the biosynthesis of ginsenoside Ro. Results of the in vitro enzyme activity assay of the heterologous expression product in E. coli of PgUGAT252645 verified the above analyses. The function of PgUGAT252645 was further verified by the result that its overexpression in ginseng adventitious roots significantly increased the content of ginsenoside Ro. The present work identified a new UGT gene involved in the biosynthesis of ginsenoside Ro, which not only enriches the functional genes in the ginsenoside synthesis pathway, but also provides the technical basis and theoretical basis for the in-depth excavation of ginsenoside-synthesis-related genes.

RLKdb: A comprehensively curated database of plant receptor-like kinase families

In summary, we accurately annotated the RLKomes and classified RLK families of 300 plant genomes with chromosome-level assemblies. The RLKdb provides comprehensive information of RLKome, RLK family, and RLKs. We also developed an online tool for genome- and transcriptome-wide identification and classification of RLKs. The valuable resources and tools will aid evolutionary and functional studies in the community.

Transcriptome-Wide Identification and Expression Analysis of bHLH Family Genes in Iris domestica under Drought and Cu Stress.

The role of bHLH transcription factors in plant response to abiotic stress and regulation of flavonoid metabolism is well documented. However, to date, the bHLH transcription factor family in Iris domestica remains unreported, impeding further research on flavonoid metabolism in this plant. To address this knowledge gap, we employed bioinformatics to identify 39 IdbHLH genes and characterised their phylogenetic relationships and gene expression patterns under both drought and copper stress conditions. Our evolutionary tree analysis classified the 39 IdbHLHs into 17 subfamilies. Expression pattern analysis revealed that different IdbHLH transcription factors had distinct expression trends in various organs, suggesting that they might be involved in diverse biological processes. We found that IdbHLH36 was highly expressed in all organs (Transcripts Per Million (TPM) > 10), while only 12 IdbHLH genes in the rhizome and four in the root were significantly upregulated under drought stress. Of these, four genes (IdbHLH05, -37, -38, -39) were co-upregulated in both the rhizome and root, indicating their potential role in drought resistance. With regards to copper stress, we found that only 12 genes were upregulated. Further co-expression analysis revealed that most bHLH genes were significantly correlated with key enzyme genes involved in isoflavone biosynthesis. Thereinto, IdbHLH06 showed a significant positive correlation with IdC4H1 and Id4CL1 (p < 0.05). Furthermore, a transient expression assay confirmed that the IdbHLH06 protein was localised in the nucleus. Our findings provide new insights into the molecular basis and regulatory mechanisms of bHLH transcription factors in isoflavone biosynthesis in I. domestica.

Transcriptome wide identification, characterization and expression analysis of PHD gene family in Crocus sativus.

The online version contains supplementary material available at 10.1007/s12298-024-01410-3.

Comprehensive Analysis of microRNA Methylation Profiles and Determination of Their Functional Significance in Colorectal Cancer: A Study Protocol

Colorectal cancer (CRC) is a leading cause of cancer-associated fatalities globally. Despite the notable progress in diagnostics and patient care, challenges persist in areas such as early detection, prognostic variable identification, metastatic disease treatment, and personalised treatment options. In CRC, microRNAs, a type of short non-coding RNA, are found to be deregulated and can significantly influence its onset and progression. However, previous microRNA research primarily focused on expression levels to ascertain their biological significance, leaving the microRNA methylation landscapes in CRC patients largely unexplored. This study aims to investigate the genome-wide methylome profiles of microRNA and clarify their roles in CRC. We will analyse the microRNA methylation profiles from our in-house data of more than 100 CRCs and correlate the differentially methylated microRNAs with clinicopathological features. To understand the biological significance of methylated microRNAs, we will perform pathway enrichment analysis and molecular dynamics simulations to examine the binding of argonaut protein to the differentially methylated microRNAs and the structural changes involved. Furthermore, we will conduct functional studies to determine the roles of selected microRNAs. CRC cell lines with hypermethylated microRNA of interest will be treated with a demethylating agent, followed by cell-based assays. Subsequent transcriptome-wide microRNA gene target identification and protein profiling will be performed to interrogate the molecular pathways affected by demethylation of the microRNA of interest. Methylation signifies a major transformation in cancer detection, as widespread epigenetic changes could potentially provide superior early-stage cancer detection and classification compared to somatic mutations. Effective CRC diagnosis ensures timely and appropriate treatment for patients, thereby improving their quality of life. The insights gained from this study could be applied to individualized health diagnostics, disease prognostication, and treatment monitoring.

Genome- and transcriptome-wide identification of trehalose-6-phosphate phosphatases (TPP) gene family and their expression patterns under abiotic stress and exogenous trehalose in soybean

BackgroundTrehalose-6-phosphate phosphatase (TPP) is an essential enzyme catalyzing trehalose synthesis, an important regulatory factor for plant development and stress response in higher plants. However, the TPP gene family in soybean has not been reported.ResultsA comprehensive analysis of the TPP gene family identified 18 GmTPPs classified into eight groups based on the phylogenetic relationships and the conservation of protein in six monocot and eudicot plants. The closely linked subfamilies had similar motifs and intron/exon numbers. Segmental duplication was the main driving force of soybean GmTPPs expansion. In addition, analysis of the cis-regulatory elements and promoter regions of GmTPPs revealed that GmTPPs regulated the response to several abiotic stresses. Moreover, RNA-seq and qRT-PCR analysis of the tissue-specific GmTPPs under different abiotic stresses revealed that most GmTPPs were associated with response to different stresses, including cold, drought, saline-alkali, and exogenous trehalose. Notably, exogenous trehalose treatment up-regulated the expression of most TPP genes under saline-alkali conditions while increasing the carbohydrate and trehalose levels and reducing reactive oxygen species (ROS) accumulation in soybean sprouts, especially in the saline-alkali tolerant genotype. Furthermore, the interaction network and miRNA target prediction revealed that GmTPPs interacted with abiotic stress response-related transcription factors.ConclusionsThe findings in this study lay a foundation for further functional studies on TPP-based breeding to improve soybean development and stress tolerance.

Transcriptome-wide identification and characterization of the regulatory landscape of NAC genes in Drimia indica

Transcriptome-wide identification and characterization of the regulatory landscape of NAC genes in Drimia indica

CRISPR-Based Functional Transcriptomics Defines the Tumor-Dependency and Molecular Determinants of Long Noncoding RNAs in Multiple Myeloma

Long noncoding RNAs (lncRNAs) constitute most elements in the human transcriptome, yet we lack a comprehensive understanding of their role in tumor cells. Here, in multiple myeloma (MM), we exploited the RNA-targeting activity of the CRISPR-Cas13d endonuclease to develop a functional transcriptomics screening platform that enabled not only the transcriptome-wide identification of tumor-promoting-lncRNAs (tp-lncRNAs) in MM cells - outperforming any prior attempt - but also provided mechanistic information about their sub-cellular site-of-function, the isoform-conferring activity, and their downstream molecular pathways. Using RNA-seq data from CD138+ plasma cells from 319 clinically annotated, homogeneously treated, newly diagnosed MM patients, we first identified 5,304 lncRNAs that were expressed in ≥10% of patients, and then designed and generated a pooled lentiviral library with 9 sgRNAs per identified lncRNA, ~500 non-targeting sgRNAs as negative controls, and 9 sgRNAs targeting known protein-coding oncogenes in MM, such as IRF4, as positive controls. We infected this library at low MOI (&amp;lt;0.3) in five MM cell lines (AMO1, H929, KMS11, OPM2, R8226), each expressing a Cas13d-GFP fusion protein. After 3 weeks, we tested for sgRNAs that were relatively depleted or enriched in the MM cell population using deep sequencing and the MAGeCK robust rank aggregation algorithm. From this, we identified ~600 tp-lncRNAs upon which MM cell lines exhibit significant growth dependency, making up ~12% of the identified lncRNA transcriptome, significantly larger than the previous estimate of 3-5%. The tp-lncRNAs overlapped across MM cell lines: 17% were observed in all cell lines tested, 26% in four cell lines, 34% in at least three cell lines, and 53% in at least two cell lines. The dependency score of many tp-lncRNAs was on a par or even superior to the dependency score of the positive control IRF4 and, as expected, the top-scoring tp-lncRNAs included RROL, MALAT1, and NEAT1. We used a small library of 3,500 gRNAs to validate the dependency on 314 tp-lncRNAs and further validated the dependency on 12 tp-lncRNAs by individually targeting them using antisense oligonucleotides or CRISPR-Cas13d. These studies were followed by downstream transcriptomic analyses using either qRT-PCR or RNA-seq, which validated the growth phenotypes and informed on function. Interestingly, when comparing CRISPR-Cas13d to the current state-of-the-art CRISPR interference screens, we found that the CRISPR-Cas13d platform was superior, with a 4- to 30-fold increase in identifying tp-lncRNAs among 913 lncRNAs of intergenic origin in the same cell lines, and with the additional ability to identify tp-lncRNAs generated at gene loci that are antisense to protein-coding genes. We further investigated the sub-cellular localization and site-of-function of the tp-lncRNAs by using a Cas13d that accumulates either in the cytosol or in the nucleus as well as sub-cellular RNA-seq and single molecule RNA FISH. This way, while confirming that most tp-lncRNAs were functional and enriched in the cell nuclei, we also identified 20 hits providing dependency in the cytosol, including the small nucleolar RNA host genes 6 and 10. We observed that the lncRNA transcriptome investigated in this study contained several transcript variants produced from the same lncRNA genes, which differ in their sequences and likely in their structures and functions. Importantly, our screening platform was able to precisely identify tp-lncRNAs isoform(s) conferring dependencies even among many isoforms, a result that was corroborated by RNA-seq and/or qRT-PCR analysis after individually targeting the tp-lncRNA isoforms with Cas13d. Finally, from our screens, we identified and validated the MM dependency on the novel lncRNA Plasma Cell Specific RNA 1 ( PLASP-1), which is one of the most abundant lncRNAs in MM and normal plasma cells (median TPM&amp;gt;25), whereas it has significantly lower expression or is absent in 54 normal tissues and cell types. PLASP-1 is an un-spliced transcript that directly interacts with spliceosome proteins, as established in living cells. We are currently investigating its functional impact on the splicing machinery and the results will be presented. Overall, this novel platform comprehensively defines tumor dependency on lncRNAs in MM and provides information to guide further mechanistic investigation.

Transcriptome-Wide Identification of TCP Transcription Factor Family Members in Pinus massoniana and Their Expression in Regulation of Development and in Response to Stress

Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and development processes. At present, TCP TFs have been widely studied in multiple plant species, but research in P. massoniana has not been carried out. In this study, 13 PmTCP TFs were identified from the transcriptomes of P. massoniana. The phylogenetic results revealed that these PmTCP members were divided into two categories: Class I and Class II. Each PmTCP TF contained a conserved TCP domain, and the conserved motif types and numbers were similar in the same subgroup. According to the transcriptional profiling analysis under drought stress conditions, it was found that seven PmTCP genes responded to drought treatment to varying degrees. The qRT-PCR results showed that the majority of PmTCP genes were significantly expressed in the needles and may play a role in the developmental stage. Meanwhile, the PmTCPs could respond to several stresses and hormone treatments at different levels, which may be important for stress resistance. In addition, PmTCP7 and PmTCP12 were nuclear localization proteins, and PmTCP7 was a transcriptional suppressor. These results will help to explore the regulatory factors related to the growth and development of P. massoniana, enhance its stress resistance, and lay the foundation for further exploration of the physiological effects on PmTCPs.

LhCLIP reveals the in vivo RNA-RNA interactions recognized by hnRNPK.

RNA-RNA interactions play a crucial role in regulating gene expression and various biological processes, but identifying these interactions on a transcriptomic scale remains a challenge. To address this, we have developed a new biochemical technique called pCp-biotin labelled RNA hybrid and ultraviolet crosslinking and immunoprecipitation (lhCLIP) that enables the transcriptome-wide identification of intra- and intermolecular RNA-RNA interactions mediated by a specific RNA-binding protein (RBP). Using lhCLIP, we have uncovered a diverse landscape of intermolecular RNA interactions recognized by hnRNPK in human cells, involving all major classes of noncoding RNAs (ncRNAs) and mRNA. Notably, hnRNPK selectively binds with snRNA U4, U11, and U12, and shapes the secondary structure of these snRNAs, which may impact RNA splicing. Our study demonstrates the potential of lhCLIP as a user-friendly and widely applicable method for discovering RNA-RNA interactions mediated by a particular protein of interest and provides a valuable tool for further investigating the role of RBPs in gene expression and biological processes.

Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm

BackgroundGenomic imprinting refers to a subset of genes that are expressed from only one parental allele during seed development in plants. Studies on genomic imprinting have revealed that intraspecific variations in genomic imprinting expression exist in naturally genetic varieties. However, there have been few studies on the functional analysis of allele-specific imprinted genes.ResultsHere, we generated three reciprocal crosses among the B73, Mo17 and CAU5 inbred lines. Based on the transcriptome-wide analysis of allele-specific expression using RNA sequencing technology, 305 allele-specific imprinting genes (ASIGs) were identified in embryos, and 655 ASIGs were identified in endosperms from three maize F1 hybrids. Of these ASIGs, most did not show consistent maternal or paternal bias between the same tissue from different hybrids or different tissues from one hybrid cross. By gene ontology (GO) analysis, five and eight categories of GO exhibited significantly higher functional enrichments for ASIGs identified in embryo and endosperm, respectively. These functional categories indicated that ASIGs are involved in intercellular nutrient transport, signaling pathways, and transcriptional regulation of kernel development. Finally, the mutation and overexpression of one ASIG (Zm305) affected the length and width of the kernel.ConclusionIn this study, our data will be helpful in gaining further knowledge of genes exhibiting allele-specific imprinting patterns in seeds. The gain- and loss-of-function phenotypes of ASIGs associated with agronomically important seed traits provide compelling evidence for ASIGs as crucial targets to optimize seed traits in crop plants.

Genome-wide and transcriptome-wide identification of the APX gene family in rapeseed (Brassica napus L.) and their expression features under low temperature stress

Ascorbate peroxidase (APX) is a crucial H2O2 scavenger that utilizes ascorbic acid as an electron donor and plays a significant role in plant stress resistance. This study aims to identify and characterize the Brassica napus L. APX gene family through genome and transcriptome sequencing, while also revealing their expression profile under low-temperature stress via transcriptome and proteome analysis. The results indicate the presence of 18 genes with three different conserved domains distributed in Brassica napus L., which can be classified into three major branches based on phylogenetic analysis. Eleven members were predicted to have the low-temperature response component (LTR). Most APX genes exhibit up-regulated transcriptional expression under low temperature stress, particularly APX2, APX4, APX12, and APX18. In terms of proteomics data, only six members (APX2, APX4, APX8, APX12, APX17, and APX18) showed temporal specificity in their expression patterns. Therefore, this study provides valuable insights into the complexity of the APX family in the functional characterization of its genes for future research.

Transcriptome-Wide Identification of Cytochrome P450s and GSTs from Spodoptera exigua Reveals Candidate Genes Involved in Camptothecin Detoxification

The application of camptothecin (CPT) and its derivatives to control insect pests has generated significant interest. This study investigated the enzymatic response of cytochrome P450 monooxygenase (CYP) and glutathione S-transferase (GST) genes in the fat body cells of Spodoptera exigua after 10 μM CPT treatment. Additionally, we examined the effects of CPT on the growth and development of S. exigua larvae and detected the relative expression levels of selected CYP and GST genes during the CPT treatment period. Twenty-one CYP and 17 GST genes were identified from the fat body cells of S. exigua by comparative transcriptomic analyses. The relative expression of ten CYP and seven GST genes changed significantly, which suggested that these CPYs and GSTs may be involved in CPT metabolism. During exposure to CPT for 10 days, the development of S. exigua larvae was delayed and was characterized by weight inhibition and a prolonged period of development. The relative expression levels of the selected four CYP genes, CYP9A27, CYP9A186, CYP337B5, CYP321A8, and one GST gene, GSTe7, were significantly changed by CPT treatment compared to the control group. These generated data provide a basis for identifying the CPT metabolism/detoxification genes of S. exigua at the molecular level.