Search Results (46)

The PLATZ gene family influences plant growth, development, and responses to both biotic and abiotic stresses. Flax (Linum usitatissimum L.), an important oilseed and fiber crop, has not been extensively studied for its PLATZ genes. In this study, 27 LuPLATZ genes were identified in the recently assembled T2T (Telomere-to-Telomere) flax genome through bioinformatics analyses. Phylogenetic analysis grouped these genes into five subfamilies. Examination of gene structure and motifs showed conserved exon–intron arrangements and similar motif compositions within the same clade. Promoter analysis revealed that most cis-elements are associated with plant hormone responses (such as MeJA and ABA) and abiotic stresses, including anaerobic induction, drought, and low temperature. Duplication analysis identified 33 segmental duplication events, and miRNA target prediction indicated that lus-miR167 is the primary regulator of LuPLATZ genes. Expression profiling based on RNA-seq data showed high expression levels of most LuPLATZ genes in leaves and roots, and qRT-PCR confirmed their stress-responsive expression under cold, drought, and salt conditions, with LuPLATZ14 and LuPLATZ21 significantly upregulated in all treatments. Furthermore, overexpression of these two genes enhanced drought tolerance in yeast transformants. Full article

Colletotrichum spp. are the causative agents of anthracnose of rubber trees, one of the most destructive diseases, resulting in substantial economic losses. To investigate the evolutionary characteristics of these pathogenic species, we first assembled the complete mitogenomes of four dominant pathogens, i.e., C. siamense, C. fructicola, C. wanningense and C. bannaense. Comparative analyses revealed that variations in their mitogenome size were primarily driven by intron expansion and expansion/contraction within the cox1, cob and nad genes. Moreover, we observed the strong conservation of gene content, mitochondrial DNA copy number, gene order and intron features within species complexes, but a clear divergence between them. Notably, further studies indicated that patterns such as genomic organization, selective pressures and codon usage were consistent across the genus, suggesting that Colletotrichum species complexes had followed distinct evolutionary trajectories, particularly in the arrangement of protein-coding genes. Therefore, this study systematically characterized the mitogenomes of the four major Colletotrichum species associated with rubber tree anthracnose and provided novel insights into the broad evolutionary mechanisms shaping Colletotrichum species complexes. Full article

The ATP-binding cassette (ABC) gene family represents one of the most extensive and evolutionarily conserved groups of proteins, characterized by ATP-dependent transporters that mediate the movement of substrates across cellular membranes. Despite their well-documented functions in various biological processes, the specific contributions of ABC transporters in eggplant (Solanum melongena L.) remain unexplored. To address this gap, we conducted a comprehensive genome-wide identification and expression profiling of ABC transporter-encoding genes in eggplant. Our investigation identified 159 SmABC genes encoding ABC transporter that were irregularly dispersed across all 12 chromosomes. The encoded proteins exhibited considerable diversity in size, with amino acid lengths varying from 55 to 2628 residues, molecular weights ranging between 4.04 and 286.42 kDa, and isoelectric points spanning from 4.89 to 11.62. Phylogenetic analysis classified the SmABC transporters into eight distinct subfamilies, with the ABCG subfamily being the most predominant. Subcellular localization predictions revealed that most SmABC proteins were localized to the plasma membrane. Members within the same subfamily exhibited conserved motif arrangements and exon–intron structures, suggesting functional and evolutionary conservation. Promoter analysis identified both shared and unique cis-regulatory elements associated with transcriptional regulation. We identified 9 tandem duplication gene pairs and 20 segmental duplication pairs in the SmABC gene family, with segmental duplication being the major mode of expansion. Non-synonymous to synonymous substitutions (Ka/Ks) analysis revealed that paralogs of SmABC family genes underwent mainly purifying selection during the evolutionary process. Comparative genomic analysis demonstrated collinearity between eggplant, Arabidopsis thaliana, and tomato (Solanum lycopersicum), confirming homology among SmABC, AtABC, and SlABC genes. Tissue-specific expression profiling revealed differential SmABC expression patterns, with three distinct genes, SmABCA16, SmABCA17 and SmABCG15, showing preferential expression in purple-peeled fruits (A1, A3, and A5 accessions), implicating their potential involvement in anthocyanin transport. Functional validation via SmABCA16 silencing led to a significant downregulation of SmABCA16 and reduced purple coloration, indicating its regulatory role in anthocyanin transport in eggplant fruit peel. This comprehensive genomic and functional characterization of ABC transporters in eggplant establishes a critical foundation for understanding their biological roles and supports targeted breeding strategies to enhance fruit quality traits. Full article

Bougainvillea spp. possesses vibrantly pigmented bracts that exhibit high ornamental value. Zinc finger proteins (ZFPs), one of the most extensive transcription factor families in plants, are implicated in diverse biological functions, including plant morphogenesis, transcriptional regulation, and responses to abiotic stress. Nevertheless, their regulatory roles in bract pigmentation in Bougainvillea remain unexplored. In the present investigation, 105 BbZFP genes were identified from the Bougainvillea genome via bioinformatic analyses and subsequently categorized into five subgroups according to the quantity and arrangement of their structural domains. Analysis of physicochemical characteristics demonstrated that the BbZFP family encompasses both acidic and basic proteins, all of which are hydrophilic and predominantly classified as unstable proteins. Gene structure analysis revealed that the majority of BbZFP genes comprise between one and five– introns. Cis-regulatory element analysis suggested that BbZFP promoter regions harbor multiple elements associated with abiotic stress responses, hormonal regulation, and light responsiveness, implying their possible participation in these physiological processes. Transcriptomic data analysis revealed distinct expression patterns of BbZFP genes among bracts of different colors. A quantitative real-time polymerase chain reaction (RT-qPCR) further confirmed that Bou_68928, Bou_1096, Bou_4400, and Bou_17631 were markedly upregulated in yellow bracts relative to white bracts, suggesting their involvement in flavonoid biosynthesis regulation. Meanwhile, Bou_1096 and Bou_17631 exhibited markedly elevated expression in red-purple bracts compared to white bracts, potentially regulating betacyanin biosynthesis in Bougainvillea. These findings offer candidate genes for molecular breeding strategies aimed at enhancing floral coloration in Bougainvillea. The next step will involve elucidating the functions of these genes in bract coloration. Full article

G-quadruplexes (G4s) are unique nucleic acid structures composed of guanine-rich (G-rich) sequences that can form diverse topologies based on the arrangement of their four strands. G4s have attracted attention for their potential roles in various biological processes and human diseases. In this review, we focus on the G4 structures formed by human telomeric sequences, (GGGTTA)_n, and the hexanucleotide repeat expansion, (GGGGCC)_n, in the first intron region of the chromosome 9 open reading frame 72 (C9orf72) gene, highlighting their structural diversity and biological significance. Human telomeric G4s play crucial roles in telomere retention and gene regulation. In particular, we provide an in-depth summary of known telomeric G4s and focus on our recently discovered chair-type conformation, which exhibits distinct folding patterns. The chair-type G4s represent a novel folding pattern with unique characteristics, expanding our knowledge of telomeric G4 structural diversity and potential biological functions. Specifically, we emphasize the G4s formed by the (GGGGCC)_n sequence of the C9orf72 gene, which represents the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The thorough structural analysis in this review advances our comprehension of the disease mechanism and provides valuable insights into developing targeted therapeutic strategies in ALS/FTD. Full article

Background/Objectives: The ShiLan domain was previously identified as an insertion sequence in a phage DNA methylase gene that exhibited similar evolutionary patterns to that of an active intein or self-splicing intron but could not be identified as either. It produces no internal stop codons when read in frame with its host methylase gene, leading to the thought that it may not be an intron and rather be an abnormal type of intein. However, the sequence has no detectable self-splicing domains, which are essential for intein persistence, as preventing an intein from successfully splicing is often detrimental to proper host protein function. Methods: The analysis of alternate open reading frames for the full nucleotide sequence of this insertion element revealed the insertion to be an out-of-frame histidine-asparagine-histidine (HNH) endonuclease. A GTG start codon is located 18 bp into the insertion, and a TAA stop codon within the last four bases of the insertion (TAAC). When this frame is read, an HNH endonuclease is revealed. In-depth computational analysis could not retrieve support for this element being any known type of self-splicing element, neither intein nor intron. When read in-frame with the methylase gene, this insertion is predicted to take on a looping structure that may be able to avoid interference with the DNA methylase activity. We performed searches for sequences similar in nature to the inserted out-of-frame HNH and found several in other phages and prokaryotes. We present our survey of these out-of-frame endonuclease insertion elements as well as some speculation on how these endonucleases are getting translated to facilitate their homing activity. Conclusions: These findings expand our understanding of the possible arrangements for and prevalence of unorthodox mobile genetic elements and overlapping open reading frames in phages. Full article

Tieguanyin tea, a renowned oolong tea, is one of the ten most famous teas in China. The Squamosa Promoter Binding Protein (SBP)-box transcription factor family, widely present in plants, plays a crucial role in plant development, growth, and stress responses. In this study, we identify and analyze 22 CsSBP genes at the genome-wide level. These genes were distributed unevenly across 11 chromosomes. Using Arabidopsis thaliana and Solanum lycopersicum L. as model organisms, we constructed a phylogenetic tree to classify these genes into six distinct subfamilies. Collinearity analysis revealed 20 homologous gene pairs between AtSBP and CsSBP, 21 pairs between SiSBP and CsSBP, and 14 pairs between OsSBP and CsSBP. Cis-acting element analysis indicated that light-responsive elements were the most abundant among the CsSBP genes. Protein motif, domain, and gene architecture analyses demonstrated that members of the same subgroup shared similar exon–intron structures and motif arrangements. Furthermore, we evaluated the expression profiles of nine CsSBP genes under light, shade, and cold stress using qRT-PCR analysis. Notably, CsSBP1, CsSBP17, and CsSBP19 were significantly upregulated under all three stresses. This study provides fundamental insights into the CsSBP gene family and offers a novel perspective on the mechanisms of SBP transcription factor-mediated stress responses, as well as Tieguanyin tea’s adaptation to environmental variations. Full article

Tree peony (Paeonia ostii T. Hong et J. X. Zhang) is an important medicinal and ornamental plant. It would be useful to propagate this plant in tissue culture, but it is difficult to induce root formation. Auxin plays a pivotal role in adventitious root formation, and ABCB transporter proteins are involved in auxin transport. To elucidate the function of the ABCB transporter family in P. ostii, we identified members of the ABCB gene family in the P. ostii genome and analyzed the functional characteristics of the putative proteins. In total, 29 ABCB genes were identified in P.ostii, distributed on five chromosomes. In a phylogenetic analysis, the PoABCBs were grouped into four subfamilies, with the largest being Subfamily I, characterized by their MDR structure. PoABCB genes in the same subfamily exhibited similar intron/exon arrangements and motif composition. The promoters of PoABCBs contained cis-acting elements associated with the photoresponse and hormone signaling. qRT-PCR analyses showed that, after treatment of tissue-cultured P. ostii seedlings with auxin, five PoABCB gene family members (PoABCB6, PoABCB10, PoABCB11, PoABCB12, and PoABCB16) were significantly upregulated during adventitious root development. These genes may play roles in the auxin response and adventitious root development of P. ostii in vitro. Full article

Members of the genus Moelleriella (Hypocreales, Clavicipitaceae) are insect pathogens with specificity for scale insects and whiteflies. However, no mitochondrial genomes are available for these fungi. Here, we assembled seven mitogenomes from M. zhongdongii, M. libera, M. raciborskii, M. gracilispora, M. oxystoma, Moelleriella sp. CGMCC 3.18909, and Moelleriella sp. CGMCC 3.18913, which varied in size from 40.8 to 95.7 Kb. Synteny and codon usage bias was relatively conserved, with the mitochondrial gene arrangement being completely homologous to the gene order of 21 other species within the Hypocreales. Nevertheless, significant intron polymorphism was observed between Moelleriella species. Evolutionary analyses revealed that all 15 core protein–coding genes had ka/ks < 1, indicating purifying selection pressure. Sequence variation within the mitochondrial ATP synthase F0 subunit 6 (atp6) gene showed the largest genetic distance, with the ATP synthase F0 subunit 9 (atp9) gene showing the smallest. Comparative analyses of mitogenomes revealed that introns were the primary factor contributing to the size variation in Moelleriella and, more broadly, within Hypocreales mitogenomes. Phylogenetic analyses indicated that the seven Moelleriella species examined form a well–supported clade, most closely related to Metarhizium. These data present the first mitogenomes from Moelleriella and further advance research into the taxonomy, origin, evolution, and genomics of Moelleriella. Full article

Chinese kale is a native vegetable from the Brassicaceae family that is grown extensively in Southeast Asia and Southern China. Its low genetic transformation and gene editing efficiency hinder gene function research and molecular biology in Chinese kale. CRISPR/Cas9 is a useful tool for plant genome research due to its rapid development and optimization. This study targeted BocPDSs, (BocPDS1, BocPDS2) to establish an effective CRISPR/Cas9 system in Chinese kale. A tandemly arranged tRNA-sgRNA construct was used to express numerous sgRNAs to induce BocPDS1 and BocPDS2 double and single mutations, with a mutation rate of 61.11%. As predicted, several mutant plants showed an albino phenotype with a harbored mutation in an exon and intron region, highlighting the relevance of the intron. The presence of mutations in the intron region suggests that the cleavage process in Chinese kale, utilizing CRISPR/Cas9 shows a preference for AT-rich regions. The distinct and somewhat redundant functions of BocPDS1 and BocPDS2 are demonstrated by the complete albino phenotype of the double mutants and the mosaic albino phenotype of the individual BocPDS1 and BocPDS2 mutants. Specific gene editing modes, including base deletion, base substitution, and base insertion, were identified in the sequence of the target gene. Among them, short nucleotide insertions were the most common type of insertion, with base insertions having the highest frequency (61.54%). Furthermore, no instances of off-target gene editing were detected. The current work demonstrated that the CRISPR/Cas9 gene editing system, which relies on endogenous tRNA processing, can effectively induce mutagenesis in Chinese kale. This finding establishes a theoretical basis and technical backbone for the more effective implementation of CRISPR/Cas9 gene-editing technology in Chinese kale and Brassica plants. Full article

The species of Purpureocillium are cosmopolitan and multitrophic fungi that can infect a wide range of invertebrate hosts. This study reports the mitogenome of P. atypicola, a specialized spider pathogenic fungus. The 112,465 bp mitogenome encoded genes typically found in fungal mitogenomes, and a total of 52 introns inserted into seven genes. A comparison with three other Purpureocillium species revealed significant differences in length and intron number, primarily due to intron variation; however, there was no dynamic variation in the introns of the cox1 gene within the same species of the Purpureocillium genus. Different mitochondrial protein-coding genes showed variable degrees of genetic differentiation among these species, but they were all under purifying selection. Additionally, frequent intron loss or gain events were detected to have occurred during the evolution of the Ophiocordycipitaceae mitogenomes, yet the gene arrangement remains conserved. A phylogenetic analysis of the combined mitochondrial gene set gave identical and well-supported tree topologies. The estimated age of the crown of Ophiocordycipitaceae and Purpureocillium were around the Early Cretaceous period (127 Mya) and Late Cretaceous period (83 Mya), respectively. The results of this study advance our understanding of the genomics, evolution, and taxonomy of this important fungal group. Full article

Andrographis paniculata is known for its diterpenoid medicinal compounds with antibacterial and anti-inflammatory properties. However, it faces production and cultivation challenges due to low temperatures (LTs). Cytochrome P450 monooxygenases (CYPs) are key enzymes in diterpenoid accumulation. Nevertheless, the functions and LT-related expression patterns of diterpenoid pathway CYPs in Andrographis paniculata remain poorly understood. In this study, 346 CYPs were discovered in Andrographis paniculata. Among them, 328 CYPs belonged to 42 known subfamilies. The remaining 17 CYPs might have represented novel subfamilies unique to this species. A total of 65 candidate CYPs associated with diterpenoid modification were identified. Of these, 50 were transmembrane proteins, and 57 were localized to chloroplasts. The CYP71 subfamily was the most abundant and had the highest motif diversity. Promoters of all candidate CYPs commonly contained elements responsive to gibberellins (GAs), methyl jasmonate (MeJA), and abiotic stresses. Notably, the XP_051152769 protein, corresponding to a CYP gene over 40,000 bp in length, featured an extraordinarily long intron (40,751 nts). Functional elements within this intron were related to LT, GAs, and dehydration pathways. Based on the promoter element arrangement and subfamily classification, 10 representative candidate CYPs were selected. Under LT stress, significant expression changes were observed in three representative CYPs: CYP71D, ent-kaurenoic acid oxidase (KAO), and ent-kaurene oxidase (KO). KAO and KO were significantly upregulated during early LT stress. KAO and KO interacted with each other and jointly interacted with GA20OX2-like. CYP71D acted as a negative response factor to LT stress. Among the 37 proteins interacting with CYP71D, 95% were CYPs. This study provides a critical preliminary foundation for investigating the functions of diterpenoid pathway CYPs in Andrographis paniculata, thereby facilitating the development of LT-tolerant cultivars. Full article

The maize Snf2 gene family plays a crucial role in chromatin remodeling and response to environmental stresses. In this study, we identified and analyzed 35 members of the maize Snf2 gene family (ZmCHR1 to ZmCHR35) using the Ensembl Plants database. Each protein contained conserved SNF2-N and Helicase-C domains. Phylogenetic analysis revealed six groups among the Snf2 proteins, with an uneven distribution across subfamilies. Physicochemical analysis indicated that the Snf2 proteins are hydrophilic, with varied amino acid lengths, isoelectric points, and molecular weights, and are predominantly localized in the nucleus. Chromosomal mapping showed that these genes are distributed across all ten maize chromosomes. Gene structure analysis revealed diverse exon–intron arrangements, while motif analysis identified 20 conserved motifs. Collinearity analysis highlighted gene duplication events, suggesting purifying selection. Cis-regulatory element analysis suggested involvement in abiotic and biotic stress responses. Expression analysis indicated tissue-specific expression patterns and differential expression under various stress conditions. Specifically, qRT-PCR validation under drought stress showed that certain Snf2 genes were upregulated at 12 h and downregulated at 24 h, revealing potential roles in drought tolerance. These findings provide a foundation for further exploration of the functional roles of the maize Snf2 gene family in development and stress responses. Full article

Suillus is one of the most important genera of ectomycorrhizal fungi. As a model for studying host specificity, its molecular fragments and nuclear genome have been analyzed. However, its mitochondrial genome has not yet been reported. In this study, we assembled five mitogenomes of Suillus and analyzed and compared their basic characteristics. Owing to the large number of introns as well as intergenic regions, the mitogenomic lengths of species of Suillus were greater than those of other species of Boletales. We identified two main patterns of gene order arrangement in the members of the order Boletales. The Ka/Ks values of 15 protein-coding genes were <1 for the mitochondrial genes of 39 Boletales species, indicating their conserved evolution. Phylogenetic trees, reconstructed using the mitogenomes, indicated that the genus Suillus was monophyletic. Phylogenetic results based on the internal transcribed spacer region and mitogenome were used to confirm the distribution of Suillus placidus in China. The results showed that the mitogenome was superior in distinguishing species compared with a single molecular fragment. This is the first study to investigate the mitogenome of Suillus, enriching the mitogenome information and providing basic data for the phylogeny, resource conservation, and genetic diversity of this genus. Full article

RNC1, a plant-specific gene, is known for its involvement in splicing group II introns within maize chloroplast. However, its role in chloroplast development and global gene expression remains poorly understood. This study aimed to investigate the role of RNC1 in chloroplast development and identify the genes that mediate its function in the development of entire tomato plants. Consistent with findings in maize, RNC1 silencing induced dwarfism and leaf whitening in tomato plants. Subcellular localization analysis revealed that the RNC1 protein is localized to both the nucleus and cytoplasm, including the stress granule and chloroplasts. Electron microscopic examination of tomato leaf transverse sections exposed significant disruptions in the spatial arrangement of the thylakoid network upon RNC1 silencing, crucial for efficient light energy capture and conversion into chemical energy. Transcriptome analysis suggested that RNC1 silencing potentially impacts tomato plant development through genes associated with all three categories (biological processes, cellular components, and molecular functions). Overall, our findings contribute to a better understanding of the critical role of RNC1 in chloroplast development and its significance in plant physiology. Full article