Search Results (76)

Sucrose phosphate synthase (SPS) is a rate-limiting enzyme in plant sucrose biosynthesis. However, the SPS gene family in luffa remains unidentified, and its functional involvement in sugar metabolism is unexplored. Here, we present the first genome-wide identification and functional analysis of the LaSPSs in luffa. We identified nine LaSPS genes, characterized their physicochemical and evolutionary properties, and analyzed their expression patterns in different tissues and response to ethylene and drought treatments. Nine tandem-duplicated LaSPS genes formed four clusters (T1(1/2), T2(3/4), T3(5/6), T4(7–9)) with conserved architectures. RNA-seq analysis indicated a ubiquitous downregulation of LaSPS genes in senescing luffa, wherein sucrose content correlated significantly with all LaSPS members except LaSPS1/2. Exogenous ethylene substantially repressed LaSPSs transcription, while 1-methylcyclopropene (1-MCP) treatment showed induction. Notably, LaSPS3/4 displayed high activation under drought stress. Functional validation via heterologous expression in tobacco confirmed that LaSPS3/4 positively regulates drought resistance. In summary, this study provides a novel perspective for the in-depth investigation of the molecular evolutionary mechanism of the LaSPS gene family and its biological functions in luffa. Full article

The phosphatidylethanolamine-binding protein (PEBP) gene family is critical for regulating plant growth, development, and flowering. Sunflower (Helianthus annuus L.) is the fourth most important oilseed crop globally. However, the genomic structure and functional diversity of PEBP genes in sunflower remain unexplored. Leveraging the recently assembled telomere-to-telomere (T2T) sunflower genome, a genome-wide analysis of the HaPEBP family was carried out. A total of 12 PEBP genes were identified in sunflower and categorized into three subfamilies: TFL1-like, FT-like, and MFT-like. Phylogenetic and synteny analyses revealed that tandem duplication events have substantially contributed to the evolution and expansion of the HaPEBP gene family. Furthermore, the analysis of the promoter regions revealed 77 distinct cis-acting elements, including 35 related to light signaling and growth regulation, highlighting their potential involvement in the regulation of flowering and development in sunflower. Expression profile analysis using RNA-seq data across various tissues indicated that FT-like and TFL1-like HaPEBP genes may be the key regulators of flowering time and plant architecture in sunflower varieties. This study offers valuable insights into the structural, evolutional, and functional dynamics of the HaPEBP gene family and holds significant implications for sunflower breeding strategies aimed at optimizing flowering time and plant architecture traits. Full article

Background: Lonchodidae is the largest family within the order Phasmatodea, and although many studies have been conducted on this family, the monophyly of the family has not been established. Methods: Eight mitogenomes from Lonchodidae, including the first complete mitogenomes of four genera, were sequenced and annotated to explore their features and phylogenetic relationships. Results: The total length ranged from 15,942–18,021 bp, and the mitogenome consisted of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region (CR). atp8 had the highest A + T content in Lonchodidae, except for Neohirasea stephanus and Asceles clavatus, in which the highest A + T contents were detected in nad6. The phylogenetic trees were reconstructed via Bayesian inference (BI) and maximum likelihood (ML) based on the PCG123 and PCG12 datasets. As the phylogenetic trees show, Necrosciinae is recognized as monophyletic, but the monophyly of Lonchodinae has not been supported. Gene deletion and rearrangement have occurred mainly in Lonchodidae and Aschiphasmatidae. The most common reason for gene rearrangements was tandem duplication random loss (TDRL), but trnI of Stheneboea repudiosa inverted into the CR. In addition, genes within the same family or genus share related sequences and conserved gene blocks. Conclusions: we expanded the mitochondrial genomic data for this family, thereby establishing a foundational dataset for future studies. Full article

Regulating chloroplast gene expression is crucial for maintaining chloroplast function and plant development. Pentatricopeptide repeat (PPR) proteins form a vast protein family that regulates organelle genes and has multiple functions during plant development. Here, we found that two P-type PPR proteins, YS1 (yellow-green seedling 1) and YS2, jointly regulated seedling development in rice. The loss of YS1 and YS2 exhibited the collapsed chloroplast thylakoids and decreased photosynthetic activity, leading to the yellowing and death of rice seedlings. YS1 and YS2 could directly bind to the transcript of the psbH-petB intergenic region to facilitate the splicing of petB intron, thereby affecting the splicing efficiency of petD, which is located downstream of petB in the five-cistronic transcription unit psbB-psbT-psbH-petB-petD. The mutations in YS1 and YS2 led to decreased mature transcripts of petB and petD after splicing, significantly reducing the protein levels of PetB and PetD. This further led to deficiencies in the cytochrome b6/f and photosystem I complexes of the electron transport chain (ETC), ultimately resulting in decreased ETC-produced NADPH and reduced contents of carbohydrates in ys mutants. Moreover, transcriptome sequencing analysis revealed that YS1 and YS2 were vital for chloroplast organization and carbohydrate metabolism, as well as chloroplast RNA processing. In previous studies, the mechanism of petB intron splicing in the five-cistronic transcription unit psbB-psbT-psbH-petB-petD of rice is unclear. Our study revealed that the two highly conserved proteins YS1 and YS2 were functionally redundant and played critical roles in photosynthesis and seedling development through their involvement in petB intron splicing to maintain chloroplast homeostasis in rice. This work broadened the perspective on PPR-mediated chloroplast development and laid a foundation for exploring the biofunctions of duplicated genes in higher plants. Full article

Canna, the sole member of the Cannaceae family, is widely cultivated as an ornamental plant for its decorative flowers and foliage and is also a potential tuber crop due to its high starch content. This study sequenced, assembled, and analyzed the complete chloroplast (cp) genomes of three common Canna species with distinct leaf colors (green, purple, and variegated). The four cp genomes ranged from 164,427 to 164,509 bp in length, had a GC content of 36.23–36.25%, and exhibited identical gene content and codon preferences. Each genome contained 130 genes, including 110 unique genes (78 protein-coding genes, four of unknown function, four rRNAs, and 28 tRNAs), 18 duplicated genes located in the IR regions (six protein-coding genes, two of unknown function, four rRNAs, and eight tRNAs), and two trnM-CAU genes in the LSC region. SSR and long-repeat showed differences in long repeats numbers and distributions among the four cp genomes, highlighting potential molecular markers for Canna species identification and breeding. Comparative analysis showed high conservation across Canna cp genomes. Phylogenetic analysis confirmed a close relationship between Cannaceae and Marantaceae and supported a [Musaeceae (Cannaceae + Marantaceae)] clade as a sister group to Costaceae. The cp genome data generated in this study provide valuable insights for developing molecular markers, resolving taxonomic classifications, and advancing phylogenetic and population genetic studies in Canna species. Full article

Tamarix chinensis (T. chinensis), an esteemed salt-tolerant plant, holds significant importance in elucidating mechanisms of plant stress adaptation. The ALKBH genes family, which is involved in RNA N⁶-methyladenosine (m⁶A) demethylation, plays a crucial role in plant growth, development, and stress responses. This study performed a genome-wide identification and analysis of the ALKBH genes family in T. chinensis using bioinformatics methodologies. A total of eight ALKBH genes were identified and named TcALKBH1 to TcALKBH8 based on their chromosomal positions. Phylogenetic analysis divided the TcALKBH genes family into different subgroups, revealing that, in comparison to Arabidopsis and other plants, T. chinensis lacks members of the ALKBH6 and ALKBH10 families. Further analysis of gene structure, conserved domain, and motif analysis elucidated the basic features of the TcALKBH gene family. Gene duplication analysis identified TcALKBH3 and TcALKBH7 as homologous gene pairs, and collinearity analysis indicated a closer relationship between T. chinensis and Populus compared to Arabidopsis. In addition, gene expression analysis revealed tissue-specific expression patterns of the TcALKBH genes, with significant upregulation observed under abiotic stress conditions such as ABA, NaCl, and NaHCO₃. It is noteworthy that the expression of TcALKBH4 increased nearly 30-fold after 6 h of ABA stress, suggesting that TcALKBH4 may play a key regulatory role in the ABA response. These results indicate that the TcALKBH genes might be crucial for stress responses in T. chinensis. This research offers a theoretical foundation for a deeper exploration of the roles and molecular mechanisms of the TcALKBH genes family in stress adaptation. It also presents valuable candidate genes for enhancing stress resistance in plants through breeding programs. Full article

Plant-specific transcription factors known as SQUAMOSA promoter binding protein-like (SPL) genes are essential for development, growth, and abiotic stress responses. While the SPL gene family has been extensively studied in various plant species, a systematic characterization in Zanthoxylum bungeanum (Zb) is lacking. This study used transcriptomic and bioinformatics data to conduct a thorough genomic identification and expression investigation of the ZbSPL gene family. Eight subfamilies including 73 ZbSPL members were identified, most of which are predicted to be localized in the nucleus. Ka/Ks ratio analysis indicates that most ZbSPL genes have undergone purifying selection. According to evolutionary research, segmental duplication is a major factor in the amplification of the ZbSPL gene family. Gene structures, conserved motifs, and domains were found to be highly conserved among paralogs. Cis-element research revealed that ZbSPLs may be implicated in hormone and abiotic stress responses. Codon usage pattern analysis showed that the ZbSPL gene family was more inclined to A/T base endings; the higher the A/T content, the stronger the preference of the codons; and the use pattern was mainly affected by natural selection. Additionally, 36 ZbSPLs were found to be potential targets of miR156. RNA-seq demonstrated that SPL genes in Zb are differentially expressed in response to distinct abiotic stressors. Two ZbSPL genes (ZbSPL10 and ZbSPL17) were implicated in the response to salt stress, while four ZbSPL genes (ZbSPL06, ZbSPL43, ZbSPL60, and ZbSPL61) showed response to drought stress, based on a qRT-PCR investigation of the ZbSPL genes under various abiotic stress conditions. This study will help us gain a deeper understanding of the functions of ZbSPLs and lay a genetic foundation for future breeding of high-quality, highly abiotic resistant varieties of Z. bungeanum. Full article

The Coelogyne s.l. is one of the emblematic genera of the Asian orchids, with high horticultural and medicinal values. However, the phylogenetic relationships of the genus inferred from previous studies based on a limited number of DNA markers remain ambiguous. In this study, we newly sequenced and assembled the complete plastomes of seven Coelogyne species: C. bulleyia, C. fimbriata, C. flaccida, C. prolifera, C. tricallosa, C. uncata, and an unknown taxa, Coelogyne sp. The plastomes of Coelogyne exhibited a typical quadripartite structure, varying in length between 157,476 bp and 160,096 bp, accompanied by a GC content spanning from 37.3% to 37.5%. A total of 132 genes were annotated for each plastome, including 86 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Among these, 19 genes underwent duplication within the inverted repeat (IR) regions, and 18 genes exhibited the presence of introns. Additionally, we detected 54 to 69 simple sequence repeats (SSRs) and 30 to 49 long repeats. In terms of codon usage frequency, leucine (Leu) emerged with the highest frequency, while cysteine (Cys) exhibited the lowest occurrence. Furthermore, eight hypervariable regions (atpB-rbcL, psbK-psbI, rps8-rpl14, rps16-trnQ^UUG, psaC-ndhE, ndhF-rpl32, psbB-psbT, and ycf1) were identified. Phylogenetic analyses using complete plastomes and protein-coding genes indicated that Coelogyne s.l. was monophyletic. Moreover, the results robustly supported the division of Coelogyne s.l. into five clades. This study provides a comprehensive analysis of the structural variation and phylogenetic analysis of the Coelogyne s.l. based on plastome data. The findings offer significant insights into the plastid genomic characteristics and the phylogenetic relationships of Coelogyne s.l., contributing to a deeper understanding of its evolutionary history. Full article

Scientists study the molecular activities of the hepatitis B virus (HBV). However, in vivo experiments are scarce. Some microRNAs are HBV-related, but their exact mechanisms are unknown. Our study provides an up-to-date view of the associations between microRNAs and HBV-DNA levels in chronically infected individuals. We conducted this large-scale research on five databases according to PRISMA guidance. Joanna Briggs Institute tools and Newcastle Ottawa Quality Assessment scores helped with quality evaluations. R 4.2.2 performed statistical computations for the meta-analysis. DIANA-microT 2023 and g:Profiler enriched the predictions of liver genes associated with miR-122 and miR-192-5p. From the 1313 records, we eliminated those irrelevant to our theme, non-article methodologies, non-English entries, and duplicates. We assessed associations between microRNAs and HBV-DNA levels. Overall, the pooled correlations favoured the general idea of the connection between non-coding molecules and viremia levels. MiR-122 and miR-192-5p were the most researched microRNAs, significantly associated with HBV-DNA levels. The connections between miR-122, miR-192-5p, let-7, miR-215, miR-320, and viral loads need further in vivo assessment. To conclude, this study evaluates systematically, for the first time, the correlations between non-coding molecules and viremia levels in patients. Our meta-analysis emphasizes potentially important pathways toward new inhibitors of the viral replication cycle. Full article

The tomato leafminer, Tuta absoluta (Lepidoptera: Gelechiidae), is a highly destructive invasive pest targeting Solanaceae crops. Its olfactory system plays a crucial role in host location, mate finding, and other behavioral activities. However, there is a notable gap in the literature regarding the characterization of its chemosensory genes. In this study, we conducted a genome-wide identification of 58 odorant receptors (ORs) of T. absoluta. The identified ORs exhibit coding sequence (CDS) lengths ranging from 1062 bp to 1419 bp, encoding proteins of 354 to 473 amino acids. Gene structure analysis showed that the majority of these ORs consist of five, seven, eight, or nine exons, collectively representing 67% of the total ORs identified. Through chromosomal mapping, we identified several tandemly duplicate genes, including TabsOR12a, TabsOR12b, TabsOR12c, TabsOR21a, TabsOR21b, TabsOR34a, TabsOR34b, TabsOR34c, TabsOR62a, and TabsOR62b. The phylogenetic analysis indicated that six TabsORs were clustered within the lepidopteran sex pheromone receptor clade, while an expansion clade containing ten TabsORs resulted from tandem duplication events. Additionally, five TabsORs were classified into a specific OR clade in T. absoluta. Furthermore, through RNA-Seq and RT-qPCR analyses, we identified five TabsORs (TabsOR21a, TabsOR26a, TabsOR34a, TabsOR34c, and TabsOR36) exhibiting female-antennae-biased expression. Our study provides a valuable foundation to further investigations into the molecular and ecological functions of TabsORs, particularly in relation to oviposition behavior. These findings provide foundational data for the future exploration of the functions of female-biased expression OR genes in T. absoluta, thereby facilitating the further development of eco-friendly attract-and-kill techniques for the prevention and control of T. absoluta. Full article

Based on the nucleotide sequences of the mitochondrial genome (mitogenome) of specimens taken from two mussel species (Arcuatula senhousia and Mytilus coruscus), an investigation was performed by means of the complex approaches of the genomics, molecular phylogenetics, and evolutionary genetics. The mitogenome structure of studied mussels, like in many other invertebrates, appears to be much more variable than in vertebrates and includes changing gene order, duplications, and deletions, which were most frequent for tRNA genes; the mussel species’ mitogenomes also have variable sizes. The results demonstrate some of the very important properties of protein polypeptides, such as hydrophobicity and its determination by the purine and pyrimidine nucleotide ratio. This fact might indirectly indicate the necessity of purifying natural selection for the support of polypeptide functionality. However, in accordance with the widely accepted and logical concept of natural cutoff selection for organisms living in nature, which explains its action against deleterious nucleotide substitutions in the nonsynonymous codons (mutations) and its holding of the active (effective) macromolecules of the polypeptides in a population, we were unable to get unambiguous evidence in favor of this concept in the current paper. Here, the phylogeny and systematics of mussel species from one of the largest taxons of bivalve mollusks are studied, the family known as Mytilidae. The phylogeny for Mytilidae (order Mytilida), which currently has no consensus in terms of systematics, is reconstructed using a data matrix of 26–27 mitogenomes. Initially, a set of 100 sequences from GenBank were downloaded and checked for their gender: whether they were female (F) or male (M) in origin. Our analysis of the new data confirms the known drastic differences between the F/M mitogenome lines in mussels. Phylogenetic reconstructions of the F-lines were performed using the combined set of genetic markers, reconstructing only protein-coding genes (PCGs), only rRNA + tRNA genes, and all genes. Additionally, the analysis includes the usage of nucleotide sequences composed of other data matrices, such as 20–68 mitogenome sequences. The time of divergence from MRCA, estimated via BEAST2, for Mytilidae is close to 293 Mya, suggesting that they originate in the Silurian Period. From all these data, a consensus for the phylogeny of the subfamily of Mytilinae and its systematics is suggested. In particular, the long-debated argument on mussel systematics was resolved as to whether Mytilidae, and the subfamily of Mytilinae, are monophyletic. The topology signal, which was strongly resolved in this paper and in the literature, has refuted the theory regarding the monophyly of Mytilinae. Full article

For patients with hereditary breast and ovarian cancer, the probability of carrying two pathogenic variants (PVs) in dominant cancer-predisposing genes is rare. Using targeted next-generation sequencing (NGS), we investigated a 49-year-old Caucasian woman who developed a highly aggressive breast tumor. Our analyses identified an intragenic germline heterozygous duplication in BRCA1 with an additional likely PV in the TP53 gene. The BRCA1 variant was confirmed by multiplex ligation probe amplification (MLPA), and genomic breakpoints were characterized at the nucleotide level (c.135-2578_442-1104dup). mRNA extracted from lymphocytes was amplified by RT-PCR and then Sanger sequenced, revealing a tandem duplication r.135_441dup; p.(Gln148Ilefs*20). This duplication results in the synthesis of a truncated and, most likely, nonfunctional protein. Following functional studies, the TP53 exon 5 c.472C > T; p.(Arg158Cys) missense variant was classified as likely pathogenic by the Li-Fraumeni Syndrome (LFS) working group. This type of unexpected association will be increasingly identified in the future, with the switch from targeted BRCA sequencing to hereditary breast and ovarian cancer (HBOC) panel sequencing, raising the question of how these patients should be managed. It is therefore important to record and investigate these rare double-heterozygous genotypes. Full article

Anthocyanins are ubiquitous pigments derived from the phenylpropanoid compound conferring red, purple and blue pigmentations to various organs of horticultural crops. The metabolism of flavonoids in the cytoplasm leads to the biosynthesis of anthocyanin, which is then conveyed to the vacuoles for storage by plant glutathione S-transferases (GST). Although GST is important for transporting anthocyanin in plants, its identification and characterization in eggplant (Solanum melongena L.) remains obscure. In this study, a total of 40 GST genes were obtained in the eggplant genome and classified into seven distinct chief groups based on the evolutionary relationship with Arabidopsis thaliana GST genes. The seven subgroups of eggplant GST genes (SmGST) comprise: dehydroascorbate reductase (DHAR), elongation factor 1Bγ (EF1Bγ), Zeta (Z), Theta(T), Phi(F), Tau(U) and tetra-chlorohydroquinone dehalogenase TCHQD. The 40 GST genes were unevenly distributed throughout the 10 eggplant chromosomes and were predominantly located in the cytoplasm. Structural gene analysis showed similarity in exons and introns within a GST subgroup. Six pairs of both tandem and segmental duplications have been identified, making them the primary factors contributing to the evolution of the SmGST. Light-related cis-regulatory elements were dominant, followed by stress-related and hormone-responsive elements. The syntenic analysis of orthologous genes indicated that eggplant, Arabidopsis and tomato (Solanum lycopersicum L.) counterpart genes seemed to be derived from a common ancestry. RNA-seq data analyses showed high expression of 13 SmGST genes with SmGSTF1 being glaringly upregulated on the peel of purple eggplant but showed no or low expression on eggplant varieties with green or white peel. Subsequently, SmGSTF1 had a strong positive correlation with anthocyanin content and with anthocyanin structural genes like SmUFGT (r = 0.9), SmANS (r = 0.85), SmF3H (r = 0.82) and SmCHI2 (r = 0.7). The suppression of SmGSTF1 through virus-induced gene silencing (VIGs) resulted in a decrease in anthocyanin on the infiltrated fruit surface. In a nutshell, results from this study established that SmGSTF1 has the potential of anthocyanin accumulation in eggplant peel and offers viable candidate genes for the improvement of purple eggplant. The comprehensive studies of the SmGST family genes provide the foundation for deciphering molecular investigations into the functional analysis of SmGST genes in eggplant. Full article

BAHD acyltransferases are involved in catalyzing and regulating the secondary metabolism in plants. Despite this, the members of BAHD family and their functions have not been reported in the Taxus species. In this study, a total of 123 TwBAHD acyltransferases from Taxus wallichiana var. mairei genome were identified and divided into six clades based on phylogenetic analysis, of which Clade VI contained a Taxus-specific branch of 52 members potentially involved in taxol biosynthesis. Most TwBAHDs from the same clade shared similar conserved motifs and gene structures. Besides the typical conserved motifs within the BAHD family, the YPLAGR motif was also conserved in multiple clades of T. mairei. Moreover, only one pair of tandem duplicate genes was found on chromosome 1, with a Ka/Ks ratio < 1, indicating that the function of duplicate genes did not differentiate significantly. RNA-seq analysis revealed different expression patterns of TwBAHDs in MeJA induction and tissue-specific expression experiments. Several TwBAHD genes in the Taxus-specific branch were highly expressed in different tissues of T. mairei, suggesting an important role in the taxol pathway. This study provides comprehensive information for the TwBAHD gene family and sets up a basis for its potential functions. Full article

The genus Neopestalotiopsis consists of obligate parasites that cause ring spot, scab, and leaf blight diseases in higher plant species. We assembled the three complete mitogenomes for the guava fruit ring spot pathogen, Neopestalotiopsis cubana. The mitogenomes are circular, with sizes of 38,666 bp, 33,846 bp, and 32,593 bp. The comparative analyses with Pestalotiopsis fici showed that N. cubana differs greatly from it in the length of the mitogenomes and the number of introns. Moreover, they showed significant differences in the gene content and tRNAs. The two genera showed little difference in gene skewness and codon preference for core protein-coding genes (PCGs). We compared gene sequencing in the mitogenomes of the order Xylariales and found large-scale gene rearrangement events, such as gene translocations and the duplication of tRNAs. N. cubana shows a unique evolutionary position in the phylum Ascomycota constructed in phylogenetic analyses. We also found a more concentrated distribution of evolutionary pressures on the PCGs of Neopestalotiopsis in the phylum Ascomycota and that they are under little selective pressure compared to other species and are subjected to purifying selection. This study explores the evolutionary dynamics of the mitogenomes of Neopestalotiopsis and provides important support for genetic and taxonomic studies. Full article