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Translation fidelity relies on accurate aminoacylation of transfer RNAs (tRNAs) by aminoacyl-tRNA synthetases (AARSs). AARSs specific for alanine (Ala), leucine (Leu), serine, and pyrrolysine do not recognize the anticodon bases. Single nucleotide anticodon variants in their cognate tRNAs can lead to mistranslation. Human genomes include both rare and more common mistranslating tRNA variants. We investigated three rare human tRNALeu variants that mis-incorporate Leu at phenylalanine or tryptophan codons. Expression of each tRNALeu anticodon variant in neuroblastoma cells caused defects in fluorescent protein production without significantly increased cytotoxicity under normal conditions or in the context of proteasome inhibition. Using tRNA sequencing and mass spectrometry we confirmed that each tRNALeu variant was expressed and generated mistranslation with Leu. To probe the flexibility of the entire genetic code towards Leu mis-incorporation, we created 64 yeast strains to express all possible tRNALeu anticodon variants in a doxycycline-inducible system. While some variants showed mild or no growth defects, many anticodon variants, enriched with G/C at positions 35 and 36, including those replacing Leu for proline, arginine, alanine, or glycine, caused dramatic reductions in growth. Differential phenotypic defects were observed for tRNALeu mutants with synonymous anticodons and for different tRNALeu isoacceptors with the same anticodon. A comparison to tRNAAla anticodon variants demonstrates that Ala mis-incorporation is more tolerable than Leu at nearly every codon. The data show that the nature of the amino acid substitution, the tRNA gene, and the anticodon are each important factors that influence the ability of cells to tolerate mistranslating tRNAs.

The efficiency with which aminoacyl-tRNA and GTP-bound translation elongation factor EF-Tu recognizes the A-site codon of the ribosome is dependent on codons and tRNA species present in the polypeptide (P) and exit (E) codon sites. To understand how codon context affects the efficiency of codon recognition by tRNA-bound EF-Tu, a genetic system was developed to select for fast translation through slow-translating codon combinations. Selection for fast translation through the slow-translated UCA-UAC pair, flanked by histidine codons, resulted in the isolation of an A25G base substitution mutant in the D-stem of an essential tRNA LeuZ, which recognizes the UUA and UUG leucine codons. The LeuZ(A25G) substitution allowed for faster translation through all codon pairs tested that included the UCA codon. Insertion of leucine at the UCA serine codon was enhanced in the presence of LeuZ(A25G) tRNA. This work, taken in context with the Hirsh UGA nonsense suppressor G24A mutation in TrpT tRNA, provides genetic evidence that the post-GTP hydrolysis proofreading step by elongation factor Tu may be controlled by structural interactions in the hinge region of tRNA species. Our results support a model in which the tRNA bending component of the accommodation step in mRNA translation allows EF Tu time to enhance its ability to differentiate tRNA interactions between cognate and near-cognate mRNA codons. Author summary: The translation of mRNA into protein by the ribosome is one of the most fundamental processes in Biology. GTP-bound elongation factor EF-Tu brings charged aminoacyl-tRNAs to the A-site in the ribosome decoding center to determine if the anti-codon of the tRNA is correct for a given codon being read. Differentiating proper cognate codon recognition from near-cognate codons is coupled to GTP hydrolysis and a conformational bending of the tRNA in the hinge region of the tRNA structure. We show that a tRNA mutant with a single base substitution in the hinge region of the tRNA allows for enhanced near-cognate codon recognition and an increase in the speed of codon translation. This result suggests an evolutionary trade-off between speed of codon recognition by the translation machinery and fidelity of the translation process. [ABSTRACT FROM AUTHOR]

Mosquitoes such as Aedes aegypti must consume a blood meal for the nutrients necessary for egg production. Several transcriptome and proteome changes occur post‐blood meal that likely corresponds with codon usage alterations. Transfer RNA (tRNA) is the adapter molecule that reads messenger RNA codons to add the appropriate amino acid during protein synthesis. Chemical modifications to tRNA enhance codon decoding, improving the accuracy and efficiency of protein synthesis. Here, we examined tRNA modifications and transcripts associated with the blood meal and subsequent periods of vitellogenesis in A. aegypti. More specifically, we assessed tRNA transcript abundance and modification levels in the fat body at critical times post blood‐feeding. Based on a combination of alternative codon usage and identification of particular modifications, we discovered that increased transcription of tyrosine tRNAs is likely critical during the synthesis of egg yolk proteins in the fat body following a blood meal. Altogether, changes in both the abundance and modification of tRNA are essential factors in the process of vitellogenin production after blood‐feeding in mosquitoes. [ABSTRACT FROM AUTHOR]

Background and Purpose: Renal interstitial fibrosis is a frequent pathological manifestation of lupus nephritis (LN). tRNA halves (tiRNAs) are acquired from tRNA‐derived small non‐coding RNAs (sncRNAs) and are associated with fibrosis. Our previous study indicated enhanced tiRNA‐Gly‐GCC‐002 (tiRNA002) levels in kidneys were positively related to LN‐related fibrosis. However, the precise molecular mechanism remains unclear. Experimental Approach: The mimic and agomiR of tiRNA002 were introduced into tubular epithelial cells (TECs) and MRL/lpr mice by transfection. The levels of gene and protein expressions were quantified using real‐time quantitative polymerase chain reaction (RT‐qPCR), Western blot and immunofluorescence assays. Key Results: In TECs treated with LN serum, as well as in the kidneys of MRL/lpr mice, high levels of tiRNA002 directly influenced the epithelial‐mesenchymal transition (EMT) and extracellular matrix (ECM) deposition. Furthermore, tiRNA002 overexpression promoted EMT in TECs and accelerated renal interstitial fibrosis in MRL/lpr mice via Smad signalling. The target gene of tiRNA002, FKBP prolyl isomerase 5 (FKBP5), improved Smad signalling by interacting with phosphorylated Smad2/3. Silencing FKBP5 alleviated LN serum‐ or tiRNA002‐mimic‐induced EMT in TECs. In addition, FKBP5 overexpression reversed the tiRNA002 knockdown‐mediated reduction of EMT and ECM accumulation. Conclusions and Implications: These findings indicated that tiRNA002 is markedly increased in LN, which facilitates renal fibrosis by promoting EMT via FKBP5‐mediated Smad signalling. Therefore, targeting tiRNA002 may be an innovative approach to treat renal interstitial fibrosis in LN. [ABSTRACT FROM AUTHOR]

The genomic-level characteristics play a pivotal role as genetic assets for the identification of species and phylogenetic analysis. Here, we sequenced and analyzed the mitochondrial genome of Scambus vesicarius (Ratzeburg), which was first morphologically described in "Die Ichneumonen der Forstinsecten in forstlicher und entomologischer Beziehung." The motivation for this research arises from the necessity to comprehend the genetic composition and evolutionary history of S. vesicarius, a genus of parasitic wasps with potential agricultural significance, which. The circular genome is 26,103bp in length with an overall base composition of 42.02% for A, 43.71% for T, 8.64% for C, and 5.63% for G. The mitochondrial genome of S. vesicarius contained 13 protein-coding genes that initiated by the ATN codon, 22 transfer RNA genes, two ribosomal RNA genes (rRNAs), and a control region (CR). Phylogenetic analyses using Maximum-likelihood methods supported that S. vesicarius is closely related to Pimpla luctuosa, both of which belong to the subfamily Pimplinae, forming a clade that is sister to other subfamilies of Ichneumonidae. This study provides value not only into the genetic diversity and evolutionary history of S. vesicarius at the mitochondrial level but basic research on parasitic wasp biology and applied efforts in biological control. [ABSTRACT FROM AUTHOR]

Rubus swinhoei Hance is an important plant owing to its medicinal root and edible fruit, and extensively distributed in China. In this study, we reported the complete chloroplast genome of R. swinhoei. The chloroplast genome was 156,335 bp in size with the overall GC content of 37.15%, having a circular and quadripartite structure, which contained a large single-copy (LSC) and a small single-copy (SSC) regions of 85,897 bp and 18,858 bp separated by a pair of 25,790 bp inverted repeat (IR) regions. The complete chloroplast genome comprised 131 unique genes of which 86 and 37 were protein-coding genes and tRNA genes, respectively, and also eight rRNA genes. The phylogenetic analysis revealed that R. swinhoei was closely related to R. kawakamii. The genome information reported in this paper will be beneficial for further investigation on the evolution of this species. [ABSTRACT FROM AUTHOR]

Solanum melongena 'Yunqie 9' was selected by the Horticultural Research Institute of Yunnan Academy of Agricultural Sciences based on the local environment of Yunnan Province. It is excellent in fruit quality and yield, but it is relatively weak in disease resistance. No information on complete chloroplast genome and position in the phylogeny of Solanum to restrict its genetic improvement. In this study, the chloroplast genome of 'Yunqie 9' was sequenced using Illumina high-throughput sequencing technology. The size of the complete chloroplast genome was 155,579 bp in length with an GC content of 37.70%, composed of a large single-copy region (86,189 bp), a small single-copy region (18,504 bp), and a pair of inverted repeat regions (25,443 bp). A total of 134 coding genes were annotated in the entire chloroplast genome, including 89 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis based on chloroplast genome sequences of 20 species in the Solanaceae family indicated that except for the cultivated Solanum, 'Yunqie 9' was closely related to Solanum melongena×Solanum torvum and Solanum insanum. [ABSTRACT FROM AUTHOR]

Genomic resources for Barringtonia asiatica (L.) Kurz, a pantropical beach forest species native to the Philippines, have not been published to date, despite its medicinal importance and potential for biomedical applications. In this study, we assembled and characterized the first complete chloroplast genome of B. asiatica using Illumina paired-end sequencing technology. It displayed a typical quadripartite structure with a sequence length of 158,794 bp, comprised of a large single copy of 88,196 bp, small single-copy of 18,448 bp, and a pair of inverted repeat regions of 26,075 bp each. The cp genome contained 35 tRNA genes, eight rRNA genes, and 86 protein-coding genes with an overall GC content of 36.8%. Phylogenetic analysis revealed a close evolutionary relationship between B. racemosa and B. fusicarpa, forming a monophyletic group with B. asiatica with high bootstrap support, thereby enhancing our understanding of the phylogeny, systematics, and genetics of Asian Lecythidaceae species. [ABSTRACT FROM AUTHOR]

Persicaria jucunda is a plant distributed at meadow or wetland. Our study reports the complete chloroplast genome. The chloroplast genome of P. jucunda is a typical tetrameric structure with a total length of 159,843 bp, containing a large single-copy (LSC) region of 84,350 bp, a small single-copy (SSC) region of 13,151 bp, and two inverted repeat regions (IRs) of 31,171 bp. The total GC content was 38.2%, 36.5% for the LSC region, 33.2% for the SSC region, and 41.5% for the IR region. The P. jucunda chloroplast genome contains 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 36 chloroplast genomes showed similarity to P. foliosa and P. kawagoeana among the species analyzed. The chloroplast genome provides a valuable genetic resource for phylogenetic studies. [ABSTRACT FROM AUTHOR]

Cathetus clarkei, a significant folk medicinal plant, is utilized to treat a variety of ailments. In this study, we reported the complete chloroplast genome sequence of this species. The length of the complete chloroplast genome was 155,810 bp, included a pair of inverted repeat (IR) regions (26,340 bp), a large single-copy region (LSC, 84,853 bp), and a small single-copy region (SSC, 18,277 bp). It comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The total GC content was 36.8%. The phylogenetic tree revealed that C. clarkei had a close relationship with P. cochinchinensis, followed by P. reticulatus. This study provides a reference for important medicinal plants within the Phyllanthaceae, and we can gain a deeper understanding of how the species adapts to changes in the environment, helping us to identify and protect it. [ABSTRACT FROM AUTHOR]

N7-methylguanosine (m7G) is an important RNA modification involved in epigenetic regulation that is commonly observed in both prokaryotic and eukaryotic organisms. Their influence on the synthesis and processing of messenger RNA, ribosomal RNA, and transfer RNA allows m7G modifications to affect diverse cellular, physiological, and pathological processes. m7G modifications are pivotal in human diseases, particularly cancer progression. On one hand, m7G modification-associated modulate tumour progression and affect malignant biological characteristics, including sustained proliferation signalling, resistance to cell death, activation of invasion and metastasis, reprogramming of energy metabolism, genome instability, and immune evasion. This suggests that they may be novel therapeutic targets for cancer treatment. On the other hand, the aberrant expression of m7G modification-associated molecules is linked to clinicopathological characteristics, including tumour staging, lymph node metastasis, and unfavourable prognoses in patients with cancer, indicating their potential as tumour biomarkers. This review consolidates the discovery, identification, detection methodologies, and functional roles of m7G modification, analysing the mechanisms by which m7G modification-associated molecules contribute to tumour development, and exploring their potential clinical applications in cancer diagnostics and therapy, thereby providing innovative strategies for tumour identification and targeted treatment. [ABSTRACT FROM AUTHOR]

Primary mitochondrial disorders are most often caused by deleterious mutations in the mitochondrial DNA (mtDNA). Here, we used a mitochondrial DddA-derived cytosine base editor (DdCBE) to introduce a compensatory edit in a mouse model that carries the pathological mutation in the mitochondrial transfer RNA (tRNA) alanine (mt-tRNAAla) gene. Because the original m.5024C→T mutation (G→A in the mt-tRNAAla) destabilizes the mt-tRNAAla aminoacyl stem, we designed a compensatory m.5081G→A edit (C→T in the mt-tRNAAla) that could restore the secondary structure of the tRNAAla aminoacyl stem. For this, the DdCBE gene construct was initially tested in an m.5024C→T mutant cell line. The reduced mt-tRNAAla amounts in these cells were increased after editing up to 78% of the mtDNA. Then, DdCBE was packaged in recombinant adeno-associated virus 9 (AAV9) and intravenously administered by retro-orbital injections into mice. Expression of the transduced DdCBE was observed in the heart and skeletal muscle. Total mt-tRNAAla amounts were restored in heart and muscle by the m.5081G→A edit in a dose-dependent manner. Lactate amounts, which were increased in the heart, were also decreased in treated mice. However, the highest dose tested of AAV9-DdCBE also induced severe adverse effects in vivo because of the extensive mtDNA off-target editing that it generated. These results show that although DdCBE is a promising gene therapy tool for mitochondrial disorders, the doses of the therapeutic constructs must be carefully monitored to avoid deleterious off-target editing. Editor's summary: Mitochondrial disorders are inherited and often linked to mitochondrial DNA (mtDNA) mutations. Pathologically mutated mtDNA can cause diverse physiological dysfunction that is limited to palliative care. Barrera-Paez et al. used a mitochondrial DddA-derived cytosine base editor (DdCBE) to correct a mutation in the mtDNA encoding a mitochondrial transfer RNA (tRNA) alanine. The mutation disrupted the aminoacyl stem of the tRNA. Correction with DdCBE restored the structure and amounts of the tRNA in cell culture and in mouse heart and muscle tissue. Mice carrying the mtDNA mutation had low mitochondrial tRNA alanine and increased lactate in heart, and editing with DdCBE reversed these abnormalities. At the highest amounts of editing, DdCBE also induced off-target edits that resulted in severe adverse effects in mice. These data suggest that while DdCBE is a promising therapeutic avenue for mitochondrial gene editing, caution and further study are warranted to avoid damaging off-target effects. —Brandon Berry [ABSTRACT FROM AUTHOR]

While all native tRNAs undergo extensive post-transcriptional modifications as a mechanism to regulate gene expression, mapping these modifications remains challenging. The critical barrier is the difficulty of readthrough of modifications by reverse transcriptases (RTs). Here we use Induro—a new group-II intron-encoded RT—to map and quantify genome-wide tRNA modifications in Induro-tRNAseq. We show that Induro progressively increases readthrough over time by selectively overcoming RT stops without altering the misincorporation frequency. In a parallel analysis of Induro vs. a related RT, we provide comparative datasets to facilitate the prediction of each modification. We assess tRNA modifications across five human cell lines and three mouse tissues and show that, while the landscape of modifications is highly variable throughout the tRNA sequence framework, it is stabilized for modifications that are required for reading of the genetic code. The coordinated changes have fundamental importance for development of tRNA modifications in protein homeostasis. Here the authors report genome-wide profiling of tRNA modifications using Induro-tRNAseq and uncover coordinated changes across cell types and tissues that underlie the basis of protein homeostasis. [ABSTRACT FROM AUTHOR]

RNA helicase DEAD-box helicase 1 (DDX1) forms a complex with the RNA ligase 2´,3´-cyclic phosphate and 5´-OH ligase (RTCB), which plays a vital role in non-spliceosomal splicing of tRNA and X-box binding protein 1 (XBP1) mRNA. However, the importance of DDX1 in non-spliceosomal splicing has not been clarified. To analyze the functions of DDX1 in mammalian cells, we generated DDX1 cKO cells from the polyploid human U2OS cell line and found that splicing of intron-containing tRNAs was significantly disturbed in DDX1-deficient cells, whereas endoplasmic reticulum (ER) stress-induced splicing of XBP1 mRNA was unaffected. Additionally, the enforced expression of DDX1, but not of its helicase-inactive mutant, rescued the splicing defects of tRNAs in DDX1-deficient cells. These results indicate that RTCB is required for the splicing of both tRNA and XBP1 mRNA, whereas the DDX1 enzymatic activity is specifically required for tRNA splicing in vivo. RTCB is required for the splicing of both tRNA and XBP1 mRNA, whereas the DDX1 enzymatic activity is specifically required for tRNA splicing in vivo. [ABSTRACT FROM AUTHOR]

Background: Pleuronectiformes, also known as flatfish, are important model and economic animals. However, a comprehensive genome survey of their important organelles, mitochondria, has been limited. Therefore, we aim to analyze the genomic structure, codon preference, nucleotide diversity, selective pressure and repeat sequences, as well as reconstruct the phylogenetic relationship using the mitochondrial genomes of 111 flatfish species. Results: Our analysis revealed a conserved gene content of protein-coding genes and rRNA genes, but varying numbers of tRNA genes and control regions across species. Various gene rearrangements were found in flatfish species, especially for the rearrangement of nad5-nad6-cytb block in Samaridae family, the swapping rearrangement of nad6 and cytb gene in Bothidae family, as well as the control region translocation and tRNA-Gln gene inversion in the subfamily Cynoglossinae, suggesting their unique evolutionary history and/or functional benefit. Codon usage showed obvious biases, with adenine being the most frequent nucleotide at the third codon position. Nucleotide diversity and selective pressure analysis suggested that different protein-coding genes underwent varying degrees of evolutionary pressure, with cytb and cox genes being the most conserved ones. Phylogenetic analysis using both whole mitogenome information and concatenated independently aligned protein-coding genes largely mirrored the taxonomic classification of the species, but showed different phylogeny. The identification of simple sequence repeats and various long repetitive sequences provided additional complexity of genome organization and offered markers for evolutionary studies and breeding practices. Conclusions: This study represents a significant step forward in our comprehension of the flatfish mitochondrial genomes, providing valuable insights into the structure, conservation and variation within flatfish mitogenomes, with implications for understanding their evolutionary history, functional genomics and fisheries management. Future research can delve deeper into conservation biology, evolutionary biology and functional usages of variations. [ABSTRACT FROM AUTHOR]

The utilization of chemical pesticides recovers 30%−40% of food losses. However, their application has also triggered a series of problems, including food safety, environmental pollution, pesticide resistance, and incidents of poisoning. Consequently, green pesticides are increasingly seen as viable alternatives to their chemical counterparts. Among these, Plant Growth-Promoting Rhizobacteria (PGPR), which are found within plant rhizosphere, stand out for their capacity to stimulate plant growth. Recently, we isolated a strain, BN, with broad-spectrum antimicrobial activity from the rhizosphere of Lilium brownii. Identification revealed that this strain belongs to the species Bacillus velezensis and exhibits significant inhibitory effects against various fungal plant pathogens. The complete genome sequence of B. velezensis BN consists of a circular chromosome with a length of 3,929,791 bp, includes 3,747 protein-coding genes, 81 small RNAs, 27 rRNAs, and 86 tRNAs. Genomic analysis revealed that 29% of the genes are directly involved in plant growth, while 70% of the genes are indirectly involved. In addition, 12 putative biosynthetic gene clusters were identified, responsible for the synthesis of secondary metabolites, such as non-ribosomal peptides, lanthipeptides, polyketides, siderophores, and terpenes. These findings provide a scientific basis for the development of efficient antimicrobial agents and the construction of biopesticide production platforms in chassis cells. [ABSTRACT FROM AUTHOR]

In addition to the 20 canonical amino acids encoded in the genetic code, there are two non-canonical ones: selenocysteine and pyrrolysine. The discovery of pyrrolysine synthetases (PylRSs) was a key event in the field of genetic code expansion research. The importance of this discovery is mainly due to the fact that the translation systems involving PylRS, pyrrolysine tRNA (tRNAPyl) and pyrrolysine are orthogonal to the endogenous translation systems of organisms that do not use this amino acid in protein synthesis. In addition, pyrrolysine synthetases belonging to different groups are also mutually orthogonal. This orthogonality is based on the structural features of PylRS and tRNAPyl, which include identical elements, such as a condensed core, certain base pairs and the structural motifs of tRNAPyl. This suggests that targeted structural changes in these molecules enable changes in their specificity for the amino acid and the codon. Such modifications were successfully used to obtain different aaRS/tRNA pairs that allow the incorporation of unnatural amino acids into peptides. This review presents the results of recent studies related to the correlation between the structure and activity of PylRS and tRNAPyl and the use of pyrrolysine synthetases to extend the genetic code. [ABSTRACT FROM AUTHOR]

Highlights: tsRNAs are small RNAs generated through specific cleavage of parent tRNAs, found across all domains of life, including protozoan parasites. tsRNAs are classified into tRNA halves formed by cleavage of a mature tRNA molecule at the anti-codon loop, or tRNA fragments, formed by cleavage of both pre- and mature- tRNAs at various positions. Various functions of tsRNAS have been identified including modulation of gene expression, translation inhibition, and response to cellular stress. tsRNAs have also been found to be packaged into extracellular vesicles and transported into host cells to modulate their gene expression. tRFs are formed by cleaving parent tRNA molecules into halves or smaller fragments. tRNA molecules are among the most fundamental and evolutionarily conserved RNA types, primarily facilitating the translation of genetic information from mRNA into proteins. Beyond their canonical role as adaptor molecules during protein synthesis, tRNAs have evolved to perform additional functions. One such non-canonical role for tRNAs is through the generation of tRNA-derived fragments via specific cleavage processes. These tRNA-derived small RNAs (tsRNAs) are present across all three domains of life, including in protozoan parasites. They are formed through the cleavage of the parent tRNA molecules at different sites, resulting in either tRNA halves or smaller fragments. The precise mechanisms underlying the synthesis of various tRNA-derived fragments, including the specific RNases involved, as well as their distinct functions and roles in parasite physiology, are not yet fully understood and remain an active area of ongoing research. However, their role in modulating gene expression, particularly during stress responses, is becoming increasingly evident. In this context, we discuss recent findings on the roles of tRNA-derived small RNA in various protozoan parasites. Furthermore, we investigate how these tsRNAs either modulate gene expression within the parasite itself or are packaged into extracellular vesicles to alter host gene expression, thereby promoting parasite survival and adaptation. [ABSTRACT FROM AUTHOR]

RNA modifications are conserved chemical features found in all domains of life and across diverse RNA biotypes, shaping gene expression profiles and enabling rapid responses to environmental changes. Their broad chemical diversity and dynamic nature pose significant challenges for studying them comprehensively. These limitations can now be addressed through direct RNA nanopore sequencing (DRS), which allows simultaneous identification of diverse RNA modification types at single-molecule and single-nucleotide resolution. Here, we review recent efforts pioneering the use of DRS to better understand the epitranscriptomic landscape. We highlight how DRS can be applied to investigate different RNA biotypes, emphasizing the use of specialized library preparation protocols and downstream bioinformatic workflows to detect both natural and synthetic RNA modifications. Finally, we provide a perspective on the future role of DRS in epitranscriptomic research, highlighting remaining challenges and emerging opportunities from improved sequencing yields and accuracy enabled by the latest DRS chemistry. Direct RNA sequencing (DRS) enables systematic profiling of RNA modifications at an unprecedented resolution. Here, Diensthuber and Novoa review key efforts made to date pioneering the use of DRS for epitranscriptomic profiling in distinct RNA biotypes and provide an overview of key biological insights learned, unresolved controversies, and future directions. [ABSTRACT FROM AUTHOR]

Anisarchus medius (Reinhardt, 1837) is a widely distributed Arctic fish, serving as an indicator of climate change impacts on coastal Arctic ecosystems. This study presents a chromosome-level genome assembly for A. medius using PacBio sequencing and Hi-C technology. The PacBio assembly totaled 739.07 Mb across 697 contigs, with a Contig N50 of 10.004 Mb. Hi-C mapping yielded 23 chromosomes, with a successful mapping rate of 90.53% and a Scaffold N50 of 30.20 Mb. Genome BUSCO integrity was 97.05%. Repetitive sequences accounted for 240.83 Mb (32.58%) of the genome. Non-coding RNA annotations included 4,928 rRNAs, 9,663 tRNAs, 347 snRNAs, and 21 snoRNAs. A total of 30,345 protein-coding genes were identified, encoding 46,603 proteins, with a BUSCO completeness of 94.98%. Molecular pathway related to the endocrine system, carbohydrate metabolism, folding, sorting, and degradation, signal transduction, and transport and catabolism contribute to A. medius adaptation to extreme Arctic environments. This high-quality genome provides valuable genetic resources for understanding Arctic adaptations and supporting polar ecological conservation and management. [ABSTRACT FROM AUTHOR]

Ischemic retinopathies are the major causes of blindness, yet effective early-stage treatments remain limited due to an incomplete understanding of the underlying molecular mechanisms. Significant changes in gene expression often precede structural and functional alterations. Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are emerging as novel gene regulators, involved in various biological processes and human diseases. In this study, tsRNA-Gln-i-0095 was identified as a novel regulator, which was significantly upregulated in retinal ischemia/reperfusion (I/R) injury. Reducing the levels of tsRNA-Gln-i-0095 suppressed reactive gliosis, lowered inflammatory cytokine levels, and protected retinal ganglion cells from I/R injury. These effects led to reduced structural and functional damage, inhibited glial activation and inflammation, and enhanced neuronal function. Mechanistically, tsRNA-Gln-i-0095 downregulated the expression of NFIA and TGFBR2 through a miRNA-like mechanism. Collectively, this study highlights the potential of targeting tsRNA-Gln-i-0095 as a novel therapeutic approach to reduce retinal I/R injury and preserve visual function. [ABSTRACT FROM AUTHOR]

The TRAMP complex contains two enzymatic activities essential for RNA processing upstream of the nuclear exosome. Within TRAMP, RNA is 3' polyadenylated by a subcomplex of Trf4/5 and Air1/2 and unwound 3' to 5' by Mtr4, a DExH helicase. The molecular mechanisms of TRAMP assembly and RNA shuffling between the two TRAMP catalytic sites are poorly understood. Here, we report solution hydrogen-deuterium exchange data with thermodynamic and functional assays to uncover these mechanisms for yeast TRAMP with Trf4 and Air2 homologs. We show that TRAMP assembly constrains RNA-recognition motifs that are peripheral to catalytic sites. These include the Mtr4 Arch and Air2 zinc knuckles 1, 2, and 3. While the Air2 Arch-interacting motif likely constrains the Mtr4 Arch via transient interactions, these do not fully account for the importance of the Mtr4 Arch in TRAMP assembly. We further show that tRNA binding by single active-site subunits, Mtr4 and Trf4-Air2, differs from the double active-site TRAMP. TRAMP has reduced tRNA binding on the Mtr4 Fist and RecA2 domains, offset by increased tRNA binding on Air2 zinc knuckles 2 and 3. Competition between these RNA-binding sites may drive tRNA transfer between TRAMP subunits. We identify dynamic changes upon TRAMP assembly and RNA-recognition motifs that transfer RNA between TRAMP catalytic sites. [ABSTRACT FROM AUTHOR]

Transgenic expression of a double-stranded RNA in plants can induce silencing of homologous mRNAs in fungal pathogens. Although such host-induced gene silencing is well documented, the molecular mechanisms by which RNAs can move from the cytoplasm of plant cells across the plasma membrane of both the host cell and fungal cell are poorly understood. Indirect evidence suggests that this RNA transfer may occur at a very early stage of the infection process, prior to breach of the host cell wall, suggesting that silencing RNAs might be secreted onto leaf surfaces. To assess whether Arabidopsis plants possess a mechanism for secreting RNA onto leaf surfaces, we developed a protocol for isolating leaf surface RNA separately from intercellular (apoplastic) RNA. This protocol yielded abundant leaf surface RNA that displayed an RNA banding pattern distinct from apoplastic RNA, suggesting that it may be secreted directly onto the leaf surface rather than exuded through stomata or hydathodes. Notably, this RNA was not associated with either extracellular vesicles or protein complexes; however, RNA species longer than 100 nucleotides could be pelleted by ultracentrifugation. Furthermore, pelleting was inhibited by the divalent cation chelator EGTA, suggesting that these RNAs may form condensates on the leaf surface. These leaf surface RNAs are derived almost exclusively from Arabidopsis, but come from diverse genomic sources, including rRNA, tRNA, mRNA, intergenic RNA, microRNAs, and small interfering RNAs, with tRNAs especially enriched. We speculate that endogenous leaf surface RNA plays an important role in the assembly of distinct microbial communities on leaf surfaces. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N²,N²-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes. [ABSTRACT FROM AUTHOR]

Senescence is a tumor suppressor mechanism triggered by oncogene expression and chemotherapy treatment. It orchestrates a definitive cessation of cell proliferation through the activation of the p53‐p21 and p16‐Rb pathways, coupled with the compaction of proliferative genes within heterochromatin regions. Some cancer cells have the ability to elude this proliferative arrest but the signaling pathways involved in circumventing senescence remain to be characterized. We have recently described that malignant cells capable of evading senescence have an increased expression of specific tRNAs, such as tRNA‐Leu‐CAA and tRNA‐Tyr‐GTA, alongside the activation of their corresponding tRNA ligases, namely LARS and YARS. We have previously shown that YARS promotes senescence escape by activating proliferation and cell cycle genes but its functions during this proliferative arrest remain largely unknown. In this study, we have continued to characterize the functions of YARS, describing non‐canonical transcriptional functions of the ligase. Our results show that YARS is present in the nucleus of proliferating and senescent cells and interacts with the Trim28 transcriptional regulator. Importantly, YARS binds to the LIN9 promoter, a critical member of the Dream complex responsible for regulating cell cycle gene transcription. The ligase facilitates the binding and the phosphorylation of the type II RNA polymerase and promotes the deposition of activating epigenetic marks on the LIN9 promoter. Consequently, during senescence escape, YARS activates LIN9 expression and both proteins are necessary to induce the proliferation of emergent cells. These results underscore unconventional transcriptional functions of YARS in activating LIN9 expression in proliferating cells and during senescence escape. [ABSTRACT FROM AUTHOR]

Tgt is the enzyme modifying the guanine (G) in tRNAs with GUN anticodon to queuosine (Q). tgt is required for optimal growth of Vibrio cholerae in the presence of sub-lethal aminoglycoside concentrations. We further explored here the role of the Q34 in the efficiency of codon decoding upon tobramycin exposure. We characterized its impact on the overall bacterial proteome, and elucidated the molecular mechanisms underlying the effects of Q34 modification in antibiotic translational stress response. Using molecular reporters, we showed that Q34 impacts the efficiency of decoding at tyrosine TAT and TAC codons. Proteomics analyses revealed that the anti-SoxR factor RsxA is better translated in the absence of tgt. RsxA displays a codon bias toward tyrosine TAT and overabundance of RsxA leads to decreased expression of genes belonging to SoxR oxidative stress regulon. We also identified conditions that regulate tgt expression. We propose that regulation of Q34 modification in response to environmental cues leads to translational reprogramming of transcripts bearing a biased tyrosine codon usage. In silico analysis further identified candidate genes which could be subject to such translational regulation, among which DNA repair factors. Such transcripts, fitting the definition of modification tunable transcripts, are central in the bacterial response to antibiotics. [ABSTRACT FROM AUTHOR]

Transfer RNAs (tRNAs) are noncoding RNAs involved in protein biosynthesis and have noncanonical roles in cellular metabolism, such as RNA silencing and the generation of transposable elements. Extensive tRNA gene duplications, modifications to mature tRNAs, and complex secondary and tertiary structures impede tRNA sequencing. As such, a comparative genomic analysis of complete tRNA sets is an alternative to understanding the evolutionary processes that gave rise to the extant tRNA sets. Although the tRNA gene (tDNA) structure and distribution in prokaryotes and eukaryotes, specifically in vertebrates, yeasts, and flies, are well understood, there is little information regarding plants. A detailed and comprehensive analysis and annotation of tDNAs from the genomes of 44 eudicots, 20 monocots, and five other non-eudicot and non-monocot species belonging to the Ceratophyllaceae and the ANA (Amborellales, Nymphaeales, and Austrobaileyales) clade will provide a global picture of plant tDNA structure and organization. Plant genomes exhibit varying numbers of nuclear tDNAs, with only the monocots showing a strong correlation between nuclear tDNA numbers and genome sizes. In contrast, organellar tDNA numbers varied little among the different lineages. A high degree of tDNA duplication in eudicots was detected, whereby most eudicot nuclear genomes (91%) and only a modest percentage of monocot (65%) and ANA nuclear genomes (25%) contained at least one tDNA cluster. Clusters of tRNATyr–tRNASer and tRNAIle genes were found in eudicot and monocot genomes, respectively, while both eudicot and monocot genomes showed clusters of tRNAPro genes. All plant genomes had intron-containing tRNAeMet and tRNATyr genes with modest sequence conservation and a strictly conserved tRNAAla-AGC species. Regulatory elements found upstream (TATA-box and CAA motifs) and downstream (poly(T) signals) of the tDNAs were present in only a fraction of the detected tDNAs. A and B boxes within the tDNA coding region show varying consensus sequences depending on the tRNA isotype and lineage. The chloroplast genomes, but not the mitogenomes, possess relatively conserved tRNA gene organization. These findings reveal differences and patterns acquired by plant genomes throughout evolution and can serve as a foundation for further studies on plant tRNA gene function and regulation. [ABSTRACT FROM AUTHOR]

In this study, we report the complete mitogenome of Nothrus silvestris Nicolet, 1855 (Acari, Oribatida, Nothridae) sequenced from Illumina sequencing data. The full length of this mitogenome is 14,592 bp with the nucleotide composition A (41.0%), C (22.2%), G (13.1%), and T (23.7%). The N. silvestris mitogenome comprises 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region. To elucidate the phylogenetic position of N. silvestris, a phylogenetic tree of 77 mite species were analyzed by maximum likelihood (ML) methods. According to phylogenetic analysis based on 13 protein-coding genes of mitogenomes, N. silvestris and Nothrus reticulatus were found the most basal Crotonioidea in the given dataset. This mitogenome not only enriches the genetic information of Nothridae, but also will be useful in the phylogenic and evolutional studies on oribatid mites. [ABSTRACT FROM AUTHOR]

Simple Summary: The genus Chlorophorus, the second largest genus of Clytini, belongs to Coleoptera, Cerambycidae. However, phylogenetic relationships within the genus remain unclear and the classification of subgenera based on elytral marking patterns remains untested. The mitochondrial genome has been widely used to reveal insect phylogeny and evolution. In this study, the complete mitochondrial genomes of 21 Chlorophorus species were sequenced, assembled, and annotated. A detailed comparative analysis was conducted on mitochondrial features, including nucleotide composition, relative synonymous codon usage (RSCU), and the evolutionary rates of protein-coding genes. Phylogenetic analysis was performed using mitochondrial genome data from 35 species, which included 12 outgroup species. The findings support the monophyly of the genus Chlorophorus and provide insights into certain subgenera. Additionally, a comparative examination of male genitalia revealed that the sclerites of the endophallus might exhibit phylogenetic signals relevant to the genus. The results of this study enhance our understanding of taxonomy and phylogenetic relationships within the genus Chlorophorus. Chlorophorus Chevrolat, 1863, one of the most species-rich genera of Clytini, comprises 36 subgenera and 302 species/subspecies, with some species being of significant economic importance. To assess the monophyly and subgeneric system of this genus, we newly obtained mitochondrial genomic data from 21 species of Chlorophorus via high-throughput sequencing and reconstructed the phylogeny of this genus using ML and BI methods. The mitochondrial genomes of all sequenced Chlorophorus species were found to comprise 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one non-coding region (control region, CR), reflecting a highly conserved gene arrangement. The mitochondrial genomes of the 21 Chlorophorus species range from 15,387 bp to 15,779 bp in length, and all exhibited AT bias. Analysis of the non-synonymous and synonymous substitution rates revealed that ATP8 has the highest evolution rate, whereas COI has the lowest. Further, phylogenetic analyses were performed based on different datasets (13 PCGs + 2 rRNAs, 13 PCGs + 2 rRNAs + 22 tRNAs, PCG123, PCG12) using maximum likelihood (ML) and Bayesian inference (BI) methods. The results indicate that Chlorophorus is monophyletic, but the subgenera Humeromaculatus Özdikmen, 2011; Immaculatoides Özdikmen, 2022; Brevenotatus Özdikmen, 2022; and Chlorophorus (s. str.) Chevrolat, 1863, are not monophyletic. Based on the comparison of male genitalia, we found that the sclerites of the endophallus may exhibit phylogenetic signals for the genus. [ABSTRACT FROM AUTHOR]

Simple Summary: Species of the family Echeneidae are known for their unique ability to adhere to various hosts using a sucking disc. However, little is known about the mitochondrial genome and evolutionary relationships within this family. This study analyzed the mitochondrial genome characteristics of three species (Echeneis naucrates, Remora albescens, and Remora remora) from the Echeneidae family and their phylogenetic relationships. The results showed that these species share similar mitochondrial features. Additionally, we found that R. osteochir and R. brachyptera were grouped together as sister taxa. This research provides valuable genetic data that will help improve the classification of the Echeneidae family and offer new insights into their evolutionary history. Species of the family Echeneidae are renowned for their capacity to adhere to various hosts using a sucking disc. This study aimed to examine the mitochondrial genome characteristics of three fish species (Echeneis naucrates, Remora albescens, and Remora remora) within the family Echeneidae and determine their phylogenetic relationships. The findings revealed that the mitochondrial genome lengths of the three species were 16,611 bp, 16,648 bp, and 16,623 bp, respectively, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a D-loop region. Most PCGs utilized ATG as the initiation codon, while only cox I used the GTG as the initiation codon. Additionally, seven genes employed incomplete termination codons (T and TA). The majority of PCGs in the three species displayed negative AT-skew and GC-skew values, with the GC-skew amplitude being greater than the AT-skew. The Ka/Ks ratios of the 13 PCGs did not exceed 1, demonstrating these species had been subjected to purification selection. Furthermore, only tRNA-Ser (GCT) lacked the D arm, while other tRNAs exhibited a typical cloverleaf secondary structure. Bayesian inference (BI) and maximum likelihood (ML) methods were utilized to construct a phylogenetic tree of the three species based on the 13 PCGs. Remora remora was identified as a distinct group, while R. osteochir and R. brachyptera were classified as sister taxa. This study contributes to the mitochondrial genome database of the family Echeneidae and provides a solid foundation for further systematic classification research in this fish group. [ABSTRACT FROM AUTHOR]

The species Niphon spinosus (Cuvier, 1829) is the only representative of the family Niphonidae and the genus Niphon, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome of N. spinosus (OP391482), which was determined to be 16,503 bp long with biased A + T contents (53.8%) using next-generation technology. The typical set of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region (D-loop) are included in the mitochondrial genome. The H-strand encoded 28 genes (14 tRNA, 2 rRNA, and 12 PCGs), and D-loop, whereas the L-strand encoded the remaining 9 genes (8 tRNA and ND6). Its nucleotide composition, gene arrangement, codon usage patterns, and tRNA secondary structures are identical with other members of the Percoidei suborder. Furthermore, we reconstructed phylogenetic trees based on the 13 PCGs. The resulting phylogenetic trees showed N. spinosus placing as a separate lineage within the family Niphonidae, its close relationship to Trachinus draco (Trachinidae), and the clustering of major subfamilies like Luciopercinae and Percinae of the Percoidei suborder. These findings will contribute to future studies on the evolutionary history, population genetics, molecular taxonomy, and phylogeny of N. spinosus and related species. [ABSTRACT FROM AUTHOR]

Mitochondrial genomes provide powerful insights into insect phylogeny and molecular evolution, aiding in the clarification of complex taxonomic relationships. Within the swallowtail butterfly subfamily Parnassiinae (Lepidoptera: Papilionidae), an insect group of significant environmental and economic importance, essential aspects of phylogenetic positioning remain unresolved. This study presents the first sequencing and annotation of the complete mitogenome for Parnassius stubbendorfii from two geographically distinct populations in Gansu Province, China. Both mitogenomes are circular, double-stranded molecules, measuring 15,377 bp and 15,348 bp in length, each encoding 37 standard mitochondrial genes: 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich control region. The gene arrangement is highly conserved and typical of Lepidoptera. Phylogenetic analyses based on both the 13 PCGs and the complete set of 37 mitochondrial genes supported the placement of Parnassiinae as a subfamily within Papilionidae, with Parnassini and Zerynthini identified as two distinct clades within Parnassiinae. Notably, tree topologies derived from the 13 PCGs alone exhibited slight deviations from those based on the full mitogenome, underscoring the need for expanded mitogenomic data across Papilionidae to further refine evolutionary relationships. [ABSTRACT FROM AUTHOR]

Since the discovery of RNA in the early 1900s, scientific understanding of RNA form and function has evolved beyond protein coding. Viruses, particularly retroviruses like human T-cell leukemia virus type 1 (HTLV-1), rely heavily on RNA and RNA post-transcriptional modifications to regulate the viral lifecycle, pathogenesis, and evasion of host immune responses. With the emergence of new sequencing technologies in the last decade, our ability to dissect the intricacies of RNA has flourished. The ability to study RNA epigenetic modifications and splice variants has become more feasible with the recent development of third-generation sequencing technologies, such as Oxford nanopore sequencing. This review will highlight the dynamic roles of known RNA and post-transcriptional RNA epigenetic modifications within HTLV-1 biology, including viral hbz, long noncoding RNAs, microRNAs (miRNAs), transfer RNAs (tRNAs), R-loops, N6-methyladenosine (m6A) modifications, and RNA-based therapeutics and vaccines. [ABSTRACT FROM AUTHOR]

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part of the taxonomically challenging genus Desmidorchis, are well‐known for their ecological resilience and medicinal significance. This study sequences the first complete chloroplast genomes of these species, shedding light on their genomic characteristics and evolutionary relationships. The circular genomes of D. penicillata (161 776 bp) and D. retrospiciens (162 277 bp) display a quadripartite structure typical of Angiosperms. Gene content, order, and GC content are consistent, featuring 114 unique genes, including 80 protein‐coding, 30 transfer RNAs, and four ribosomal RNAs genes. Codon usage analysis underscores A/U‐rich preferences, while RNA editing sites, predominantly in ndhB and ndhD genes, suggest post‐transcriptional modifications. Analysis of long repeated sequences reveals a predominance of forward and palindromic repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are abundant, with high presence of mononucleotide, offering potential molecular markers. Comparative analysis with their relatives in subtribe Stapeliinae identifies mutational hotspots such as ycf1, ndhF, trnG(GCC)‐trnfM(CGA) and ndhG‐ndhI that could be potential DNA barcoding markers. The inverted repeat (IR) boundaries analysis revealed an expansion of IR on the small single copy region, leading to the formation of a pseudogene. Overall, substitution rate analysis indicated purifying selection, with a few genes (rpl22, clpP and rps11) showing signatures of positive selection. Additionally, the phylogenetic analysis positioned Desmidorchis within the Stapeliinae clade and strongly supported the sister relationship between D. penicillata and D. retrospiciens. This study provides comprehensive molecular data for future research in Desmidorchis. [ABSTRACT FROM AUTHOR]

Objective: We aim to investigate transcriptomic and immunophenotypic features of muscle specimens from patients with idiopathic inflammatory myopathy (IIM). Methods: Bulk RNA‐sequencing was performed on muscle biopsy samples from 16 patients with dermatomyositis (DM) and 9 patients with polymyositis (PM). Seven tested positive for anti‐aminoacyl transfer RNA synthetase antibodies in the patients with DM (ARS‐DM). We conducted weighted gene coexpression network analysis (WGCNA), differentially expressed gene (DEG) analysis, and gene set variation analysis to assess contributions of specific pathways. Cell proportions in muscle specimens were estimated using a deconvolution approach. Results: WGCNA revealed significant positive correlations between serum creatine kinase (CK) levels and gene modules involved in cellular respiration, phagocytosis, and oxidative phosphorylation (OXPHOS). Significant positive correlations were also observed between CK levels and proportions of CD16‐positive and negative monocytes and myeloid dendritic cells. Notably, patients with DM demonstrated enrichment of complement and interferon‐α and γ pathway genes compared with those with PM. Furthermore, ARS‐DM demonstrated a higher proportion of Th1 cells and DEGs related to OXPHOS. Additionally, serum Krebs von den Lungen‐6 levels correlated with gene modules associated with extracellular matrix and the transforming growth factor‐β signaling pathway. Conclusion: Our study highlights a significant involvement of monocytes in muscle damage and delineates pathologic differences among IIM subtypes. DM was characterized by complement and interferon‐α and γ signaling, whereas ARS‐DM was associated with OXPHOS. Distinctive gene expression variations in muscle specimens suggest that different pathologic mechanisms underlie muscle damage in each IIM phenotype. [ABSTRACT FROM AUTHOR]

Introduction: The large-scale mullet, Parachelon grandisquamis (Teleostei: Mugilidae), is a monotypic species endemic to the eastern Atlantic Ocean, playing a crucial role in tropical ecosystems. Despite its ecological significance, the systematic classification of Mugilidae remains unresolved, largely due to their diverse morphology, which necessitates the integration of molecular data. Methods: This study aimed to achieve a comprehensive molecular characterization of the species and establish its matrilineal taxonomic placement using complete mitogenome data. Next-generation sequencing was employed to generate the de novo mitogenome of P. grandisquamis , which spans 16,859 bp and includes 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNAs, and a non-coding AT-rich control region (CR). Results: Most PCGs use ATG as the start codon, with the exception of COI , which begins with GTG. Analysis of amino acids abundance revealed high frequencies for leucine, serine, proline, threonine, and alanine with distinctive codon usage. The proportion of nonsynonymous and synonymous substitutions suggests strong purifying selection in most PCGs, except for ND4L , ND5 , and ND6. Most transfer RNAs exhibited typical cloverleaf secondary structures, with the exception of tRNA-Ser1 (GCT), which lacks base pairing in the DHU arm. Mitogenome-based phylogenetic analysis using the Bayesian approach revealed that the monotypic P. grandisquamis is closely related to the genera Chelon and Planiliza within Mugilidae. Furthermore, analysis of the CRs with polymorphic nucleotides in conserved blocks provides additional insight into the development of distinct molecular markers for species identification and population structure analysis of mullets. Discussion: Overall, this study provides a comprehensive analysis of the mitogenomic structure and variation of P. grandisquamis and other mullets , confirming its maternal evolutionary relationships and offering valuable insights for advancing SNP-based species discrimination within the Mugilidae lineage. [ABSTRACT FROM AUTHOR]

The article in Cell Discovery explores the structural basis for tRNA mimicry by mascRNA and menRNA, two long noncoding RNAs associated with cancer and metastasis. The maturation of these RNAs involves processing by RNase P, RNase Z, and CCA addition, resembling tRNA maturation. Crystal structures of human mascRNA and menRNA reveal a 3D L-shaped conformation similar to tRNA, with conserved elements and interactions crucial for processing. The study provides insights into how mascRNA and menRNA mimic tRNA, potentially recruiting RNase P and RNase Z for processing and maturation. [Extracted from the article]

The complete plastome size of Citrus hystrix DC. 1813 was 159,893 bp in length and has a typical quadripartite structure. The 87,148-bp-long large single-copy and the 18,763-bp-long small single-copy regions were separated by a pair of inverted repeats (each 26,991 bp). The plastome was predicted to contain 132 genes, of which 87 were CDS, 37 were tRNA, and eight were rRNA genes. The plastome was A/T biassed, and the overall GC content was 38.4%. Using maximum likelihood and Bayesian inference methods, the phylogenetic analysis of the complete plastome sequence revealed a close relationship between C. hystrix and C. aurantiifolia, placing them under the same clade as C. micrantha. [ABSTRACT FROM AUTHOR]

Aster scaber Thunb. (1784) is primarily distributed in eastern Asia, has a total length of 152,778 bp and consists of a large single copy (LSC) region of 84,517 bp, a small single copy (SSC) region of 18,277 bp, and two inverted repeat (IRs) regions of 24,992 bp. The GC content is 37.31%. A total of 133 genes were annotated, including 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis using the maximum likelihood method showed that A. scaber is closely related to Aster species. This study provides chloroplast genome resource for further research on the phylogenetics and resource development of A. scaber. [ABSTRACT FROM AUTHOR]

Clivia mirabilis Rourke 2002 is an evergreen herbaceous flower with high ornamental value. In this study, we sequenced the complete chloroplast (cp) genome of C. mirabilis and reported it for the first time. The cp genome was 158,914 base pairs (bp) in total length, including two inverted repeats (IRs, 27,052 bp), separated by a large single-copy region (LSC, 86,519 bp) and a small single-copy region (SSC, 18,291 bp). There are 133 different genes in the cp genome of Clivia mirabilis, including 87 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. The overall GC content of the cp genome was 37.9%. Our phylogenetic analysis showed that C. mirabilis formed a monophyletic clade with the other sampled species of Clivia, falling into the Amaryllidoideae clade. Our findings could be used to identify and analyze the genetic diversity of C. mirabilis and provide new data for taxonomic and phylogenetic studies of Clivia. [ABSTRACT FROM AUTHOR]

Rehmannia glutinosa, an extensively utilized Chinese herbal medicine, is highly valued for its medicinal properties. In this study, the complete mitochondrial genome (mitogenome) of R. glutinosa was sequenced and assembled for the first time. The mitogenome is 547,032 bp in length, with an overall GC content of 44.97%. The mitogenome contains 67 unique genes, comprising 43 protein-coding, three rRNA, and 21 tRNA genes, with six protein-coding and nine tRNA genes being chloroplast-derived. The phylogenetic analysis, based on the maximum-likelihood criterion, demonstrated that R. glutinosa is closely related to Aeginetia indica and Castilleja paramensis within the family Orobanchaceae. [ABSTRACT FROM AUTHOR]

Trichosanthes sunhangii (Cucurbitaceae) is an endemic species native to the Shennongjia forestry district of China, whose plastid genome was reported in this study. The whole genome exhibits the typical quadripartite structure with 156,906 bp in size. A total of 130 genes were identified, containing 85 protein-coding genes (CDS), 37 tRNA, and 8 rRNA genes. Phylogenetic reconstruction based on 83 shared CDS sequences reaffirmed the status of T. sunhangii within the Sect. Foliobracteola, revealing close relationships with morphologically similar species, T. kirilowii and T. rosthornii. Our findings will provide a significant foundation for future investigations into the evolution, conservation, and potential utilization of this species. [ABSTRACT FROM AUTHOR]

Vaccinium henryi Hemsl. 1889 is an endemic deciduous shrub in China, belonging to the family Ericaceae. In this study, the first complete chloroplast genome of V. henryi was assembled and annotated. The genome was 176,339 bp in size containing a large single-copy region of length 106,115 bp, a small single-copy region of length 3022 bp, and a pair of inverted repeat regions of 33,601 bp each. It contained 139 genes, including 91 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis exhibited that V. henryi and V. oldhamii were phylogenetic closely related. The chloroplast genome of V. henryi would provide valuable information for phylogenetic and evolutionary research on genus Vaccinium. [ABSTRACT FROM AUTHOR]