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1.
Insect Sci ; 2024 Apr 09.
Article in English | MEDLINE | ID: mdl-38594229

ABSTRACT

Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.

2.
Redox Biol ; 72: 103137, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38642502

ABSTRACT

The oncogene Aurora kinase A (AURKA) has been implicated in various tumor, yet its role in meningioma remains unexplored. Recent studies have suggested a potential link between AURKA and ferroptosis, although the underlying mechanisms are unclear. This study presented evidence of AURKA upregulation in high grade meningioma and its ability to enhance malignant characteristics. We identified AURKA as a suppressor of erastin-induced ferroptosis in meningioma. Mechanistically, AURKA directly interacted with and phosphorylated kelch-like ECH-associated protein 1 (KEAP1), thereby activating nuclear factor erythroid 2 related factor 2 (NFE2L2/NRF2) and target genes transcription. Additionally, forkhead box protein M1 (FOXM1) facilitated the transcription of AURKA. Suppression of AURKA, in conjunction with erastin, yields significant enhancements in the prognosis of a murine model of meningioma. Our study elucidates an unidentified mechanism by which AURKA governs ferroptosis, and strongly suggests that the combination of AURKA inhibition and ferroptosis-inducing agents could potentially provide therapeutic benefits for meningioma treatment.


Subject(s)
Aurora Kinase A , Ferroptosis , Forkhead Box Protein M1 , Meningioma , NF-E2-Related Factor 2 , Piperazines , Ferroptosis/drug effects , Ferroptosis/genetics , Forkhead Box Protein M1/metabolism , Forkhead Box Protein M1/genetics , Aurora Kinase A/metabolism , Aurora Kinase A/genetics , Humans , NF-E2-Related Factor 2/metabolism , NF-E2-Related Factor 2/genetics , Animals , Mice , Meningioma/metabolism , Meningioma/genetics , Meningioma/pathology , Piperazines/pharmacology , Cell Line, Tumor , Gene Expression Regulation, Neoplastic/drug effects , Signal Transduction/drug effects , Kelch-Like ECH-Associated Protein 1/metabolism , Kelch-Like ECH-Associated Protein 1/genetics , Meningeal Neoplasms/metabolism , Meningeal Neoplasms/genetics , Meningeal Neoplasms/pathology , Meningeal Neoplasms/drug therapy , Drug Resistance, Neoplasm/genetics
3.
Cell Mol Life Sci ; 81(1): 136, 2024 Mar 13.
Article in English | MEDLINE | ID: mdl-38478033

ABSTRACT

BACKGROUND: Metazoan adenosine-to-inosine (A-to-I) RNA editing resembles A-to-G mutation and increases proteomic diversity in a temporal-spatial manner, allowing organisms adapting to changeable environment. The RNA editomes in many major animal clades remain unexplored, hampering the understanding on the evolution and adaptation of this essential post-transcriptional modification. METHODS: We assembled the chromosome-level genome of Coridius chinensis belonging to Hemiptera, the fifth largest insect order where RNA editing has not been studied yet. We generated ten head RNA-Seq libraries with DNA-Seq from the matched individuals. RESULTS: We identified thousands of high-confidence RNA editing sites in C. chinensis. Overrepresentation of nonsynonymous editing was observed, but conserved recoding across different orders was very rare. Under cold stress, the global editing efficiency was down-regulated and the general transcriptional processes were shut down. Nevertheless, we found an interesting site with "conserved editing but non-conserved recoding" in potassium channel Shab which was significantly up-regulated in cold, serving as a candidate functional site in response to temperature stress. CONCLUSIONS: RNA editing in C. chinensis largely recodes the proteome. The first RNA editome in Hemiptera indicates independent origin of beneficial recoding during insect evolution, which advances our understanding on the evolution, conservation, and adaptation of RNA editing.


Subject(s)
Adenosine , RNA , Humans , Animals , RNA/genetics , Adenosine/genetics , Introns , Proteomics , Inosine/genetics , Insecta/genetics
4.
Insects ; 15(3)2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38535361

ABSTRACT

Due to the variability of body coloration and morphological similarity among closely related species, unresolved issues and debates still persist in the taxonomic study of the genus Sycanus from China. In this study, we conducted phylogenetic analyses and species delimitation for Sycanus in China based on a COI DNA barcoding dataset comprising 81 samples. The results revealed that all the samples could be classified into 12 species by integrating molecular analyses with morphological comparison. This paper provides a comprehensive systematic review of the Sycanus species found in China, including descriptions of three new species: S. taiwanensis Zhao & Cai sp. nov., S. flavicorius Li & Cai sp. nov., and S. hainanensis Wang & Cai sp. nov. Furthermore, it is proposed that S. croceovittatus Dohrn, 1859, S. leucomesus Walker, 1873, and S. villicus Stål, 1863, are three synonyms of S. bifidus (Fabricius, 1787); S. bicolor Hsiao, 1979, is a synonym of S. versicolor Dohrn, 1859; and S. hsiaoi Maldonado-Capriles, 1990, is a synonym of S. marginellus Putshkov, 1987. Additionally, brief biological information is provided for two species, S. falleni Stål, 1863, and S. croceus Hsiao, 1979.

5.
Epigenetics ; 19(1): 2333665, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38525798

ABSTRACT

Although A-to-I RNA editing leads to similar effects to A-to-G DNA mutation, nonsynonymous RNA editing (recoding) is believed to confer its adaptiveness by 'epigenetically' regulating proteomic diversity in a temporospatial manner, avoiding the pleiotropic effect of genomic mutations. Recent discoveries on the evolutionary trajectory of Ser>Gly auto-editing site in insect Adar gene demonstrated a selective advantage to having an editable codon compared to uneditable ones. However, apart from pure observations, quantitative approaches for justifying the adaptiveness of individual RNA editing sites are still lacking. We performed a comparative genomic analysis on 113 Diptera species, focusing on the Adar Ser>Gly auto-recoding site in Drosophila. We only found one species having a derived Gly at the corresponding site, and this occurrence was significantly lower than genome-wide random expectation. This suggests that the Adar Ser>Gly site is unlikely to be genomically replaced with G during evolution, and thus indicating the advantage of editable status over hardwired genomic alleles. Similar trends were observed for the conserved Ile>Met recoding in gene Syt1. In the light of evolution, we established a comparative genomic approach for quantitatively justifying the adaptiveness of individual editing sites. Priority should be given to such adaptive editing sites in future functional studies.


Subject(s)
Drosophila Proteins , RNA Editing , Animals , Proteomics , DNA Methylation , Mutation , Drosophila/genetics , Adenosine Deaminase/genetics , Adenosine Deaminase/metabolism , Drosophila Proteins/genetics
6.
Gigascience ; 13(1)2024 Jan 02.
Article in English | MEDLINE | ID: mdl-38372702

ABSTRACT

BACKGROUND: Lice (Psocodea: Phthiraptera) are one important group of parasites that infects birds and mammals. It is believed that the ancestor of parasitic lice originated on the ancient avian host, and ancient mammals acquired these parasites via host-switching from birds. Here we present the first chromosome-level genome of Menopon gallinae in Amblycera (earliest diverging lineage of parasitic lice). We explore the transition of louse host-switching from birds to mammals at the genomic level by identifying numerous idiosyncratic genomic variations. RESULTS: The assembled genome is 155 Mb in length, with a contig N50 of 27.42 Mb. Hi-C scaffolding assigned 97% of the bases to 5 chromosomes. The genome of M. gallinae retains a basal insect repertoire of 11,950 protein-coding genes. By comparing the genomes of lice to those of multiple representative insects in other orders, we discovered that gene families of digestion, detoxification, and immunity-related are generally conserved between bird lice and mammal lice, while mammal lice have undergone a significant reduction in genes related to chemosensory systems and temperature. This suggests that mammal lice have lost some of these genes through the adaption to environment and temperatures after host-switching. Furthermore, 7 genes related to hematophagy were positively selected in mammal lice, suggesting their involvement in the hematophagous behavior. CONCLUSIONS: Our high-quality genome of M. gallinae provides a valuable resource for comparative genomic research in Phthiraptera and facilitates further studies on adaptive evolution of host-switching within parasitic lice.


Subject(s)
Amblycera , Parasites , Animals , Poultry , Chromosomes , Mammals
7.
Nat Commun ; 15(1): 1379, 2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38355730

ABSTRACT

Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit crop loss. However, the consequences of large-scale releasing of captive A. gifuensis, such as genetic erosion and reduced fitness in wild populations of this species, remains unclear. Here, we sequence the genomes of 542 A. gifuensis individuals collected across China, including 265 wild and 277 human-intervened samples. Population genetic analyses on wild individuals recovered Yunnan populations as the ancestral group with the most complex genetic structure. We also find genetic signature of environmental adaptation during the dispersal of wild populations from Yunnan to other regions. While comparative genomic analyses of captive wasps revealed a decrease in genetic diversity during long-term rearing, population genomic analyses revealed signatures of natural selection by several biotic (host plants) or abiotic (climate) factors, which support maintenance of the gene pool of wild populations in spite of the introduction of captive wasps. Therefore, the impact of large-scale release is reduced. Our study suggests that A. gifuensis is a good system for exploring the genetic and evolutionary effects of mass rearing and release on species commonly used as biocontrol agents.


Subject(s)
Aphids , Wasps , Humans , Animals , Wasps/genetics , China , Selection, Genetic , Aphids/genetics , Genetic Variation , Host-Parasite Interactions
8.
Nucleus ; 15(1): 2304503, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38286757

ABSTRACT

Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Adar gene has uneditable Ser codons in ancestral nodes, indicating the selective advantage to having an editable status. Here, we extended this case study to more metazoan species, and also looked for all Drosophila recoding events with potential uneditable synonymous codons. Interestingly, in D. melanogaster, the abundant nonsynonymous editing is enriched in the codons that have uneditable counterparts, but the Adar Ser>Gly case suggests that the editable orthologous codons in other species are not necessarily edited. The use of editable versus ancestral uneditable codon is a smart way to infer the selective advantage of RNA editing, and priority might be given to these editing sites for functional studies due to the feasibility to construct an uneditable allele. Our study proposes an idea to narrow down the candidates of beneficial recoding sites. Meanwhile, we stress that the matched transcriptomes are needed to verify the conservation of editing events during evolution.


Subject(s)
Drosophila Proteins , RNA , Animals , RNA/genetics , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , RNA Editing/genetics , Inosine/genetics , Codon , Adenosine Deaminase/genetics , Adenosine Deaminase/metabolism , Drosophila Proteins/genetics
9.
Oncogene ; 43(1): 61-75, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37950039

ABSTRACT

The molecular mechanism of glioblastoma (GBM) radiation resistance remains poorly understood. The aim of this study was to elucidate the potential role of Melanophilin (MLPH) O-GlcNAcylation and the specific mechanism through which it regulates GBM radiotherapy resistance. We found that MLPH was significantly upregulated in recurrent GBM tumor tissues after ionizing radiation (IR). MLPH induced radiotherapy resistance in GBM cells and xenotransplanted human tumors through regulating the NF-κB pathway. MLPH was O-GlcNAcylated at the conserved serine 510, and radiation-resistant GBM cells showed higher levels of O-GlcNAcylation of MLPH. O-GlcNAcylation of MLPH protected its protein stability and tripartite motif containing 21(TRIM21) was identified as an E3 ubiquitin ligase promoting MLPH degradation whose interaction with MLPH was affected by O-GlcNAcylation. Our data demonstrate that MLPH exerts regulatory functions in GBM radiation resistance by promoting the NF-κB signaling pathway and that O-GlcNAcylation of MLPH both stabilizes and protects it from TRIM21-mediated ubiquitination. These results identify a potential mechanism of GBM radiation resistance and suggest a potential therapeutic strategy for GBM treatment.


Subject(s)
Glioblastoma , NF-kappa B , Humans , NF-kappa B/genetics , Cell Line, Tumor , Glioblastoma/genetics , Glioblastoma/radiotherapy , Glioblastoma/pathology , Neoplasm Recurrence, Local , Ubiquitination
10.
Mol Biol Evol ; 40(12)2023 Dec 01.
Article in English | MEDLINE | ID: mdl-38039153

ABSTRACT

Müllerian mimicry provides natural replicates ideal for exploring mechanisms underlying adaptive phenotypic divergence and convergence, yet the genetic mechanisms underlying mimetic variation remain largely unknown. The current study investigates the genetic basis of mimetic color pattern variation in a highly polymorphic bumble bee, Bombus breviceps (Hymenoptera, Apidae). In South Asia, this species and multiple comimetic species converge onto local Müllerian mimicry patterns by shifting the abdominal setal color from orange to black. Genetic crossing between the orange and black phenotypes suggested the color dimorphism being controlled by a single Mendelian locus, with the orange allele being dominant over black. Genome-wide association suggests that a locus at the intergenic region between 2 abdominal fate-determining Hox genes, abd-A and Abd-B, is associated with the color change. This locus is therefore in the same intergenic region but not the same exact locus as found to drive red black midabdominal variation in a distantly related bumble bee species, Bombus melanopygus. Gene expression analysis and RNA interferences suggest that differential expression of an intergenic long noncoding RNA between abd-A and Abd-B at the onset setal color differentiation may drive the orange black color variation by causing a homeotic shift late in development. Analysis of this same color locus in comimetic species reveals no sequence association with the same color shift, suggesting that mimetic convergence is achieved through distinct genetic routes. Our study establishes Hox regions as genomic hotspots for color pattern evolution in bumble bees and demonstrates how pleiotropic developmental loci can drive adaptive radiations in nature.


Subject(s)
Biological Mimicry , Genome-Wide Association Study , Bees/genetics , Animals , Phenotype , Biological Mimicry/genetics , Gene Editing , DNA, Intergenic/genetics
11.
Int J Mol Sci ; 24(24)2023 Dec 05.
Article in English | MEDLINE | ID: mdl-38138955

ABSTRACT

Adenosine-to-inosine (A-to-I) RNA editing is the most prevalent RNA modification in the nervous systems of metazoans. To study the biological significance of RNA editing, we first have to accurately identify these editing events from the transcriptome. The genome-wide identification of RNA editing sites remains a challenging task. In this review, we will first introduce the occurrence, regulation, and importance of A-to-I RNA editing and then describe the established bioinformatic procedures and difficulties in the accurate identification of these sit esespecially in small sized non-model insects. In brief, (1) to obtain an accurate profile of RNA editing sites, a transcriptome coupled with the DNA resequencing of a matched sample is favorable; (2) the single-cell sequencing technique is ready to be applied to RNA editing studies, but there are a few limitations to overcome; (3) during mapping and variant calling steps, various issues, like mapping and base quality, soft-clipping, and the positions of mismatches on reads, should be carefully considered; (4) Sanger sequencing of both RNA and the matched DNA is the best verification of RNA editing sites, but other auxiliary evidence, like the nonsynonymous-to-synonymous ratio or the linkage information, is also helpful for judging the reliability of editing sites. We have systematically reviewed the understanding of the biological significance of RNA editing and summarized the methodology for identifying such editing events. We also raised several promising aspects and challenges in this field. With insightful perspectives on both scientific and technical issues, our review will benefit the researchers in the broader RNA editing community.


Subject(s)
RNA , Transcriptome , RNA/genetics , RNA Editing , Reproducibility of Results , Adenosine/genetics , Adenosine/metabolism , DNA , Inosine/genetics , Inosine/metabolism
12.
Front Biosci (Landmark Ed) ; 28(10): 256, 2023 10 20.
Article in English | MEDLINE | ID: mdl-37919076

ABSTRACT

Metazoan adenosine-to-inosine (A-to-I) RNA editing is a highly conserved mechanism that diversifies the transcriptome by post-transcriptionally converting adenosine to inosine. Millions of editing sites have been identified in different species and, based on abnormal editing observed in various disorders, it is intuitive to conclude that RNA editing is both functional and adaptive. In this review, we propose the following major points: (1) "Function/functional" only represents a molecular/phenotypic consequence and is not necessarily connected to "adaptation/adaptive"; (2) Adaptive editing should be judged in the light of evolution and emphasize advantages of temporal-spatial flexibility; (3) Adaptive editing could, in theory, be extended from nonsynonymous sites to all potentially functional sites. This review seeks to conceptually bridge the gap between molecular biology and evolutionary biology and provide a more objective understanding on the biological functions and evolutionary significance of RNA editing.


Subject(s)
RNA Editing , RNA , Animals , RNA/genetics , RNA/metabolism , Adenosine/genetics , Adenosine/metabolism , Inosine/genetics , Inosine/metabolism , Transcriptome
13.
Zookeys ; 1182: 331-338, 2023.
Article in English | MEDLINE | ID: mdl-37900705

ABSTRACT

Renicorisgen. nov. and its type species Renicorisrobustussp. nov. (Hemiptera: Heteroptera: Reduviidae: Harpactorinae) from Yunnan, China, are described and illustrated. A key to separate the new genus and its closely related genera is provided.

14.
Biology (Basel) ; 12(10)2023 Sep 30.
Article in English | MEDLINE | ID: mdl-37887009

ABSTRACT

Species in Ectrichodiinae are known for their prey specialization on millipedes. However, knowledge of the morphological adaptations to this unique feeding habit was limited. In the current study, we examined the microstructures of the antennae, mouthparts, and legs of four millipede feeding ectrichodiines, Ectrychotes andreae (Thunberg, 1888), Haematoloecha limbata Miller, 1953, Labidocoris pectoralis (Stål, 1863), and Neozirta eidmanni (Taueber, 1930), and compared them with those of three species of tribelocephalines, a group closely related to Ectrichodiinae. On the antennae, we found four types of antennal sensilla. On the mouthparts, we recognized four types of labial sensilla. Sampled ectrichodiines have distinctly more and denser slightly transverse ridges on the external side of mandibles than tribelocephalines. E. andreae and H. limbata possess numerous small papillae fringed with densely arranged finger-print-like grains on the trochanter and femur; these probably facilitate the immobilization of prey. Overall, our study illustrates, at a microstructural level, the remarkable morphological adaption of prey manipulation in ectrichodiine, and has enhanced our understanding about stenophagy in the family Reduviidae.

15.
RNA Biol ; 20(1): 703-714, 2023 01.
Article in English | MEDLINE | ID: mdl-37676051

ABSTRACT

Adenosine-to-inosine (A-to-I) RNA editing, mediated by metazoan ADAR enzymes, is a prevalent post-transcriptional modification that diversifies the proteome and promotes adaptive evolution of organisms. The Drosophila Adar gene has an auto-recoding site (termed S>G site) that forms a negative-feedback loop and stabilizes the global editing activity. However, the evolutionary trajectory of Adar S>G site in many other insects remains largely unknown, preventing us from a deeper understanding on the significance of this auto-editing mechanism. In this study, we retrieved the well-annotated genomes of 375 arthropod species including the five major insect orders (Lepidoptera, Diptera, Coleoptera, Hymenoptera and Hemiptera) and several outgroup species. We performed comparative genomic analysis on the Adar auto-recoding S>G site. We found that the ancestral state of insect S>G site was an uneditable serine codon (unSer) and that this state was largely maintained in Hymenoptera. The editable serine codon (edSer) appeared in the common ancestor of Lepidoptera, Diptera and Coleoptera and was almost fixed in the three orders. Interestingly, Hemiptera species possessed comparable numbers of unSer and edSer codons, and a few 'intermediate codons', demonstrating a multi-step evolutionary trace from unSer-to-edSer with non-synchronized mutations at three codon positions. We argue that the evolution of Adar S>G site is the best genomic evidence supporting the 'proteomic diversifying hypothesis' of RNA editing. Our work deepens our understanding on the evolutionary significance of Adar auto-recoding site which stabilizes the global editing activity and controls transcriptomic diversity.


Subject(s)
Coleoptera , Drosophila Proteins , Hemiptera , Animals , Hemiptera/genetics , Proteomics , RNA Editing , Insecta , Genes, Insect , Drosophila/genetics , Adenosine Deaminase/genetics , Drosophila Proteins/genetics
16.
Int J Biol Macromol ; 253(Pt 2): 126742, 2023 Dec 31.
Article in English | MEDLINE | ID: mdl-37689283

ABSTRACT

Insect mitochondrial genomes (mitogenome) generally present a typical gene order, which is considered as the ancestral arrangement. All sequenced mitogenomes in the Thysanoptera display high levels of gene rearrangement. Due to limited number of thrips mitogenomes sequenced, how gene rearrangement may be shaped by evolution remain unclear. Here, we analyzed 33 thrips mitogenomes, including 14 newly sequenced. These mitogenomes were diverse in organization, nucleotides substitution and gene arrangements. We found 28 highly rearranged gene orders with the breakpoints of gene rearrangements from 25 to 33. Reconstruction of the ancestors mitochondrial gene arrangements states indicated that Tubulifera have more complex pathways than Terebrantia in the gene order evolution. Molecular calibration estimated that divergence of two suborders occurred in the middle Triassic while the radiation of thrips was associated with the arose and flourish of angiosperm. Our evolutionary hypothesis testing suggests that relaxation of selection pressure enabled the early phase of Thysanoptera evolution, followed by a stronger selective pressure fixed diversification. Our analyses found gene inversion increases the nonsynonymous substitution rates and provide an evolutionary hypothesis driving the diverse gene orders.


Subject(s)
Genome, Mitochondrial , Thysanoptera , Animals , Thysanoptera/genetics , Genome, Mitochondrial/genetics , Phylogeny , Insecta/genetics , Gene Rearrangement , Gene Order , Evolution, Molecular
17.
Insects ; 14(8)2023 Jul 31.
Article in English | MEDLINE | ID: mdl-37623389

ABSTRACT

The assassin bug genus Argolis Stål, 1861 (Hemiptera: Reduviidae: Stenopodainae) has a disjunct distribution in Sub-Saharan Africa and Asia. In the present study, the Asian species of Argolis are revised. Two species are recognized, redescribed, and illustrated, with the following new subjective synonyms and new combination proposed: Argolis Stål, 1861 = Bardesanes Distant, 1909, syn. nov. = Neoklugia Distant, 1919, syn. nov.; A. farinator (Reuter, 1882) = N. typica Distant, 1919, syn. nov. = B. sericenotatus Livingstone & Ravichandran, 1989, syn. nov.; A. signata (Distant, 1909), comb. nov. (transferred from Bardesanes) = Caunus noctulus Hsiao, 1977, syn. nov. Lectotypes for C. farinator, B. signatus, and N. typica are designated. A key to separate the two Asian species of Argolis is provided. The sexual dimorphism, systematic relationships, and distribution of Argolis are discussed. Argolis is newly recorded from Laos, Pakistan, and Vietnam.

18.
Biol Direct ; 18(1): 47, 2023 08 17.
Article in English | MEDLINE | ID: mdl-37592344

ABSTRACT

BACKGROUND: C-to-U RNA editing in plants is believed to confer its evolutionary adaptiveness by reversing unfavorable DNA mutations. This "restorative hypothesis" has not yet been tested genome-wide. In contrast, A-to-I RNA editing in insects like Drosophila and honeybee is already known to benefit the host by increasing proteomic diversity in a spatial-temporal manner (namely "diversifying hypothesis"). METHODS: We profiled the RNA editomes of multiple tissues of Arabidopsis thaliana, Drosophila melanogaster, and Apis melifera. We unprecedentedly defined the haplotype diversity (HD) of RNA molecules based on nonsynonymous editing events (recoding sites). RESULTS: Signals of adaptation is confirmed in Arabidopsis by observing higher frequencies and levels at nonsynonymous editing sites over synonymous sites. Compared to A-to-I recoding sites in Drosophila, the C-to-U recoding sites in Arabidopsis show significantly lower HD, presumably due to the stronger linkage between C-to-U events. CONCLUSIONS: C-to-U RNA editing in Arabidopsis is adaptive but it is not designed for diversifying the proteome like A-to-I editing in Drosophila. Instead, C-to-U recoding sites resemble DNA mutations. Our observation supports the restorative hypothesis of plant C-to-U editing which claims that editing is used for fixing unfavorable genomic sequences.


Subject(s)
Arabidopsis , Drosophila melanogaster , Bees , Animals , Drosophila melanogaster/genetics , Arabidopsis/genetics , Haplotypes , Proteomics , RNA Editing , Insecta , Drosophila , RNA
19.
RNA ; 29(10): 1509-1519, 2023 10.
Article in English | MEDLINE | ID: mdl-37451866

ABSTRACT

As one of the most prevalent RNA modifications in animals, adenosine-to-inosine (A-to-I) RNA editing facilitates the environmental adaptation of organisms by diversifying the proteome in a temporal-spatial manner. In flies and bees, the editing enzyme Adar has independently gained two different autorecoding sites that form an autofeedback loop, stabilizing the overall editing efficiency. This ensures cellular homeostasis by keeping the normal function of target genes. However, in a broader range of insects, the evolutionary dynamics and significance of this Adar autoregulatory mechanism are unclear. We retrieved the genomes of 377 arthropod species covering the five major insect orders (Hemiptera, Hymenoptera, Coleoptera, Diptera, and Lepidoptera) and aligned the Adar autorecoding sites across all genomes. We found that the two autorecoding sites underwent compensatory gains and losses during the evolution of two orders with the most sequenced species (Diptera and Hymenoptera), and that the two editing sites were mutually exclusive among them: One editable site is significantly linked to another uneditable site. This autorecoding mechanism of Adar could flexibly diversify the proteome and stabilize global editing activity. Many insects independently selected different autorecoding sites to achieve a feedback loop and regulate the global RNA editome, revealing an interesting phenomenon during evolution. Our study reveals the evolutionary force acting on accurate regulation of RNA editing activity in insects and thus deepens our understanding of the functional importance of RNA editing in environmental adaptation and evolution.


Subject(s)
RNA Editing , RNA , Animals , RNA/genetics , RNA Editing/genetics , Proteome/genetics , Base Sequence , Insecta/genetics , Adenosine Deaminase/genetics , Adenosine Deaminase/metabolism , Inosine/genetics , Inosine/metabolism
20.
Int J Mol Sci ; 24(13)2023 Jun 24.
Article in English | MEDLINE | ID: mdl-37445747

ABSTRACT

The recently reorganized classification of Mantodea has made significant progress in resolving past homoplasy problems, although some relationships among higher taxa remain uncertain. In the present study, we utilized newly sequenced mitogenomes and nuclear gene sequences of 23 mantid species, along with published data of 53 mantises, to perform familial-sampling structural comparisons of mantodean mitogenomes and phylogenomic studies. Our rstructural analysis revealed generally conserved mitogenome organizations, with a few cases of tRNA gene rearrangements, including the detection of trnL2 duplication for the first time. In our phylogenetic analysis, we found a high degree of compositional heterogeneity and lineage-specific evolutionary rates among mantodean mitogenomes, which frequently corresponded to several unexpected groupings in the topologies under site-homogeneous models. In contrast, the topologies obtained using the site-heterogeneous mixture model fit the currently accepted phylogeny of Mantodea better. Topology tests and four-cluster likelihood mapping analyses further determined the preferred topologies. Our phylogenetic results confirm the monophyly of superfamilial groups Schizomantodea, Amerimantodea, Heteromantodea, Promantidea, and Mantidea and recover the early-branching relationships as (Mantoidoidea + (Amerimantodea + (Metallyticoidea + Cernomantodea))). Additionally, the results suggest that the long-unresolved phylogenetic position of Majangidae should be placed within Mantidea, close to Mantoidea, rather than within Epaphroditoidea. Our findings contribute to understanding the compositional and structural diversity in mantodean mitogenomes, underscore the importance of evolutionary model selection in phylogenomic studies, and provide new insights into the high-level phylogeny of Mantodea.


Subject(s)
Genome, Mitochondrial , Mantodea , Animals , Phylogeny , Mantodea/genetics , Genome, Mitochondrial/genetics , Biological Evolution , Base Sequence
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