Synonymous Substitutions Research Articles

A novel splice-altering TNC variant (c.5247A > T, p.Gly1749Gly) in an Chinese family with autosomal dominant non-syndromic hearing loss

BackgroundThis study aims to analyze the pathogenic gene in a Chinese family with non-syndromic hearing loss and identify a novel mutation site in the TNC gene.MethodsA five-generation Chinese family from Anhui Province, presenting with autosomal dominant non-syndromic hearing loss, was recruited for this study. By analyzing the family history, conducting clinical examinations, and performing genetic analysis, we have thoroughly investigated potential pathogenic factors in this family. The peripheral blood samples were obtained from 20 family members, and the pathogenic genes were identified through whole exome sequencing. Subsequently, the mutation of gene locus was confirmed using Sanger sequencing. The conservation of TNC mutation sites was assessed using Clustal Omega software. We utilized functional prediction software including dbscSNV_AdaBoost, dbscSNV_RandomForest, NNSplice, NetGene2, and Mutation Taster to accurately predict the pathogenicity of these mutations. Furthermore, exon deletions were validated through RT-PCR analysis.ResultsThe family exhibited autosomal dominant, progressive, post-lingual, non-syndromic hearing loss. A novel synonymous variant (c.5247A > T, p.Gly1749Gly) in TNC was identified in affected members. This variant is situated at the exon–intron junction boundary towards the end of exon 18. Notably, glycine residue at position 1749 is highly conserved across various species. Bioinformatics analysis indicates that this synonymous mutation leads to the disruption of the 5' end donor splicing site in the 18th intron of the TNC gene. Meanwhile, verification experiments have demonstrated that this synonymous mutation disrupts the splicing process of exon 18, leading to complete exon 18 skipping and direct splicing between exons 17 and 19.ConclusionThis novel splice-altering variant (c.5247A > T, p.Gly1749Gly) in exon 18 of the TNC gene disrupts normal gene splicing and causes hearing loss among HBD families.

Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing.

Adenosine-to-inosine (A-to-I) RNA editing recodes the genetic information. Apart from diversifying the proteome, another tempting advantage of RNA recoding is to correct deleterious DNA mutation and restore ancestral allele. Solid evidences for beneficial restorative editing are very rare in animals. By searching for "convergent recoding" under a phylogenetic context, we proposed this term for judging the potential restorative functions of particular editing site. For the well-known mammalian Gln>Arg (Q>R) recoding site, its ancestral state in vertebrate genomes was the pre-editing Gln, and all 470 available mammalian genomes strictly avoid other three equivalent ways to achieve Arg in protein. The absence of convergent recoding from His>Arg, or synonymous mutations on Gln codons, could be attributed to the strong maintenance on editing motif and structure, but the absence of direct A-to-G mutation is extremely unexpected. With similar ideas, we found cases of convergent recoding in Drosophila genus, reducing the possibility of their restorative function. In summary, we defined an interesting scenario of convergent recoding, the occurrence of which could be used as preliminary judgements for whether a recoding site has a sole restorative role. Our work provides novel insights to the natural selection and evolution of RNA editing.

Distinct genome trichotomy in members of Hapalosiphonaceae is guided by habitat adaptation with Mastigocladus laminosus UU774 as a case study

The family Hapalosiphonaceae is grouped under subsection IV complying with International Code of Nomenclature for algae, fungi, and plants (ICN). This is a complex taxonomic group with often overlapping morphological traits. The members of this group have heterogeneous habitats and need urgent attention for de-entangling the taxon. The genome comparisons among 44 high quality drafts belonging to Hapalosiphonaceae suggests the presence of three distinct groups, one largely dominated by thermophiles (Group 1) and the other comprising of members of diverse habitats (Group 2). The third group is small with only 2 representative members (Group 3) are considered as outliers. The group containing members of diverse habitats are characterized by the presence of higher number of ORFan genes, mobilome and secondary metabolites genes. The thermophiles belonging to Group 1 are characterized by compact genome whereas the Group 2 genomes having diverse ecological habitat show genome expansion possibly due to recent acquisition. Comparison of synonymous and non-synonymous substitution of conserved genes suggest, members of Group 2 are undergoing relaxed purifying selection. There is a significant increase in the number of core genes (2075 for n = 35) when Group 1 organisms are considered alone compared to only 46 core genes when all three groups are taken together (n = 44). The presence of a huge pan genome (47,756) and a relatively tiny core genome (46) suggests that the taxon is an open and expanding. Members of Group 2 are distinct in coding for commercial metabolite shinorine that was visibly absent from other members of the Hapalosiphonaceae. Our RNAseq investigations on Mastigocladus laminosus UU774, a candidate of Group 2, showed that metabolic clusters overexpressed during stress. UU774 metabolic extracts shown potential antibacterial and anticancer cell line activity.

O-259 Seminal plasma cell-free RNA to predict testicular biopsy sperm retrieval outcome in azoospermic men

Abstract Study question Is there a way to assess seminal plasma of NOA men to predict a successful sperm retrieval at testicular biopsy? Summary answer Multi-omics approach in seminal plasma of NOA men provides reliable prediction on the spermatogenic activity within the seminiferous tubule. What is known already Microdissection testicular sperm extraction (m-TESE) in NOA men successfully retrieved spermatozoa in about 60% of the cases. While several algorithms have been investigated aiming at estimating spermatogenic progress such as age, serum FSH, inhibin B, and genetics, there is no specific assay that can do so reliably. Even histopathology is often inconclusive while equally invasive. Recently, epigenetic analysis on testicular biopsy specimens has shown a differential gene expression in relation to the origin of azoospermia and spermatogenic function (Cheung, et al, 2024, in press). Study design, size, duration Over a 4-year period, twenty-eight men were deemed azoospermic following several failed extensive semen analyses. Transcriptomic analysis was performed by RNAseq on seminal fluid and the specific gene expression were evaluated and compared. In addition, DNAseq and proteomics were carried out to confirm our findings. These patients then underwent micro-TESE by a single surgeon and were divided into two cohorts based on whether spermatozoa was successfully retrieved or not. Participants/materials, setting, methods RNA and DNA were isolated from seminal plasma using a commercial kit and sequenced by Illumina HiSeq3000/4000 platform. Differentially expressed genes (DEGs) were assessed and compared to a fertile donor control using DESeq2 and Gene Ontology analysis. An absolute log2fold change of > 1 and a P-value of < 0.0005 were considered statistically significant. Gene mutations were detected by CLC Genomic Server 9.0. Main results and the role of chance Transcriptomic in 28 ejaculates from iNOA men browsed 21,855 genes against a fertile donor. Of 3,505 imbalanced genes, 12 were consistently imbalanced in 12 men, while 19 genes were imbalanced in remaining 16. Among the 2 cohorts, 8 common imbalanced genes were found. Particularly TPTE2, a testis-specific gene that regulates spermatogenesis, was overexpressed in 10/12 men (OE-12-cohort), while underexpressed in the remainder 16 (UE-16-cohort). DNAseq showed that TPTE2 was conserved in the OE-12-cohort, while exhibiting a frameshift mutation in the UE-16-cohort. Most interestingly, NEU1, a gene involved in acrosome development and fertilization, was found to be consistently and concurrently overexpressed in the OE-12-cohort, while being convserly underexpressed in all the men in the UE-16 cohort. DNAseq confirmed the NEU1 gene exhibited a synonymous mutation in the OE-12 and a frameshift mutation in the UE-16-cohort. About 1-2 months after the DEG analysis was completed, all of the patients underwent m-TESE. The 12 men from the OE-12-cohort all had successful retrieval of spermatozoa at m-TESE, conversely the 16 men from the UE-16-cohort all consistently failed to yield spermatozoa at testicular surgery in spite of extensive search for several hours and by multiple embryologists. Moreover, histopathology confirmed spermatogenic status in both OE-12&UE-16-cohorts. Limitations, reasons for caution Using non-invasive RNAseq and DNAseq on the seminal plasma has allowed us to identify DEGs that may be used to predict whether a patient with iNOA would have a successful or failed sperm retrieval with micro-TESE. However, these results are preliminary and should be further validated in larger study cohort. Wider implications of the findings Transcriptomics on the ejaculates of men with iNOA represents a noninvasive tool to detect presence of residual spermatogenesis. If confirmed by further studies, this precision medicine method may be utilized in order to properly counsel patients regarding their future prognosis. Trial registration number Not applicable

The abnormal splicing regulation network caused by synonymous mutations in FBN1 exon 39 leads to Marfan syndrome

The abnormal splicing regulation network caused by synonymous mutations in FBN1 exon 39 leads to Marfan syndrome

Synonymous variant at the terminal nucleotide in exon 3 of F7 causes abnormal splicing: A case report.

Synonymous variants are non-pathogenic due to non-substitution of amino acids. However, synonymous exonic terminal nucleotide substitutions may affect splicing. Splicing variants are easily analyzed at RNA level for genes expressed in blood cells. Minigene analysis provides another method for splicing variant analysis of genes that are poorly or not expressed in peripheral blood. Whole exome sequencing was performed to screen for potential pathogenic mutations in the proband, which were validated within the family by Sanger sequencing. The pathogenicity of the synonymous mutation was analyzed using the minigene technology. The proband harbored the compound heterogeneous variants c. [291G >A; 572-50C >T] and c.681 + 1G >T in F7, of which the synonymous variant c.291G >A was located at the terminal position of exon 3. Minigene analysis revealed exon3 skipping due to this mutation, which may have subsequently affected protein sequence, structure, and function. Our finding confirmed the pathogenicity of c.291G >A, thus extending the pathogenic mutation spectrum of F7, and providing insights for effective reproductive counseling.

Association between rat decompression sickness resistance, transthyretin single nucleotide polymorphism, and expression: A pilot study.

Decompression sickness (DCS) is a systemic syndrome that can occur after an environmental pressure reduction. Previously, we showed that the plasmatic tetrameric form of transthyretin (TTR) nearly disappeared in rats suffering DCS but not in asymptomatic ones. In this pilot study, we assessed whether the resistance to DCS could be associated with polymorphism of the gene of TTR. For this study, Sanger sequencing was performed on purified PCR products from the liver of 14-week-old male and female standard and DCS-resistant rats (n = 5 per group). Hepatic TTR mRNA expression was assessed by RT-qPCR in 18-19 week-old male and female standard and resistant rats (n = 6 per group). There is a synonymous single nucleotide polymorphism (SNP) on the third base of codon 46 (c.138 C > T). The thymine allele was present in 90% and 100% of males and females standard, respectively. However, this allele is present in only 30% of DCS-resistant males and females (p = 0.0002301). In the liver, there is a significant effect of the resistance to DCS (p = 0.043) and sex (p = 0.047) on TTR expression. Levels of TTR mRNA were lower in DCS-resistant animals. To conclude, DCS resistance might be associated with a SNP and a lower expression of TTR.

Genetic diversity and population structure of grapevine Roditis leaf discoloration‐associated virus in Turkey vineyards

AbstractGrapevine Roditis leaf discoloration‐associated virus (GRLDaV) is a type of virus that infects grapevines. This research aimed to determine the prevalence of GRLDaV in Turkey vineyards and investigate the genetic diversity and population structure of the selected viral isolates from Turkey compared to isolates from other countries. In this study, 800 shoot samples from Turkey vineyards were collected in late spring and autumn from different regions. The samples were analysed by RT‐PCR targeting the partial RNaseH‐like gene region of the virus genome. The overall prevalence of GRLDaV was 8.1% among the samples. Phylogenetic analysis of the GRLDaV genome showed that the GRLDaV isolates were clustered into two major lineages. The nucleotide diversity (π) value of Group I, including only Mediterranean isolates, was lower than Group II, suggesting little variation among isolates. Even though π values were low among the geographical regions in Turkey, the region with the highest nucleotide diversity was the Aegean population, followed by the Eastern and Mediterranean populations. Comparison between nonsynonymous and synonymous substitutions showed that negative selection acts on synonymous amino acids. Along with neutrality tests and gene flow analyses, it was emphasized that genetic drift played an important role in shaping the GRLDaV populations. This study provides important information on the prevalence and genetic diversity of GRLDaV in Turkey vineyards. The findings will help to develop better strategies to manage and control this virus, which can cause significant economic losses in grape industries.

Exploring the mitogenomes of Batracomorphus (Hemiptera: Cicadellidae: Iassinae): new insights from structural diversity and phylogenomic analyses

Abstract Comparisons of mitogenomes are widely used for species identification and to explore the phylogenetic relationship among insect taxa. Batracomorphus is the third most diverse and widely distributed genus in the Cicadellidae (Hemiptera). However, there have been no analyses of genome structure and phylogenetic relationships within the genus. To compensate for the paucity of genomic information in this genus, we sequenced novel complete mitochondrial genomes of 11 Batracomorphus species and combined these with 23 previously sequenced mitochondrial genomes to perform structural comparisons and phylogenomic studies. Our results reveal generally conserved mitogenome organization, with one case of tRNA gene rearrangement, with trnI-trnQ reversed to trnQ-trnI when compared with the ancestral arrangement. Analysis of the ratio of nonsynonymous (Ka) to synonymous substitutions (Ks) showed ATP8 is the fastest and COI is the slowest evolving gene. ND2 and ND6 have highly variable nucleotide diversity, whereas COI and ND1 exhibit the lowest diversity. Phylogenetic analysis of nucleotide sequences grouped Batracomorphus species into a clade within the subfamily Iassinae. Within Batracomorphus, 3 clades were reconstructed consistent with the observed gene rearrangement, indicating that such rearrangements can serve as reliable molecular markers supporting phylogenetic hypotheses. These clades also correspond to clusters of species recovered by morphometric analysis of aedeagal shape, suggesting that characters of the male genitalia traditionally used for species delimitation are phylogenetically informative. Molecular divergence time estimates indicate that most speciation events within Batracomorphus occurred between the Paleogene and Neogene. This study provides insight into the population genetics, molecular biology, phylogeny, and morphological evolution of the leafhopper subfamily Iassinae and its largest genus, Batracomorphus.

Prevalence of synonymous mutations in m6A modification sites in human cancers

Prevalence of synonymous mutations in m6A modification sites in human cancers

Deformations in translating modern Ukrainian war fiction into English – A psycholinguistic study of "Інтернат"/<i>The Orphanage</i> by Serhiy Zhadan

The article is focused on analysing linguistic deformations in translating modern Ukrainian war fiction into English. The research material is the novel "Інтернат"/ The Orphanage by Serhiy Zhadan and its translation into English. Translation deformations, or "deforming tendencies" (Berman, 2000), are viewed as systemic psycholinguistic distortions, arbitrary and non-arbitrary, of formal and content source text characteristics. Three main groups of translation deformations have been identified in the text under analysis - lexical, stylistic, and grammatical. Lexical deformations include calque translation, concretisation and modulation. Due to their low frequency, they are not viewed as typical. Stylistic deformations fall into synonymous substitution, logisation, explication, expressivation, modernisation, antonymous translation, and compensation. Synonymous substitution and logisation are the most frequent types; therefore, they may be considered prototypical. They are mainly concerned with reproducing characters’ names and descriptions, names or descriptions of military and civil vehicles and tools, colloquial expressions and 'surzhyk'. Grammatical deformations constitute the most significant group. They comprise substitutions and permutations of different types, deletion of words/phrases/sentences, addition of words/phrases, and changes in punctuation. The style of Serhiy Zhadan is characterised by specific syntactical-stylistic features, such as the tendency to use extremely long sentences, high frequency of repetitions of different types, and specific punctuation. Therefore, deleting repetitions, intensifiers, discourse markers, and even sentences is the most recurrent type of grammatical deformation, followed by substitution–division of sentences, which may be treated as prototypical grammatical deformations in the analysed text. Disclosure Statement The authors reported no potential conflicts of interest. * Corresponding author: Diana Kalishchuk, 0000-0003-1952-5176diana.kalishchuk@vnu.edu.ua

Assembly and Genome Annotation of Different Strains of Apple Fruit Moth Virus (Cydia pomonella granulovirus).

Cydia pomonella granulovirus is a natural pathogen for Cydia pomonella that is used as a biocontrol agent of insect populations. The study of granulovirus virulence is of particular interest since the development of resistance in natural populations of C. pomonella has been observed during the long-term use of the Mexican isolate CpGV. In our study, we present the genomes of 18 CpGV strains endemic to southern Russia and from Kazakhstan, as well as a strain included in the commercial preparation "Madex Twin", which were sequenced and analyzed. We performed comparative genomic analysis using several tools. From comparisons at the level of genes and protein products that are involved in the infection process of virosis, synonymous and missense substitution variants have been identified. The average nucleotide identity has demonstrated a high similarity with other granulovirus genomes of different geographic origins. Whole-genome alignment of the 18 genomes relative to the reference revealed regions of low similarity. Analysis of gene repertoire variation has shown that BZR GV 4, BZR GV 6, and BZR GV L-7 strains have been the closest in gene content to the commercial "Madex Twin" strain. We have confirmed two deletions using read depth coverage data in regions lacking genes shown by homology analysis for granuloviruses BZR GV L-4 and BZR GV L-6; however, they are not related to the known genes causing viral pathogenicity. Thus, we have isolated novel CpGV strains and analyzed their potential as strains producing highly effective bioinsecticides against C. pomonella.

Comparative Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.

Male seminal fluid proteins often show signs of positive selection and divergent evolution, believed to reflect male-female coevolution. Yet, our understanding of the predicted concerted evolution of seminal fluid proteins and female reproductive proteins is limited. We sequenced, assembled, and annotated the genome of two species of seed beetles allowing a comparative analysis of four closely related species of these herbivorous insects. We compare the general pattern of evolution in genes encoding seminal fluid proteins and female reproductive proteins with those in digestive protein genes and well-conserved reference genes. We found that female reproductive proteins showed an overall ratio of nonsynonymous to synonymous substitutions (ω) similar to that of conserved genes, while seminal fluid proteins and digestive proteins exhibited higher overall ω values. Further, seminal fluid proteins and digestive proteins showed a higher proportion of sites putatively under positive selection, and explicit tests showed no difference in relaxed selection between protein types. Evolutionary rate covariation analyses showed that evolutionary rates among seminal fluid proteins were on average more closely correlated with those in female reproductive proteins than with either digestive or conserved genes. Gene expression showed the expected negative covariation with ω values, except for male-biased genes where this negative relationship was reversed. In conclusion, seminal fluid proteins showed relatively rapid evolution and signs of positive selection. In contrast, female reproductive proteins evolved at a lower rate under selective constraints, on par with genes known to be well conserved. Although our findings provide support for concerted evolution of seminal fluid proteins and female reproductive proteins, they also suggest that these two classes of proteins evolve under partly distinct selective regimes.

Declining Genetic Polymorphisms of the C-terminus Merozoite Surface Protein-1 Amidst Increased Plasmodium knowlesi Transmission in Thailand.

Recent reports from Thailand reveal a substantial surge in Plasmodium knowlesi cases over the past decade, with a more than eightfold increase in incidence by 2023 compared to 2018. This study investigates temporal changes in genetic polymorphism associated with the escalating transmission of P. knowlesi malaria in Thailand over the past two decades. Twenty-five P. knowlesi samples collected in 2018-2023 were sequenced for the 42-kDa region of pkmsp1 and compared with 24 samples collected in 2000-2009, focusing on nucleotide diversity, natural selection, recombination rate, and population differentiation. Seven unique haplotypes were identified in recent samples, compared to 15 in earlier samples. Nucleotide and haplotype diversities were lower in recent samples (π = 0.016, Hd = 0.817) than in earlier samples (π = 0.018, Hd = 0.942). Significantly higher synonymous substitution rates were observed in both sample sets (dS - dN = 2.77 and 2.43, p < 0.05), indicating purifying selection and reduced genetic diversity over time. Additionally, 8 out of 17 mutation points were located on B-cell epitopes, suggesting an adaptive response by the parasites to evade immune recognition. Population differentiation analysis using the fixation index (Fst) revealed high genetic differentiation between parasite populations in central and southern Thailand or Malaysia. Conversely, the relatively lower Fst value between southern Thailand and Malaysia suggests a closer genetic relationship, possibly reflecting historical gene flow. In conclusion, our findings highlight a decline in genetic diversity and evidence of purifying selection associated with the recently increased incidence of P. knowlesi malaria in Thailand. The minor genetic differentiation between P. knowlesi populations from southern Thailand and Malaysia suggests a shared recent ancestry of these parasites and underscores the need for coordinated efforts between the two countries for the elimination of P. knowlesi.

Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken

Abstract. Indrijani H, Hilmia N, Anang A, Pangestu MSP. 2024. Non-synonymous Single Nucleotide Polymorphism on TLR1A gene as a candidate for immune function of Indonesian indigenous chicken. Biodiversitas 25: 2434-2441. TLR1A is a candidate gene related to the immune system in chickens, which contributes to disease resilience, which could impact their productivity. This study aimed to determine mutations in the TLR1A gene in three indigenous Indonesian chickens namely, Pelung, Black Kedu and Sentul. A total of 127 DNA samples were used and consisted of 38, 41 and 48 respectively for Pelung, Black Kedu and Sentul chickens. DNA was isolated from white blood cells and amplification of TLR1A gene was conducted in part of exon 4 using PCR with specific primer. The sequencing results for the TLR1A gene were analyzed to identify mutations using the BioEdit and MEGA X programs. The results showed genetic polymorphisms in the TLR1A gene in Indonesian indigenous chicken. One synonymous mutation, g.710C&gt;T, in which amino acid coded leusine at 207th, and four non-synonymous mutation, i.e., g.822A&gt;G, altered amino acids coding from threonine to alanine (T245A), g.835C&gt;T, which altered amino acids coding 249th from threonine to methionine (T249M), g.1015G&gt;A that altered amino acids coding 309th from serine to aspargine (S309N) and g.1165T&gt;G that changed amino acid from arginine to proline R359P. All mutation frequencies for the alleles are lower than those for the non-mutation alleles. The non-synonymous mutation of the TLR1A gene might alter the metabolism of this hormone related to the immune system in chickens.

Improving clinical abbreviation sense disambiguation using attention-based Bi-LSTM and hybrid balancing techniques in imbalanced datasets.

Clinical abbreviations pose a challenge for clinical decision support systems due to their ambiguity. Additionally, clinical datasets often suffer from class imbalance, hindering the classification of such data. This imbalance leads to classifiers with low accuracy and high error rates. Traditional feature-engineered models struggle with this task, and class imbalance is a known factor that reduces the performance of neural network techniques. This study proposes an attention-based bidirectional long short-term memory (Bi-LSTM) model to improve clinical abbreviation disambiguation in clinical documents. We aim to address the challenges of limited training data and class imbalance by employing data generation techniques like reverse substitution and data augmentation with synonym substitution. We utilise a Bi-LSTM classification model with an attention mechanism to disambiguate each abbreviation. The model's performance is evaluated based on accuracy for each abbreviation. To address the limitations of imbalanced data, we employ data generation techniques to create a more balanced dataset. The evaluation results demonstrate that our data balancing technique significantly improves the model's accuracy by 2.08%. Furthermore, the proposed attention-based Bi-LSTM model achieves an accuracy of 96.09% on the UMN dataset, outperforming state-of-the-art results. Deep neural network methods, particularly Bi-LSTM, offer promising alternatives to traditional feature-engineered models for clinical abbreviation disambiguation. By employing data generation techniques, we can address the challenges posed by limited-resource and imbalanced clinical datasets. This approach leads to a significant improvement in model accuracy for clinical abbreviation disambiguation tasks.

Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection

BackgroundNematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures.ResultsGenerally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection.ConclusionsNematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.

Reversions mask the contribution of adaptive evolution in microbiomes.

When examining bacterial genomes for evidence of past selection, the results obtained depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by , the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale-dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with exactly opposite implications for dynamical intuition and applications of . Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the decay given only dozens of locally-fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of obtained from long-time scales with caution, as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short time scales.

Comparative mitogenomic analysis provides evolutionary insights into Formica (Hymenoptera: Formicidae).

Formica is a large genus in the family Formicidae with high diversity in its distribution, morphology, and physiology. To better understand evolutionary characteristics of Formica, the complete mitochondrial genomes (mitogenomes) of two Formica species were determined and a comparative mitogenomic analysis for this genus was performed. The two newly sequenced Formica mitogenomes each included 37 typical mitochondrial genes and a large non-coding region (putative control region), as observed in other Formica mitogenomes. Base composition, gene order, codon usage, and tRNA secondary structure were well conserved among Formica species, whereas diversity in sequence size and structural characteristics was observed in control regions. We also observed several conserved motifs in the intergenic spacer regions. These conserved genomic features may be related to mitochondrial function and their highly conserved physiological constraints, while the diversity of the control regions may be associated with adaptive evolution among heterogenous habitats. A negative AT-skew value on the majority chain was presented in each of Formica mitogenomes, indicating a reversal of strand asymmetry in base composition. Strong codon usage bias was observed in Formica mitogenomes, which was predominantly determined by nucleotide composition. All 13 mitochondrial protein-coding genes of Formica species exhibited molecular signatures of purifying selection, as indicated by the ratio of non-synonymous substitutions to synonymous substitutions being less than 1 for each protein-coding gene. Phylogenetic analyses based on mitogenomic data obtained fairly consistent phylogenetic relationships, except for two Formica species that had unstable phylogenetic positions, indicating mitogenomic data are useful for constructing phylogenies of ants. Beyond characterizing two additional Formica mitogenomes, this study also provided some key evolutionary insights into Formica.

The reference genome of an endangered Asteraceae, Deinandra increscens subsp. villosa, endemic to the Central Coast of California.

We present a reference genome for the federally endangered Gaviota tarplant, Deinandra increscens subsp. villosa (Madiinae, Asteraceae), an annual herb endemic to the Central California coast. Generating PacBio HiFi, Oxford Nanopore Technologies, and Dovetail Omni-C data, we assembled a haploid consensus genome of 1.67 Gb as 28.7 K scaffolds with a scaffold N50 of 74.9 Mb. We annotated repeat content in 74.8% of the genome. Long terminal repeats (LTRs) covered 44.0% of the genome with Copia families predominant at 22.9% followed by Gypsy at 14.2%. Both Gypsy and Copia elements were common in ancestral peaks of LTRs, and the most abundant element was a Gypsy element containing nested Copia/Angela sequence similarity, reflecting a complex evolutionary history of repeat activity. Gene annotation produced 33,257 genes and 68,942 transcripts, of which 99% were functionally annotated. BUSCO scores for the annotated proteins were 96.0% complete of which 77.6% was single copy and 18.4% duplicates. Whole genome duplication synonymous mutation rates of Gaviota tarplant and sunflower (Helianthus annuus) shared peaks that correspond to the last Asteraceae polyploidization event and subsequent divergence from a common ancestor at ∼27 MYA. Regions of high-density tandem genes were identified, pointing to potentially important loci of environmental adaptation in this species.