Specific Clades Research Articles

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution.

Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mt-tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mt-tRNAs with a uniform workflow. Here, we report our results on the complete reannotation of all mitogenomes available in the RefSeq database by September 2022 using mitos2. Based on the individual cases of mt-tRNA variants reported throughout the literature, our data pinpoint the respective hotspots of change, i.e. Acanthocephala (Lophotrochozoa), Nematoda, Acariformes and Araneae (Arthropoda). Less dramatic deviations of mt-tRNAs from the norm are observed throughout many other clades. Loss of arms in animal mt-tRNA clearly is a phenomenon that occurred independently many times, not limited to a small number of specific clades. The summary data here provide a starting point for systematic investigations into the detailed evolutionary processes of structural reduction and and loss of mt-tRNAs as well as a resource for further improvements of annotation workflows for mt-tRNA annotation.

Independent effects of tree diversity on aboveground and soil carbon pools after six years of experimental afforestation.

Planting diverse forests has been proposed as a means to increase long-term carbon (C) sequestration while providing many co-benefits. Positive tree diversity-productivity relationships are well established, suggesting more diverse forests will lead to greater aboveground C sequestration. However, the effects of tree diversity on belowground C storage have the potential to either complement or offset aboveground gains, especially during early stages of afforestation when potential exists for large losses in soil C due to soil decomposition. Thus, experimental tests of the effects of planted tree biodiversity on changes in whole-ecosystem C balance are needed. Here, we present changes in above- and belowground C pools 6 years after the initiation of the Forests and Biodiversity experiment (FAB1), consisting of high-density plots of one, two, five, or 12 tree species planted in a common garden. The trees included a diverse range of native species, including both needle-leaf conifer and broadleaf angiosperm species, and both ectomycorrhizal and arbuscular mycorrhizal species. We quantified the effects of species richness, phylogenetic diversity, and functional diversity on aboveground woody C, as well as on mineral soil C accumulation, fine root C, and soil aggregation. Surprisingly, changes in aboveground woody C pools were uncorrelated to changes in mineral soil C pools, suggesting that variation in soil C accumulation was not driven by the quantity of plant litter inputs. Aboveground woody C accumulation was strongly driven by species and functional identity; however, plots with higher species richness and functional diversity accumulated more C in aboveground wood than expected based on monocultures. We also found weak but significant effects of tree species richness, identity, and mycorrhizal type on soil C accumulation. To assess the role of the microbial community in mediating these effects, we further compared changes in soil C pools to phospholipid fatty acid (PLFA) profiles. Soil C pools and accumulation were more strongly correlated with specific microbial clades than with total microbial biomass or plant diversity. Our results highlight rapidly emerging and microbially mediated effects of tree biodiversity on soil C storage in the early years of afforestation that are independent of gains in aboveground woody biomass.

A New Dawn for Protist Biogeography

ABSTRACTAimBiogeographers have believed for a long time that the geographical distributions of protists are only determined by environmental conditions, because dispersal is not limited. During the past two decades, the field has come a long way to show that historical and spatial factors also significantly contribute to shaping protist distributions, calling for a reappraisal of our understanding of protist biogeography.MethodsWe review the current state‐of‐the‐art on the field of protist biogeography, highlighting several outstanding questions and opportunities. Our review brings together insights from different disciplines, ranging from morphology‐based research to environmental, population and speciation genomics.ResultsProtist communities harbour cosmopolitan and geographically restricted species and are shaped by both local environmental conditions and historical processes, yet the relative contributions of these patterns and processes likely differs depending on the geographic scale, protist lineage and the habitat that is being investigated. The field is ready to move beyond the decades‐long ubiquity versus (moderate) endemicity discourse and to instead ask why and where specific protist species and clades are more prone to widespread or restricted distributions. With the advent of next‐generation sequencing technologies, from whole‐genome sequencing to environmental and ancient DNA surveys, it is now possible to integrate insights from multiple lines of evidence and investigate protist communities, species and populations at an unprecedented scale and detail.OutlookTo further advance the field, the protist community needs to focus on understudied habitats and protist lineages, study the impact of protist traits on biogeographical patterns, perform targeted field and experimental work to disentangle the processes that underlie protist biogeographies and expand and develop databases with sequence, trait, distributional and phylogenetic information of protists. Given that a good understanding of species boundaries is central to unravelling protist biogeography, it remains crucial to invest in polyphasic taxonomic research.

Patterns of girdle shape and their correlates in Australian limb-reduced skinks.

The evolution of limb reduction in squamates is a classic example of convergence, but the skeletal morphological patterns associated with it are underexplored. To provide insights on the biomechanical and developmental consequences of transitions to limb reduction, we use geometric morphometrics to examine the morphology of pectoral and pelvic girdles in 90 species of limb-reduced skinks and their fully limbed relatives. Clavicle shapes converge towards an acute anterior bend when forelimbs are lost but hindlimbs are retained-a morphology typical of sand-swimmers. This may either indicate functional adaptations to locomotion in fine substrates, or a developmental consequence of complete limb loss. The shape of limb-bearing elements of both girdles (coracoid and pelvis) instead closely mirrors limb reduction, becoming more simplified as undulation replaces limbed locomotion. Integration between girdles decreases in taxa lacking elements of the forelimbs but not hindlimbs, indicating differential selection on each girdle in response to distinct locomotory strategies. However, this pattern becomes less clear when considering phylogenetic history, perhaps because it is limited to one specific clade (Lerista). We show how the functional demands of locomotion can induce changes at different levels of organismal organization, including both external and internal structures.

Genetic diversity, biofilm formation, and Vancomycin resistance of clinical Clostridium innocuum isolates

BackgroundClostridium innocuum, previously considered a commensal microbe, is a spore-forming anaerobic bacterium. C. innocuum displays inherent resistance to vancomycin and is associated with extra-intestinal infections, antibiotic-associated diarrhea, and inflammatory bowel disease. This study seeks to establish a multilocus sequence typing (MLST) scheme to explore the correlation between C. innocuum genotyping and its potential pathogenic phenotypes.MethodsFifty-two C. innocuum isolates from Linkou Chang Gung Memorial Hospital (CGMH) in Taiwan and 60 sequence-available C. innocuum isolates from the National Center for Biotechnolgy Information Genome Database were included. The concentrated sequence of housekeeping genes in C. innocuum was determined by amplicon sequencing and used for MLST and phylogenetic analyses. The biofilm production activity of the C. innocuum isolates was determined by crystal violet staining.ResultsOf the 112 C. innocuum isolates, 58 sequence types were identified. Maximum likelihood estimation categorized 52 CGMH isolates into two phylogenetic clades. These isolates were found to be biofilm producers, with isolates in clade I exhibiting significantly higher biofilm production than isolates in clade II. The sub-inhibitory concentration of vancomycin seemed to minimally influence biofilm production by C. innocuum isolates. Nevertheless, C. innocuum embedded in the biofilm structure demonstrated resistance to vancomycin treatments at a concentration greater than 256 µg/mL.ConclusionsThis study suggests that a specific genetic clade of C. innocuum produces a substantial amount of biofilm. Furthermore, this phenotype assists C. innocuum in resisting high concentrations of vancomycin, which may potentially play undefined roles in C. innocuum pathogenesis.

Diversity and Interactions between Picobiine Mites and Starlings.

The subfamily Picobiinae (Acariformes: Syringophilidae) comprises obligate and permanent parasites of birds found exclusively in the quills of contour feathers. We studied associations of picobiine mites with birds of the family Sturnidae (Aves: Passeriformes) across the Palaearctic, Afrotropical, Oriental, and Oceanian zoogeographical regions. Among the 414 examined bird individuals belonging to 44 species (35.2% of all sturnids), 103 individuals from 24 species (54.5% of examined species) were parasitised by quill mites. The diversity of mites was represented by five species, including one newly described, Picobia malayi Patan and Skoracki sp. n. Statistical analysis of the Picobiinae-Sturnidae bipartite network demonstrated a low connectance value (Con = 0.20) and high modularity, with significant differences in the H2' specialisation index compared to null model values. The network structure, characterised by four distinct modules, highlighted the specificity and limited host range of the Picobiinae-Sturnidae associations. The distribution of Picobia species among starlings was congruent with the phylogeny of their hosts, with different mites parasitising specific clades of starlings. Additionally, the findings suggest that the social and breeding behaviours of starlings influence quite a high prevalence. Finally, our studies support the validity of museum collections to study these parasitic interactions.

A phylogenetic approach for identifying new sources of economically important fatty acids in plants and algae

Societal Impact StatementNew sources of essential and other nutritionally and/or pharmacologically important fatty acids for human use can be discovered through bioprospecting. Demonstrating how fatty acids in plants and algae are distributed across a phylogeny is a critical first step in this process. Here, new sources of essential omega‐3 fatty acids that are critically important to human health were identified, such as green and Chromista algae, bryophytes and some angiosperm families. The identification of certain taxa that are high in critical fatty acids is important for developing new sources of these healthful compounds.Summary Essential fatty acids (EFA) including long‐chain omega‐3 and omega‐6 EFA are key nutrients that broadly support the health of individuals and the ecosystems they inhabit. Production of these EFA is critical to global nutritional security, and therefore, it is imperative to assess the distribution patterns of FA in plants to bioprospect new resources that do not threaten biodiversity. We used a meta‐analytic approach (phylogenetic signal analysis), which incorporated a wide variety of taxa to map FA profiles including both presence and abundance of specific FA and EFA onto a plant phylogeny including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. Our phylogenetic signal analysis revealed that presence/absence of most FA of interest were randomly or ubiquitously distributed, while FA content was significantly clustered in specific clades for most key FA (including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and nervonic acid). Both green and Chromista algae displayed relatively high proportions of EPA and DHA, while green algae contained higher proportional amounts of stearidonic acid (SDA). Further, signal analysis revealed high proportional content of gamma‐linoleic acid (GLA) in bryophytes and some angiosperm families, suggesting potential sources for bioprospecting GLA. This analysis provides a crucial foundation for understanding the influence of phylogenetic relationships in the relative proportions of key FA in plants and algae across a diverse phylogeny. Furthermore, in demonstrating how fatty acids in plants and algae are distributed across a phylogeny, we provide a critical first step in bioprospecting for new sources of essential and other nutritionally‐ and/or pharmacologically important fatty acids for human use.

Genome-Wide Identification, Evolution, and Female-Biased Expression Analysis of Odorant Receptors in Tuta absoluta (Lepidoptera: Gelechiidae).

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

Sacbrood viruses and select Lake Sinai virus variants dominated Apis mellifera colonies symptomatic for European foulbrood.

European foulbrood (EFB) is a prevalent disease in the European honey bee (Apis mellifera) in the United States, which can lead to colony decline and collapse. The bacterial components of EFB are well-studied, but the diversity of viral infections within infected colonies has not been explored. In this study, we use meta-transcriptomics sequencing of 12 honey bee hives, symptomatic (+, n = 6) and asymptomatic (-, n = 6) for EFB, to investigate viral infection associated with the disease. We assembled 41 viral genomes, belonging to three families (Iflaviridae, Dicistroviridae, and Sinhaliviridae), all previously reported in honey bees, including Lake Sinai virus, deformed wing virus, sacbrood virus, Black queen cell virus, and Israeli acute paralysis virus. In colonies with severe EFB, we observed a higher occurrence of viral genomes (34 genomes) in contrast to fewer recovered from healthy colonies (seven genomes) and a complete absence of Dicistroviridae genomes.We observed specific Lake Sinai virus clades associated exclusively with EFB + or EFB - colonies, in addition to EFB-afflicted colonies that exhibited an increase in relative abundance of sacbrood viruses. Multivariate analyses highlighted that a combination of site and EFB disease status influenced RNA virome composition, while EFB status alone did not significantly impact it, presenting a challenge for comparisons between colonies kept in different yards. These findings contribute to the understanding of viral dynamics in honey bee colonies compromised by EFB and underscore the need for future investigations to consider viral composition when investigating EFB.IMPORTANCEThis study on the viromes of honey bee colonies affected by European foulbrood (EFB) sheds light on the dynamics of viral populations in bee colonies in the context of a prevalent bacterial brood disease. The identification of distinct Lake Sinai virus and sacbrood virus clades associated with colonies affected by severe EFB suggests a potential connection between viral composition and disease status, emphasizing the need for further investigation into the role of viruses during EFB infection. The observed increase in sacbrood viruses during EFB infection suggests a potential viral dysbiosis, with potential implications for honey bee brood health. These findings contribute valuable insights related to beekeeping practices, offering a foundation for future research aimed at understanding and mitigating the impact of bacterial and viral infection in commercial honey bee operations and the management of EFB.

Network analyses predict major regulators of resistance to early blight disease complex in tomato

BackgroundEarly blight and brown leaf spot are often cited as the most problematic pathogens of tomato in many agricultural regions. Their causal agents are Alternaria spp., a genus of Ascomycota containing numerous necrotrophic pathogens. Breeding programs have yielded quantitatively resistant commercial cultivars, but fungicide application remains necessary to mitigate the yield losses. A major hindrance to resistance breeding is the complexity of the genetic determinants of resistance and susceptibility. In the absence of sufficiently resistant germplasm, we sequenced the transcriptomes of Heinz 1706 tomatoes treated with strongly virulent and weakly virulent isolates of Alternaria spp. 3 h post infection. We expanded existing functional gene annotations in tomato and using network statistics, we analyzed the transcriptional modules associated with defense and susceptibility.ResultsThe induced responses are very distinct. The weakly virulent isolate induced a defense response of calcium-signaling, hormone responses, and transcription factors. These defense-associated processes were found in a single transcriptional module alongside secondary metabolite biosynthesis genes, and other defense responses. Co-expression and gene regulatory networks independently predicted several D clade ethylene response factors to be early regulators of the defense transcriptional module, as well as other transcription factors both known and novel in pathogen defense, including several JA-associated genes. In contrast, the strongly virulent isolate elicited a much weaker response, and a separate transcriptional module bereft of hormone signaling.ConclusionsOur findings have predicted major defense regulators and several targets for downstream functional analyses. Combined with our improved gene functional annotation, they suggest that defense is achieved through induction of Alternaria-specific immune pathways, and susceptibility is mediated by modulating hormone responses. The implication of multiple specific clade D ethylene response factors and upregulation of JA-associated genes suggests that host defense in this pathosystem involves ethylene response factors to modulate jasmonic acid signaling.

Beneficial effect of GABA-producing Lactiplantibacillus strain LPB145 isolated from cheese starters evaluated in anxiety- and depression-like behaviours in rats.

In a previous study, we reported the in vitro potential probiotic and gamma-aminobutyric acid (GABA) production, of several strains from a collection of Lactiplantibacillus (Lpb) strains within the community of natural whey starters from the artisanal cheese industry. GABA is a non-protein amino acid widely distributed in nature and produced in animals, plants, and microorganisms. However, the best known role of GABA is its function as the major inhibitory neurotransmitter of the central nervous system. Preclinical and clinical evidence suggests that the GABAergic system has a relevant role in mental health disorders, such as anxiety and major depression. The modulation of the GABAergic system has been suggested as a potential strategy for treatment, one such mechanism of modulation is the influence of the microbiota-gut-brain axis through probiotic treatments. The present study was designed to investigate the in vivo probiotic potential of LPB145, a Lactiplantibacillus strain previously characterised as a GABA-producing potentially probiotic strain. Therefore, we evaluated the behavioural effects of chronic oral administration of LPB145 on rats' anxiety- and depression-like behaviours, using the elevated plus maze, open field, and the forced swimming test. The impact of LPB145 strain treatment on the gut microbiota structure and diversity was assessed to discern a possible mechanism of action of the LPB145 treatment through the microbiota-gut-brain axis. Our results showed that LPB145 administration induced an antidepressive-like behaviour without changes in locomotor activity. In contrast, the treatment did not modify the experimental anxiety. The structure and diversity of the intestinal microbiota remained unaffected by the treatment when compared to the control. However, specific clades that could be implicated in the behavioural changes did show differences in their relative abundance. These findings provide evidence regarding the potential of probiotic strains isolated from alimentary sources, to modulate the microbiota-gut-brain axis and positively impact mental health.

Phylogeography, Genetic Diversity and Population Structure of Echinococcus granulosus Sensu Stricto Inferred by Mitochondrial DNA Markers between Southeast of Iran and Pakistan.

Current study was designed to provide a better insight into the circulating genotypes, genetic diversity, and population structure of Echinococcus spp. between southeast of Iran and Pakistan. From Jun 2020 to Dec 2020, 46 hydatid cysts were taken from human (n: 6), camel (n: 10), goat (n: 10), cattle (n: 10) and sheep (n: 10) in various cities of Sistan and Baluchestan Province of Iran, located at the neighborhood of Pakistan. DNA samples were extracted, amplified, and subjected to sequence analysis of cox1 and nad1 genes. The phylogeny inferred by the Maximum Likelihood algorithm indicated that G1 genotype (n: 19), G3 genotype (n: 14) and G6 genotype (n: 13) assigned into their specific clades. The diversity indices showed a moderate (nad1: Hd: 0.485) to high haplotype diversity (cox1: Hd: 0.867) of E. granulosus s.s. (G1/G3) and low nucleotide diversity. The negative value of Tajima's D and Fu's Fs test displayed deviation from neutrality indicating a recent population expansion. A parsimonious network of the haplotypes of cox1 displayed star-like features in the overall population containing IR9/PAK1/G1, IR2/PAK2/G3 and IR18/G6 as the most common haplotypes. A pairwise fixation index (Fst) indicated that E. granulosus s.s. populations are genetically moderate differentiated between southeast of Iran and Pakistan. The extension of haplotypes PAK18/G1 (sheep) and PAK26/G1 (cattle) toward Iranian haplogroup revealed that there is dawn of Echinococcus flow due to a transfer of alleles between mentioned populations through transport of livestock or their domestication. The current findings strengthen our knowledge concerning the evolutionary paradigms of E. granulosus in southeastern borders of Iran and is effective in controlling of hydatidosis.

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine.

The emergence of new SARS-CoV-2 variants in Palestine highlights the need for continuous genetic surveillance and accurate screening strategies. This case series study aimed to investigate the geographic distribution and genetic variation of the SARS-CoV-2 Delta Variant in Palestine in August 2021. Samples were collected at random in August 2021 (n = 571) from eight districts in the West Bank, Palestine. All samples were confirmed as positive for COVID-19 by RT-PCR. The samples passed the quality control test and were successfully sequenced using the ARTIC protocol. The Delta Variant was revealed to have four dominant lineages: B.1.617 (19%), AY.122 (18%), AY.106 (17%), and AY.121 (13%). The study revealed eight significant purely spatial clusters (p < 0.005) distributed in the northern and southern parts of Palestine. Phylogenetic analysis of SARS-CoV-2 genomes (n = 552) showed no geographically specific clades. The haplotype network revealed three haplogroups without any geographic distribution. Chronologically, the Delta Variant peak in Palestine was shortly preceded by the one in the neighboring Israeli community and shortly followed by the peak in Jordan. In addition, the study revealed an extremely intense transmission network of the Delta Variant circulating between the Palestinian districts as hubs (SHR ≈ 0.5), with Al-Khalil, the district with the highest prevalence of COVID-19, witnessing the highest frequency of transitions. Genetic diversity analysis indicated closely related haplogroups, as haplotype diversity (Hd) is high but has low nucleotide diversity (π). However, nucleotide diversity (π) in Palestine is still higher than the global figures. Neutrality tests were significantly (p < 0.05) low, including Tajima's D, Fu-Li's F, and Fu-Li's D, suggesting one or more of the following: population expansion, selective sweep, and natural negative selection. Wright's F-statistic (Fst) showed genetic differentiation (Fst > 0.25) with low to medium gene flow (Nm). Recombination events were minimal between clusters (Rm) and between adjacent sites (Rs). The study confirms the utility of the whole genome sequence as a surveillance system to track the emergence of new SARS-CoV-2 variants for any possible geographical association and the use of genetic variation analysis and haplotype networking to delineate any minimal change or slight deviation in the viral genome from a reference strain.

Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US.

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of leptospirosis in urban settings. We investigated leptospirosis among brown rats in Boston, Massachusetts and hypothesized that rat dispersal in this urban setting influences the movement, persistence, and diversity of Leptospira . We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira . We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira isolates obtained from frozen and fresh tissue from some of the 59 Leptospira -positive rat kidneys. When isolates were not obtained, we attempted Leptospira genomic DNA capture and enrichment, which yielded 14 additional Leptospira genomes from rats. We also generated an enriched Leptospira genome from a 2018 human case in Boston. We found evidence of high genetic structure and limited dispersal among rat populations that is likely influenced by major roads and/or other unknown dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats, with specific clades tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and movement of leptospirosis in this urban rat community is driven by rat dispersal. Finally, our genomic analyses of the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other urban settings.

Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes.

Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by ACYLSUGAR ACYLTRANSFERASE (ASAT) enzymes from sugars and acyl-coenzyme A esters. Published research has revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars have been analyzed across a small fraction of the >1,200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the clade II species brinjal eggplant (Solanum melongena) led to the identification of eight unusual structures with inositol or inositol glycoside cores and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity, with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the brinjal eggplant ASAT 3-LIKE 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.

Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites.

Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans that include species that cause neglected tropical diseases, are a relevant group to study aneuploidies. Their life cycle has several stressors that could select for different patterns of chromosomal duplications and/or losses, and their nearly universal use of polycistronic transcription increases their reliance on gene expansion/contraction, as well as post-transcriptional control as mechanisms for gene expression regulation. By evaluating the data from 866 isolates covering seven trypanosomatid genera, we have revealed that aneuploidy tolerance is an ancestral characteristic of trypanosomatids but has a reduced occurrence in a specific monophyletic clade that has undergone large genomic reorganization and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite's speciation, named collectively as the trypanosomatid ancestral supernumerary chromosome (TASC). TASC has most genes in the same coding strand, is expressed as a disomic chromosome (even having four copies), and has increased potential for functional variation, but it purges highly deleterious mutations more efficiently than other chromosomes. The evidence of stringent control over gene expression in this chromosome suggests that these parasites have adapted to mitigate the fitness cost associated with this ancient chromosomal duplication.

Genome-wide identification and characterisation of hevein precursor genes in Hevea brasiliensis

Hevea brasiliensis is the primary source of natural rubber, which is obtained from its latex and used in the manufacturing of various products. Hevein is a small protein found in the latex, produced by post-translational cleavage of prohevin, which is encoded by the hevein precursor gene. It exhibits antimicrobial and agglutination properties. Several nucleotide sequences that encode the hevein precursor genes were reported, however, the sequences are not characterised well. In the present study, four full-length hevein precursor sequences (Hevein 1–4) were obtained by manually curating the sequences from different databases. All sequences show high homology with the highest identity between Hevein 1 and Hevein 3. In a phylogenetic analysis along with sequences from related plants, all sequences from H. brasiliensis were clustered into a specific clade. All hevein precursor genes were expressed in the latex samples obtained from three clones; RRIM 600, RRIM 3001 and PB 350 of less than one year old and five-year-old RRIM 3001 plants, grown in plant house, as well as field-grown trees of clone PB 350 belonging to three different ages; two years, six years and fifteen years. All hevein precursor genes in the five-year-old RRIM 3001 plants with stunted growth, maintained in the plant house showed alternative splicing. Hevein 3 was expressed with two splice variants, one with intron retention and the other without intron whereas the other genes were expressed with only intron retained variant. Differential expression analysis using nanoplate digital PCR showed that Hevein 2 and Hevein 3 were expressed with no significant difference among the three young H. brasiliensis clones. The expression of Hevein 2 and Hevein 3 among the H. brasiliensis clone PB 350 of different ages grown in field conditions showed significant difference. The present study provides a better understanding on the importance of hevein precursor genes in different physiological responses which will be useful for further research leading to the genetic improvement of H. brasiliensis.

Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia

A dataset comprising metagenomes of outpatients (n = 28) with acute leukemia (AL) and healthy controls (n = 14) was analysed to investigate the associations between gut microbiota composition and metabolic activity and AL. According to the results obtained, no significant differences in the microbial diversity between AL outpatients and healthy controls were found. However, significant differences in the abundance of specific microbial clades of healthy controls and AL outpatients were found. We found some differences at taxa level. The relative abundance of Enterobacteriaceae, Prevotellaceae and Rikenellaceae was increased in AL outpatients, while Bacteirodaceae, Bifidobacteriaceae and Lachnospiraceae was decreased. Interestingly, the abundances of several taxa including Bacteroides and Faecalibacterium species showed variations based on recovery time from the last cycle of chemotherapy. Functional annotation of metagenome-assembled genomes (MAGs) revealed the presence of functional domains corresponding to therapeutic enzymes including l-asparaginase in a wide range of genera including Prevotella, Ruminococcus, Faecalibacterium, Alistipes, Akkermansia. Metabolic network modelling revealed potential symbiotic relationships between Veillonella parvula and Levyella massiliensis and several species found in the microbiota of AL outpatients. These results may contribute to develop strategies for the recovery of microbiota composition profiles in the treatment of patients with AL.

Plant phylogenetic diversity influences arthropod communities in tropical forest restoration plots

AbstractConsideration of plant phylogenetic diversity in ecological restoration carries substantial potential, as communities with a greater diversity of lineages with older evolutionary histories can increase the diversity of niches and thus are likely to recover larger species networks than communities clustered in specific clades with reduced variation in functional traits. In this study, we experimentally assessed how arthropod communities were affected by the phylogenetic diversity of a set of tropical tree species. We established 12 experimental restoration plots with either high or low plant phylogenetic diversity while maintaining constant the number of plant species. After 1 and 3 years, arthropods with different feeding habits (herbivores, predators, pollinators, and detritivores) were collected and identified as morphospecies or operational taxonomic units using metabarcoding techniques. We provide insights on the influence of plant phylogenetic diversity on arthropod abundance and species diversity, particularly among predator, pollinator, and detritivore common and dominant species, which increased with plant phylogenetic diversity. The trend, however, was the opposite for the diversity of herbivore common and dominant species, which decreased as plant phylogenetic diversity increased. These findings highlight the importance of considering plant species richness when designing restoration strategies, but also their evolutionary histories, as the same number of plant species can produce different outcomes for higher trophic levels, as a function of their phylogenetic relationships.Abstract in Spanish is available with online material.

Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus

To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, Peptoniphilus species formed eight distinct clades, with Aedoeadaptatus and Anaerosphaera species branching between them. The observed clades designated as Peptoniphilus sensu stricto (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several Peptoniphilus species (viz. P. coxii, P. ivorii, P. nemausensis and some non-validly published species) grouped reliably with the type species of Aedoeadaptatus (A. acetigenes) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence, we are proposing the transfer of these species into the emended genus Aedoeadaptatus. Our analyses on protein sequences from Peptoniphilus genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different Peptoniphilus species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized Peptoniphilus spp. (cultured and uncultured), their affiliations to the specific Peptoniphilus clades can be accurately predicted. These results should prove useful in understanding the potential involvement of Peptoniphilus-related species in diseases.