Studying animal diets can be of great value to conservation biology; however, identifying diet items by observation can be challenging, constrained by factors like habitat structure, observer distance, and climatic conditions. Our aim was to evaluate the diet of the free-living Blue-and-yellow Macaw in an urban area of Central-West Brazil, using DNA metabarcoding. Cloacal swab samples were collected in nests during the nestlings' monitoring season. After eDNA extractions, the nuclear internal transcribed spacer (ITS) and the chloroplast psbA-trnH intergenic regions were amplified and sequenced using the Oxford Nanopore Technologies MinION. Blastn was performed using a local database to analyze our sequences. The most abundant taxa detected included pink ipê (Handroanthus impetiginosus), amate (Ficus obtusifolia), and mango (Mangifera indica), at central nest; and queen's crape myrtle (Lagerstroemia speciosa), java plum (Syzygium cumini), pequi (Caryocar brasiliense), peterebi (Cordia trichotoma), and mango at peripheral nest. Our findings showed that DNA metabarcoding provides a more comprehensive and detailed assessment of the diet of Blue-and-yellow Macaw, complementing traditional methods and underscoring its value as a powerful and sensitive tool for advancing ecological and conservation studies.
This study characterizes the cytogenetic diversity of maize landraces from Northern Argentina, a region comprising Northwestern Argentina (NWA) and Northeastern Argentina (NEA). New data from four NWA landraces were analysed using DAPI banding, fluorescence in situ hybridization (FISH), and flow cytometry. Intra- and inter-populational variation was detected in heterochromatin content (2.06-12.6%), as well as in the number (3-15), size, and chromosomal position of knobs. Genome size (2C value) ranged from 5.27 to 5.74 pg, and numerical polymorphism (0-2) of B chromosomes was observed. Consensus idiograms were constructed for each studied landrace. A quantitative analysis combining these data with previously published information on Argentine maize revealed a negative association between knob heterochromatin content and cultivation altitude. In NWA landraces, genome size was also negatively associated with altitude, whereas no such relationship was detected when NWA and NEA data were analysed together. In NEA landraces, which grow within a narrow altitudinal range, genome size variability may be influenced by local farmers selection practices, whereas in NWA landraces cytogenetic variation may reflect multifactorial anthropogenic and environmental influences. B chromosomes were recorded exclusively at altitudes above 2000 m.a.s.l. The observed cytogenetic patterns are discussed in the context of ecogeographic differentiation among maize landraces.
Drosophila suzukii, a species native to southeast Asia, is a major pest of berry and stone fruit crops. This species has invaded Europe and the Americas in just a few decades, becoming a global concern to agriculture. In contrast to other flies, D. suzukii infests ripening fruits, causing substantial economic losses worldwide. Nevertheless, genomic studies on this species remain insufficient, especially in transposable elements (TEs), which constitute nearly half of its genome and represent a substantially larger genomic fraction than in most other Drosophila species. Given their ability to reshape genome structure and influence gene regulation, TEs have been implicated in adaptive and invasive processes across diverse organisms. Therefore, this study characterized the dynamics of TEs in the genome of D. suzukii by developing a new manually curated reference TE library and generating a comprehensive genome-wide TE annotation employing bioinformatics techniques. Our analysis of TE dynamics highlights key associations between TEs and food consumption-related genes that are unique to the D. suzukii genome and absent in the model species D. melanogaster, which infests rotten fruits. These findings provide new insights about food selection in this species, offering potential targets for developing improved pest management strategies in fruit production.
Biosynthetic gene clusters (BGCs) are important for plant specialized metabolism, but remain poorly characterized in coffee. Given Brazil’s importance in coffee production, we performed a comparative genomic analysis of BGCs across the allotetraploid Coffea arabica and its diploid progenitors C. eugenioides and C. canephora. Using standardized genome filtering, annotation, orthogroup inference, and cluster classification, we identified 472 BGCs comprising 3,118 biosynthetic genes, which were grouped into 194 cluster families and integrated with 28,280 orthogroups. Of these, 7,091 orthogroups were shared across all species; Coffea canephora and subgenomes shared 10,923, while Coffea eugenioides and subgenomes shared 11,446. Most BGC-associated orthogroups (86.4%) link to a single pathway class. BGC-associated genes form a highly structured yet lineage-dynamic component of the Coffea pangenome. C. eugenioides and its derived subgenomes in Arabica contributed disproportionately to 14 BGC-associated orthogroups, including flavonoid-, lipid-, and stress-related functions. In contrast, C. canephora derivatives contributed only two terpene-related orthogroups. The parental species showed fewer secondary metabolism-related enriched GO terms (3 and 1) than their subgenomes (53 and 56). Species-specific rearrangements, expansions, and subgenome retention indicate that hybridization and polyploidy shaped BGC diversification. These results advance understanding of specialized metabolism in Coffea and identify targets for coffee improvement and climate resilience.
Cancer is a serious healthcare issue throughout the world. The rising demand for safe and efficient cancer treatments drives research on phytochemicals. Phyla nodiflora is a perennial species that contains potential anticancer compounds. Eupafolin and hispidulin from P. nodiflora demonstrated significant antitumor efficacy against several cancer types. Nonetheless, the biochemical pathways and genes encoding the enzymes required for the biosynthesis of these compounds remain unknown. Therefore, we sequenced the leaf, root, and flower transcriptomes to identify the transcripts involved in eupafolin and hispidulin biosynthesis. We assembled 113 956 transcripts and assigned 34 876 transcripts to 149 pathways. We associated 102 transcripts in the phenylpropanoid pathway with the biosynthesis of eupafolin and hispidulin. We identified 16 transcripts putatively encoding the enzymes that are associated with the biosynthesis of eupafolin and hispidulin for the first time. Together, these findings provide a transcriptomic framework for Phyla nodiflora that can guide future efforts in metabolic engineering and functional genomics, particularly in optimizing the biosynthesis of the anticancer compounds eupafolin and hispidulin.
Terrestrial arthropods are declining in most ecosystems, creating a need for efficient and scalable biodiversity monitoring tools. DNA-barcoding enables high-throughput species identification but is constrained by incomplete reference libraries for many taxa. Here, we expand the DNA barcode database for Austrian Auchenorrhyncha by combining morphological identification with Sanger-sequenced COI barcodes. A total of 1 304 specimens representing 394 species were successfully barcoded, resulting in 384 Barcode Index Numbers (BINs), including 73 newly established BINs. Elevated intraspecific COI divergence and BIN discordance in several taxa reveal species complexes and missing barcode gaps. The expanded reference library was applied to Auchenorrhyncha from Malaise trap samples collected at an agricultural lowland and an alpine site and analyzed using a high-throughput Oxford Nanopore Technologies (ONT) workflow. The improved reference library substantially increased assignment success and taxonomic resolution. Finally, we compared the ONT barcoding results from Malaise trap catches with morphology-based identifications from single-event suction sampling. Both approaches detected similar proportions of species, and differences in species composition likely reflect sampling- and method-specific biases. Overall, this study advances the development of a comprehensive DNA barcode reference library for Central European Auchenorrhyncha and underscores the importance of regionally curated databases and complementary approaches for biodiversity assessments.
Although insects are fundamental to understanding and conserving global biodiversity, they are vastly understudied. Here, we present a national inventory of Costa Rican insects based upon 3.78 million DNA barcodes representing 152 891 Barcode Index Numbers (BINs, proxies for species) from 28 localities sampled from 2017 to 2023 through the national BioAlfa program of Costa Rica. Although only 3.6% of BINs are linked to Linnean species, barcode-based community analyses revealed strong, consistent ecogeographic structure. Clustering of BIN data using bootstrapped Jaccard distances revealed seven distinct mainland assemblages and a distinct island cluster, shaped primarily by Costa Rica’s mountain ranges, elevation, and slope orientation. Separate analyses for Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera coupled with analyses focused on some of their largest families (e.g., Braconidae, Cecidomyiidae, Cicadellidae, Erebidae, and Staphylinidae) confirmed these patterns and further revealed extremely high species turnover with most BINs being exclusive to a single region or locality. Our results reveal limited overlap of insect communities across ecosystems, implying that each life zone harbors unique taxonomic assemblages. Large-scale DNA barcoding has detected fine-grained spatial structure, providing a genomic framework for biodiversity monitoring and conservation in diverse tropical regions undergoing rapid environmental change.
Lipoxygenase proteins (LOXs) play a crucial role in plant growth, development, and defense notably through their involvement in jasmonic acid (JA) biosynthesis. Here, we aimed to identify and characterize genes encoding lipoxygenases in three coffee species, Coffea arabica, Coffea canephora, and Coffea eugenioides, and to evaluate whether LOX genes are differentially expressed following hexanoic acid application in C. arabica. We found 18 LOX genes in C. arabica and 9 genes each in C. eugenioides and C. canephora. Chromosomal localization analyses revealed strong correspondence between the LOX genes of tetraploid C. arabica and those of its putative diploid progenitors, C. eugenioides and C. canephora. Transcriptomic and enzymatic analyses showed that hexanoic acid application modulates the expression of specific LOX genes and alters lipoxygenase activity in leaves and roots of C. arabica cvs. Catuaí Vermelho and Obatã. Notably, three LOX genes displayed strong correlations between transcript abundance and enzymatic activity. Together, these results indicate that a subset of LOX genes in C. arabica represents promising candidates for detailed functional analyses, as they likely contribute substantially to lipoxygenase activity and elicitor-induced defense responses in Coffea species.
The MLO gene family plays a critical role in plant-pathogen interactions, regulating susceptibility and resistance to fungal diseases. In this study, we performed a genome-wide characterization of the MLO genes in soybean (Glycine max), integrating structural analysis, phylogenetic classification, expression profiling, functional validation by virus-induced gene silencing (VIGS), and SNP mining. We identified 40 MLO genes, including a novel member (GmMLO25) with an unusually small MLO domain (93 aa). Protein length varied from 130 to 600 aa, with differences in the number of transmembrane domains and conserved motifs, including calmodulin-binding domains (CaMBDs). Analysis of SNPs in coding sequences revealed missense substitutions affecting conserved motifs and transmembrane regions, particularly in clade V genes. RNA-seq and RT-qPCR analyses revealed differential regulation of clade V members between resistant (Rpp5) and susceptible (BRS 184) genotypes during Phakopsora pachyrhizi infection. Functional validation by VIGS demonstrated that silencing multiple clade V genes did not reduce the number of uredinia but drastically reduced fungal sporulation. This study identified GmMLO38 as a functional susceptibility gene in soybean and as a prime target for gene editing or RNAi-based strategies to enhance resistance to Asian soybean rust (ASR).
Accurate characterization of human genetic diversity is essential for robust genomic analyses. We compared self-declared and genome-derived ancestry composition in 10 250 participants from the pan-Canadian HostSeq cohort using whole-genome sequencing data. Global and local ancestry were inferred at the continental super-population level using the alignment-free ntRoot algorithm and evaluated through both hard-label concordance and multiclass Brier score analyses incorporating full ancestry fraction profiles. Strong agreement was observed among East Asian / Pacific Islander (mean Brier score ± SD: 0.012 ± 0.052), Black (0.013 ± 0.042), White (0.055 ± 0.022), and South Asian (0.057 ± 0.098) participants, whereas higher scores among Hispanic (0.083 ± 0.060) and Middle Eastern or Central Asian (0.122 ± 0.034) participants reflected broader and more admixed ancestry profiles. Principal component analysis of centered log-ratio-transformed ancestry fractions revealed overlapping ancestry gradients rather than discrete continental groupings. Entropy- and dominance margin-based analyses further indicated that many discordant cases reflected diffuse admixture rather than categorical mismatch. Together, these findings support representing ancestry as a continuous compositional spectrum rather than discrete categories. Genome-derived ancestry estimates describe patterns of genomic variation and should not be interpreted as proxies for race.
Brazil is the global leader in the production and export of tropical forage seeds. The livestock sector primarily relies on tropical grasses, including species of Urochloa and Megathyrsus maximus, as well as other genera such as Paspalum, Cenchrus, and Setaria. The sustainability and competitiveness of this sector are increasingly threatened by climate change and biotic stresses. While conventional breeding has made progress, enhancing genetic gains requires advanced molecular tools due to the biological complexity of these grasses. Given the growing importance of forage genomics, this paper provides an up-to-date overview of genomic resources available for the main tropical forage species. We synthesized the state-of-the-art applications of genomics, transcriptomics, and functional genetics in forage research, consolidating findings from Brazilian and international institutions. In recent years, significant advances have been made, including the assembly of reference genomes, the development of comprehensive transcriptomic datasets, and the construction of high-density linkage maps. Despite the recent increase in genomic data, we identified significant bottlenecks, including the need for reference pangenomes, standardized phenotyping platforms, and robust functional validation pipelines for novel genes. This review serves as a critical roadmap, emphasizing that collaboration is vital to translate genomic data into resilient, nutritious, and climate-adapted tropical forage cultivars, securing the future of sustainable livestock production.
All bats in Newfoundland, Canada are insectivores. While the dietary insects of several bat species have been investigated elsewhere in Canada and North America, little is known about the insect prey of Newfoundland bats. Here, we use DNA metabarcode sequencing of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify insect prey from Myotis lucifugus guano. Among 21 guano samples from six sites in Newfoundland, 346 amplicon sequence variants (ASVs) of arthropods were identified. Among these 346 ASVs, 343 and 330 have not been documented in the barcode of life database from Newfoundland and Canada, respectively. In addition, only 34 and 54 of the 346 ASVs were identified to 19 species and 24 genera, respectively, with high confidence. Overall, Trichoptera had the highest percentage of COI sequences while Coleoptera had the most ASVs. High arthropod variabilities were observed among guano samples from both within and among sites. In eastern Newfoundland, notable difference in prey arthropod compositions was observed between two sampling times. Together, our results show tremendous undiscovered arthropod diversity in Newfoundland and that bat guano DNA metabarcoding can be an effective tool to help reveal this biodiversity. The implications of this research to bat conservation were discussed.
The Amazon River plume (ARP) impacts the Amazon Continental Shelf's (ACS) marine ecosystem, but its effect on fish larvae remains uninvestigated. To investigate the influence of the ARP on the ichthyoplankton community, MIDI Multinet net integrative tows were carried in the ACS (September 2021) and samples were identified and separated into morphotypes for molecular analysis. Morphological assessment of 343 fish larvae initially suggested 30 families, but subsequent DNA barcoding revealed a 42% discrepancy, highlighting the limitations of traditional taxonomy for larvae identification. Eighty-three fish larvae, representatives of identified morphotypes were successfully assigned to 58 Barcode Index Numbers, including sequences new to global databases and possibly five new occurrences in the region. The assemblage displayed a heterogeneous mix of neritic, oceanic, and estuarine taxa. However, no clear pattern emerged between species life-history traits and their distribution across the plume-generated hydrographic habitats. Although species composition varied across the plume's influence gradient, our sampling design cannot identify the underlying environmental drivers, underscoring the need for broader seasonal and spatial surveys in the region. These findings reveal the complexity of the ACS ecosystem and demonstrate the necessity of integrating molecular tools to accurately characterize biodiversity gaps and support conservation strategies in this dynamic region.
Atractylodes lancea in the family Asteraceae is an important plant in traditional herbal medicine. Although its genome has been reported, this species harbors B chromosomes whose DNA composition and biological significance remain largely unexplored. Here, we dissect the origin, structure, and diversification of A. lancea B chromosomes, using an integrated genomic and cytogenetic approach. Illumina sequencing of bulk samples and RepeatExplorer2 analysis identified two satellite repeats as major components of B chromosomes: CL2, a centromeric and pericentromeric repeat shared with A chromosomes, and CL47/59, a B chromosome-specific repeat localized to the interstitial region of B chromosomes. Fluorescence in situ hybridization uncovered striking variation among B chromosomes in repeat distribution, as well as in length and the arm ratio. CL47/59 abundance was positively correlated with B chromosome length, implicating its amplification during B chromosome enlargement. Integrating these genomic and cytological observations, we propose a model for B chromosome diversification in A. lancea, involving a pericentric inversion and the differential accumulation of CL2 and CL47/59 repeats.
The transposable I-element from Drosophila melanogaster encodes an RNA-binding protein ORF1p required for its retroansposition. ORF1p binds single-stranded DNA and RNA in vitro nonspecifically. If this nonspecific RNA binding occurs in the germline, then we hypothesize that it plays a role in the production of heritable retrocopies of genes other than the I-element. The goal of this study was to test this hypothesis by investigating the specificity of ORF1p RNA binding in the female germline. To this end, we cloned a D. teissieri I-element. We first tested D. melanogaster strains transgenic for this element for its RNA and protein expression, and its transposition, and demonstrated that it has similar properties to those reported for previously isolated D. teissieri and D. melanogaster I-elements. Then, using RNA immunoprecipitation of epitope-tagged HAORF1p from ovary extracts, followed by high-throughput sequencing (RIP-seq), we found that HAORF1p binds RNA in cis with high specificity. Therefore, the I-element ORF1p does not appear to play a role in generating retrocopies by binding host cellular RNAs in trans in the female germline, unless it binds these RNAs rarely or with low affinity.
The tRNA-derived RNA fragments (tRFs) have emerged as pivotal regulators of eukaryotic stress responses. These small non-coding RNAs are implicated in various biological domains. This study investigates the expression and functions of plant tRFs in response to abiotic stress with focus on Eugenia uniflora L. In silico analysis identified a diverse set of small RNAs originating from 73 conserved tRNAs. High-throughput analysis of small RNA (sRNA) libraries revealed a prevalence of 5'tRFs, with 51 947 sRNAs. RT-qPCR analysis unveiled predominant tRFs, such as those derived from tRNA-Arg-CCT. Among the 11 tRFs examined, six displayed notable differences in expression levels under high salt and osmotic stress triggered by NaCl and polyethylene glycol. Notably, 5'tRF ArgTCG and 5'tRF GlyTCC were positively regulated under both saline and water stress conditions. Additionally, we demonstrated that some previously identified targets of these tRFs showed reduced expression following both types of stress. Our findings suggest that abiotic stress-related tRFs interact with various signaling and metabolic pathways. Alterations in the expression of three tRFs and their target genes in both stress conditions highlight the potential significance of tRF changes in E. uniflora adaptation to drought and salinity.
Decades of neuroscience research utilizing Drosophila has led to enormous strides in uncovering genes that positively support the ability to form new memories or consolidate them for the long-term. However, recent research has revealed the existence of more rare but equally important memory suppressor genes whose normal function is to limit memory formation or even promote active forgetting. Here we report that RNAi targeting of diacylglycerol kinase (dgk), a regulator of lipid signaling, within the mushroom body memory circuitry, specifically enhances aversive olfactory memory retention while leaving learning and sensory-motor behavioural controls unaffected. Furthermore, memory retention is enhanced when targeting dgk in these circuits with two additional RNAi lines. Finally, using in vivo functional imaging, we offer evidence that dgk plays a role in regulating baseline synaptic transmission of memory circuits. While the exact mechanism for Dgk's synaptic effects and the implications for memory storage remain unclear, our findings implicate lipid signaling via Dgk as an important regulator of active-forgetting pathways. This work builds on our prior understanding of the importance of lipids in cognition by extended their role to memory suppression and active forgetting.
Science and research are under attack and scientists need to fight back. Public access to information is at an unprecedented high, but misinformation and disinformation are rampant and societal trust in science and research is at a historic low. Scientists need to be part of restoring trust in science and evidence-based decision making. For a variety of reasons, including time constraints, little professional recognition, and limited communication experience, too few scientists are involved in science outreach. Here, based on our experience as research scientists who engage in science outreach, we suggest ways to address these issues including four "How-To's": Take the leap, Engage, Find partners, and Explain the scientific process. Like scientific research, science communication is a craft that can be intentionally practiced and developed. Scientists can restore trust in science and research. It is in our best interest, and that of society as a whole, for us to step up and meet this challenge.
Single-locus species-delimitation methods using DNA barcoding data have made an important contribution to large scale biodiversity inventories and integrative taxonomy, allowing rapid and repeatable estimates of alpha diversity from huge numbers of individuals. A range of distance-based and tree-based methods now exist to perform these analyses, including ABGD, ASAP, GMYC, and mPTP. However, the outputs of such software are idiosyncratic and difficult to integrate and compare. The R package delimtools offers a platform capable of (1) pre-processing, cleaning, and formatting data; (2) collapsing and summarising haplotype information; (3) executing, parsing, and merging program outputs and species partitions; and (4) tabulating results, and visualizing on a phylogenetic tree. The open-source delimtools package opens up new avenues to scale up and standardize species delimitation analyses, and is available on the CRAN (https://cran.r-project.org/package=delimtools) and GitHub (https://github.com/legalLab/delimtools/) repositories.
Euterpe oleracea Mart. is a perennial wetland palm native to the eastern Amazon that produces a fruit called açaí, which is used to prepare a beverage of great social and economic importance to the region. We have sequenced the açaí genome using Oxford Nanopore long-read platform, and we have evaluated the gene expression of the fruit during the ripening process in both the white and purple varieties via RNA-Seq analysis. The assembled genome had a size of 3 066 969 163 bp, with the longest contig displaying 430 834 bp, an N50 of 54 646, and a GC content of 49.97%. The transcriptome analysis identified crucial genes that regulate the production of anthocyanins in purple açaí. For example, the upregulation of the flavonoid 3'5'-hydroxylase enzyme plays a crucial role in the synthesis of purple anthocyanins, such as delphinidin 3-glucoside, between 70 and 130 days after flowering. In contrast, a general downregulation of the enzymes responsible for the initial stages of the anthocyanin synthesis was observed in the white variety. Our findings provide a valuable contribution to the understanding of the molecular mechanisms that regulate the ripening process of açaí fruits and present the first genome of E. oleracea.
