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Aniline blue, a triphenylmethane dye, has been widely used in industrial and medical fields, leading to its gradual enrichment in environmental water. Its removal and degradation from the water is essential but very challenging. A bacterium Lysinibacillus sp. 38-6, which is able to efficiently degrade aniline blue, was isolated from the surface soil samples under withered leaves. The strain exhibited excellent decolorization capacity at high concentrations of aniline blue (91% at 1000 mg/L) and salt (90% at 75 g/L) as well as high temperature (92% at 45 °C). To investigate the dye degradation strategies of Lysinibacillus sp. 38-6 at the genomic level, its genome was sequenced and analyzed. The isolate possesses abundant genomic features responsible for degrading dyes. In particular, several genes encoding laccase, iron-dependent peroxidase, NAD(P)H-dependent FMN reductase, and short-chain dehydrogenase/reductases might contribute to the cleavage of chromophore groups and aromatic rings in aniline blue. In addition, a number of genes required for heat, salt, and oxidative stress responses were found, indicating that Lysinibacillus sp. 38-6 is able to efficiently degrade dyes at higher temperature, salty and oxidative environments. It is thus inferred that isolate 38-6 has the potential for applications in efficient degradation of aniline blue in wastewater treatment.

Natural history museums harbor invaluable resources for conserving endangered species by providing insights into the mechanism of historical population declines. We conducted data synthesis to better understand the extinction factors of the iconic Jambato Harlequin frog, Atelopus ignescens, which was widespread in the Ecuadorian Andes before 1985 but vanished in 1988. We synthesized historical data from natural history museums, the global biodiversity information facility, and mtDNA sequences to examine whether Batrachochytrium dendrobatidis (Bd) fungus infection, climate change, and/or their interaction contributed to the rapid population decline. We found excessive rare alleles reflected in the negative Tajima's D estimated from the mtDNA samples from 1984, indicating a selective sweep or population bottleneck. Sex and geography showed stronger effects on adult body sizes than Bd epizootic timing. The body sizes of adult males formed a geographic cline. Species distribution modeling based on temperature and precipitation accurately predicted the occupancy of A. ignescens in 1960-69, which further projected a rapid decline in species distribution between 1970 and 2020. This investigation revealed strong climate effect and weak epizootics effect on A. ignescens extinction, and inspires future museum genomic studies to dissect the potential climatic maladaptation behind dramatic historical extinctions.

Intramuscular fat is an important factor for the sensory quality and value of meat. However, in tropical breeds such as Nellore, the lower marbling capacity represents a challenge for its positioning in premium markets. Marbling score (MS) and the total lipid (TL) determination methods are complementary methodologies for measuring beef intramuscular fat. Longissimus thoracis samples from the 24 most extreme steers (out of 189 steers) for MS (high = 12 and low = 12) and TL (high = 12 and low = 12) traits were collected to (1) validate in Nellore cattle differentially expressed genes for MS and TL traits found in the literature in other populations using real-time PCR, and (2) verify if differentially expressed genes were translated into differentially expressed proteins through advanced mass spectrometry (LC-MS/MS). Significant differences in the expression levels of the genes FABP4, DGAT1, DGAT2, BARX2, STAT5A, and SDC were observed in the group with high intramuscular fat content. These genes play important roles in lipid metabolism, adipogenesis, and muscle development. Proteins encoded by genes (PRDM1 and COL1A2) regulated by the transcription factor STAT5A were differentially expressed and probably play a key role during intramuscular fat deposition. Our results confirm that the genes FABP4, DGAT1, DGAT2, STAT5A, and BARX2 validated here can potentially be used as biomarkers for intramuscular fat in Nellore cattle.

The genus Leptodactylus is among the most studied anurans in cytogenetics. Despite exhibiting chromosomal conservatism with 2n = 22, microstructural studies (here defined as investigations of subchromosomal features such as DNA repetitive elements, chromatin organization, and sequence-level structural arrangements) have revealed significant karyotypic diversity within the genus, primarily associated with the distribution of repetitive sequences. Additionally, complex sex chromosome systems have been identified, underscoring the importance of further studies on these species. In this context, we performed a karyotypic characterization of Leptodactylus vastus from the Amazonian region. Using conventional cytogenetics, FISH with repetitive sequences, and phylogenetic analyses, we identified extensive chromosomal rearrangements, evidenced by the distribution of heterochromatin and repetitive sequences, including microsatellites, 18S rDNA, and U2 snDNA. Meiotic analyses in males revealed the presence of multivalent chromosomal chains involving eight chromosomes, a pattern consistent with a multiple sex chromosome system (X₁Y₁X₂Y₂X₃Y₃X₄Y₄). Concerning the clusters of repetitive sequences, we observed in specific chromosome pairs underscores the potential cytotaxonomic relevance of these markers. Phylogenetically, Leptodactylus vastus belongs to the Leptodactylus pentadactylus group, which includes other species known to possess multiple sex chromosome systems, although the absence of female data prevents definitive confirmation of this system in this species. Our results suggest that chromosomal rearrangements may have contributed to the genomic diversification of the species, supporting previous hypotheses on the role of structural variation in Leptodactylus species while highlighting the need for further comparative studies involving both sexes to fully clarify the nature of the multivalent chromosomal chains observed in Leptodactylus vastus.

Environmental DNA (eDNA) has shown promise for the detection of threatened and endangered species and has been implemented for monitoring aquatic spawning events. Freshwater unionid mussels exhibit a rare form of mitochondrial inheritance, in which males possess a unique mitochondrial mitotype that is divergent from the female mitotype. As freshwater mussels are spermcasters, the detection of male mitotype eDNA may provide critical conservation information related to timing of sperm release. This study re-purposed an existing eDNA metabarcoding dataset to detail the unique detection of eDNA pertaining to the male mitotype. Water samples collected alongside an extensive mussel salvage within the Walhonding River, Ohio, detected 16 distinct male mitotypes. However, several constraints limit the proper interpretation of these detections. There is currently a lack of reporting on assay compatibility with the male mitotype within freshwater mussel eDNA literature. Reference genetic databases are critically lacking, with only four of the 16 male eDNA sequences in this study able to be discerned to a species. This study highlights the importance of detailing these detections as the unique inheritance system provides opportunities to document difficult to record spawning behaviors, and eDNA may be employed as a survey tool to evaluate patterns of metapopulation geneflow.

Medicago polymorpha (2n = 2x = 14) is a valuable forage legume, but the identification of its somatic chromosomes has been challenging due to a lack of distinctive chromosome morphological features. With appropriate probes, oligonucleotide-based FISH is a highly effective method for chromosome identification. However, there are no available probes for M. polymorpha. In this study, we isolated five tandem repeats from the M. polymorpha genome, named Mp51, Mp139, Mp167, Mp179, and Mp497. Mp51 showed two pairs of signals located at the pericentromere. Mp139 exhibited four pairs of signals, located at the pericentromere and short arm of chromosomes. Mp167 and Mp179 showed seven pairs of signals, respectively, concentrated in the pericentromere. Mp497 exhibited three pairs of signals, distributed across the pericentromere and proximal position of the chromosomes. The combined FISH results of Mp51 and Mp139 oligo probes with 5S rDNA and 18S-26S rDNA probes demonstrated distinct signal patterns for each chromosome, enabling the precise identification of all chromosome pairs. Finally, the visual identification of M. polymorpha chromosomes was resolved. This will provide useful cytological information for studying the chromosomal structure and behavior of M. polymorpha.

We present the first genome of a Brazilian bumblebee species, the bellicose bumblebee (Bombus bellicosus). This is an endemic species in southern South America facing local extinction due to habitat loss and climate change. During the COVID-19 social distancing in Brazil, we launched a citizen science initiative via social media to locate remaining bellicose bumblebee populations, leading to the collection of a specimen for genome sequencing. Analysis of the novel genome revealed lower genetic diversity in the bellicose bumblebee compared to a widespread related species (Bombus pascuorum). However, the absence of extensive runs of homozygosity indicated a lack of recent inbreeding, offering a promising perspective for the conservation of this species. Furthermore, demographic history analysis indicates population expansion during past glacial periods, in contrast to Palearctic bumblebees that suffered a stark decline during glaciations. Our findings provide invaluable information for the conservation of this species and for further studies about its biology and evolution, particularly under a scenario of rapid environmental change.

Bacteria in the genus Staphylococcus include human and animal pathogens. Although the genomic diversity of these bacteria is increasingly well characterized, the rate of protein evolution in staphylococci remains poorly understood. In this study, the genomic sequences of one representative from each of the 63 Staphylococcus species were downloaded from the RefSeq database. Homologous protein sequences were identified, and their evolutionary rates were inferred using a phylogenetic approach. The results demonstrated that some proteins evolve significantly faster than others, with several being involved in DNA-mediated transformation. Further analyses of the genomic sequences revealed that the evolutionary rate of proteins is correlated with codon adaptation of their genes, and that certain protein regions are more prone to accumulating mutations. This study highlights the more rapid evolution of specific proteins in staphylococci, likely reflecting the host diversity of these bacteria and their high adaptive capacity.

The subtribe Pronophilina (Nymphalidae: Satyrinae: Satyrini) is one of the most diverse subtribes within the Lepidoptera. In Colombia, these butterflies are distributed throughout the Andes, where they play a key role in montane ecosystems and exhibit high levels of endemism. Despite their complex genital morphology, species within the same genus often exhibit highly similar wing patterns, complicating taxonomic identification. In this study, we analyzed the concordance between DNA barcode-based species delimitation and morphological identifications using 334 cytochrome c oxidase subunit I barcodes from 94 a priori identified morphospecies in Colombia. We applied four molecular species delimitation methods (Automatic Barcode Gap Discovery, Refined Single Linkage, Poisson Tree Processes, and Assemble Species by Automatic Partitioning), delimitating between 98 and 108 molecular operational taxonomic units. Overall, the methods showed high consistency, with high congruence between morphological and molecular delimitations (81%). Additionally, 96.8% of the morphospecies exhibited a barcode gap, indicating clear genetic differentiation. However, we found some inconsistencies, including 6 cases of species merging and 12 cases of species splitting. Our findings underscore the utility of DNA barcoding for species delimitation in Pronophilina, while highlighting the need for integrative approaches to resolve taxonomic uncertainties in this diverse group.

Strains of the Italian honey bee Apis mellifera ligustica Spinola, 1806 are selectively bred for desirable apiculture traits. Ma et al. compared SNP differences in mtDNA genomes between a strain bred for enhanced royal jelly production (RJB) and an unselected strain (ITB). Kim et al. compared SNP and intergenic repeats differences between a Varroa mite resistant strain bred for high-hygienic behavior (HHB) and an unselected low-hygienic strain (LHB). Phylogenetic comparison of 23 complete A. m. ligustica mtDNA sequences, including the HHB and LHB strains and 14 RJB and ITB haplotypes, shows significant intrasubspecific clade structure for SNP differences and amino acid substitutions; however, this structure is not diagnostic of the strains under selection. RJB strains occur in three separate clades, and along with HHB are frequently identical or near-identical to other haplotypes. Differences between the selected and unselected strains appear to arise from coincidental fixation of alternative SNPs in different clades. Numbers of repeats show little or no phylogenetic signal: similarities are symplesiomorphic and differences convergent. Evaluation of the diagnostic and (or) adaptive significance of mtDNA markers requires broad knowledge of within-subspecies polymorphism.