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As one of the most important parts of plants, the genetic mechanisms of photosynthesis or the response of leaf to a single abiotic and biotic stress have been well studied. However, few researches have involved in the integration of data analysis from system level in leaf tissue under multiple abiotic stresses by utilizing biological networks. In this study, the weighted gene co-expression network analysis (WGCNA) strategy was used to integrate multiple data in leaf tissue of Populus species under different sample treatments. The gene co-expression networks were constructed and functional modules were identified by selecting the suitable soft threshold power β in the procedure of WGCNA. The identified hub genes and gene modules were annotated by agriGO, NetAffx Analysis Center, The Plant Genome Integrative Explorer (PlantGenIE) and other annotation tools. The annotation results have displayed that the highly correlated modules and hub genes are involved in the important biological processes or pathways related to module traits. The efficiency of the WGCNA strategy can generate comprehensive understanding of gene module-traits associations in leaf tissue, which will provide novel insight into the genetic mechanism of Populus species.

DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.

Complete mitochondrial genome of two species of subfamily Panchaetothripinae, Astrothrips tumiceps (16,467 bp) and Monilothrips kempi (14,773 bp) are generated by Next-Generation Sequencing Method. In this study, the detailed annotation of these mitogenomes as well as comparative analyses are carried out to explore the codon usage, gene composition, and phylogenetic relationship of subfamilies of family Thripidae. Moreover, the gene rearrangement of subfamily Panchaetothripinae of family Thripidae is also studied. Both the mitogenomes featured by 37 genes including 13 PCGs, 22 tRNAs, 2 rRNAs and with single putative control region with a positive AT-skew and negative GC-skew. trnS1 without DHU arm in both species, trnV without DHU arm in M. kempi, and trnE without TΨC loop in As. tumiceps. Further, codon based comparative analysis depicted the existence of natural selection pressure on all the PCGs in all the subfamilies of family Thripidae. The phylogenetic analyses, using the Bayesian inference (BI) and Maximum likelihood (ML) supported the monophyly of two suborders and family Phlaeothripidae. The family Thripidae is recovered as paraphyletic and subfamily Panchaetothripinae is in sister relationship with family Aeolothripidae and Stenurothripidae rather than the other subfamilies of family Thripidae. The gene order of the order Thysanoptera is highly rearranged, while few members of the subfamily Panchaetothripinae showed similar gene order to family Stenurothripidae. Therefore, this study suggests that the phylogenetic relationship between the subfamily Panchaetothripinae and other families is uncertain, necessitating a whole genome-based study to clarify the position of Panchaetothripinae within the suborder Terebrantia.

Eucalyptol is one of the major insecticidal active ingredients in a variety of plant essential oils, and has good killing and avoidance effects on Tribolium castaneum. The presence of detoxifying enzymes glutathione S-transferase (GST) in T. castaneum makes it resistant to a variety of insecticides. However, whether GST is involved in regulating the sensitivity of eucalyptol by T. castaneum is not well understood. In our previous study, a glutathione S-transferase, TcGSTu1, was significantly up-regulated in RNA sequencing data when T. castaneum was exposed to eucalyptol. Therefore, in this study, the role of TcGSTu1 in the regulating the sensitivity of T. castaneum to eucalyptol was studied. The enzyme activities of GST and the transcription levels of TcGSTu1 were significantly increased following stimulation with eucalyptol. When using RNA interference technology knockdown TcGSTu1 heightens the sensitivity of T. castaneum to eucalyptol, demonstrating a link between TcGSTu1 and eucalyptol detoxification metabolism. Furthermore, TcGSTu1 is expressed in all developmental stages of T. castaneum, with higher expression levels observed particularly in the late egg stage. There was significant expression of TcGSTu1 in various tissues of different organisms, including larval head, fat body, and adult head. This observation indicated a possible connection between high TcGSTu1 expression and eucalyptol detoxification. The present findings suggest that TcGSTu1 may be involved in regulating the sensitivity and response of T. castaneum to treatment with eucalyptol, providing new research insight into pest control.

Molecular characterization was conducted to characterise 'Nattukuttai', a native cattle population of the north-eastern agro-climatic zone of Tamil Nadu (India), using thirty microsatellite markers. The analyses revealed a high level of genetic diversity, with a total of 294 alleles observed across all the loci, averaging 9.8 alleles per locus. The allele sizes ranged from 83 bp to 302 bp, with frequencies ranging from 0.010 to 0.875. The microsatellite markers demonstrated high polymorphism, as indicated by an average polymorphic information content (PIC) of 0.763. Deviation from Hardy-Weinberg equilibrium was observed in a significant number of loci, indicating possible genetic influences such as selection or population structure. Bottleneck analysis suggested that the Nattukuttai population did not undergo any recent significant population contraction. Comparative analyses with three other cattle populations (Kangayam, Malai Madu, and Malnad Gidda) revealed varying genetic distances. Nattukuttai showed a distinct genetic profile, diverging from a common source that also gave rise to the Kangayam and Malai Madu clusters. Multivariate statistical analyses and phylogenetic reconstruction supported the genetic differentiation of Nattukuttai from the other populations, while Malai Madu and Kangayam were found to be genetically closer to each other. Overall, these findings provide insights into the genetic structure and relationships of the Nattukuttai cattle population, highlighting its distinct genetic identity and potential conservation significance.

Xylanase inhibitor proteins (XIP) are widely distributed in the plant kingdom, and also exist in rice. However, a systematic bioinformatics analysis of this gene family in rice (OsXIP) has not been conducted to date. In this study, we identified 32 members of the OsXIP gene family and analyzed their physicochemical properties, chromosomal localization, gene structure, protein structure, expression profiles, and interaction networks. Our results indicated that OsXIP genes exhibit an uneven distribution across eight rice chromosomes. These genes generally feature a low number of introns or are intronless, all family members, except for OsXIP20, contain two highly conserved motifs, namely Motif 8 and Motif 9. In addition, it is worth noting that the promoter regions of OsXIP gene family members feature a widespread presence of abscisic acid response elements (ABRE) and gibberellin response elements (GARE-motif and TATC-box). Quantitative Real-time PCR (qRT-PCR) analysis unveiled that the expression of OsXIP genes exhibited higher levels in leaves and roots, with considerable variation in the expression of each gene in these tissues both prior to and following treatments with abscisic acid (ABA) and gibberellin (GA3). Protein interaction studies and microRNA (miRNA) target prediction showed that OsXIP engages with key elements within the hormone-responsive and drought signaling pathways. The qRT-PCR suggested osa-miR2927 as a potential key regulator in the rice responding to drought stress, functioning as tissue-specific and temporally regulation. This study provides a theoretical foundation for further analysis of the functions within the OsXIP gene family.

The Universal Stress Protein (USP) primarily participates in cellular responses to biotic and abiotic stressors, playing a pivotal role in plant growth, development, and Stress responses to adverse environmental conditions. Totals of 23, 26 and 26 USP genes were recognized in Arabidopsis thaliana, Zea mays, and Oryza sativa, respectively. According to USP genes physicochemical properties, proteins from USP I class were identified as hydrophilic proteins with high stability. Based on phylogenetic analysis, USP genes family were classified into nine groups, USP II were rich in motifs. Additionally, members of the same subgroup exhibited similar numbers of introns/exons, and shared conserved domains, indicating close evolutionary relationships. Motif analysis results demonstrated a high degree of conservation among USP genes. Chromosomal distribution suggested that USP genes might have undergone gene expansion through segmental duplication in Arabidopsis thaliana, Zea mays, and Oryza sativa. Most Ka/Ks ratios were found to be less than 1, suggesting that USP genes in Arabidopsis thaliana, Zea mays, and Oryza sativa have experienced purifying selection. Expression profile analysis revealed that USP genes primarily respond to drought stress in Oryza sativa, temperature, and drought stress in Zea mays, and cold stress in Arabidopsis thaliana. Gene collinearity analysis can reveal correlations between genes, aiding subsequent in-depth investigations. This study sheds new light on the evolution of USP genes in monocots and dicots and lays the foundation for a better understanding of the biological functions of the USP genes family.

Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.

DnaJs/Hsp40s/JPDs are obligate co-chaperones of heat shock proteins (Hsp70), performing crucial biological functions within organisms. A comparative genome analysis of four genomes (Vitis vinifera, Eucalyptus grandis, Lagerstroemia indica, and Punica granatum) revealed that the DnaJ gene family in L. indica has undergone expansion, although not to the extent observed in P. granatum. Inter-genome collinearity analysis of four plants indicates that members belonging to Class A and B are more conserved during evolution. In L. indica, the expanded members primarily belong to Class-C. Tissue expression patterns and the biochemical characterization of LiDnaJs further suggested that DnaJs may be involved in numerous biological processes in L. indica. Transcriptome and qPCR analyses of salt stressed leaves identified at least ten LiDnaJs that responded to salt stress. In summary, we have elucidated the expansion mechanism of the LiDnaJs, which is attributed to a recent whole-genome triplication. This research laid the foundation for functional analysis of LiDnaJs and provides gene resources for breeding salt-tolerant varieties of L. indica.

The high dynamism of repetitive DNAs is a major driver of chromosome evolution. In particular, the accumulation of repetitive DNA sequences has been reported as part of the differentiation of sex-specific chromosomes. In turn, the fish species of the genus Megaleporinus are a monophyletic clade in which the presence of differentiated ZZ/ZW sex chromosomes represents a synapomorphic condition, thus serving as a suitable model to evaluate the dynamic evolution of repetitive DNA classes. Therefore, transposable elements (TEs) and in tandem repeats were isolated and located on chromosomes of Megaleporinus obtusidens and M. reinhardti to infer their role in chromosome differentiation with emphasis on sex chromosome systems. Despite the conserved karyotype features of both species, the location of repetitive sequences - Rex 1, Rex 3, (TTAGGG)_n, (GATA)_n, (GA)n, (CA)_n, and (A)_n - varied both intra and interspecifically, being mainly accumulated in Z and W chromosomes. The physical mapping of repetitive sequences confirmed the remarkable dynamics of repetitive DNA classes on sex chromosomes that might have promoted chromosome diversification and reproductive isolation in Megaleporinus species.