RESUMO

Background: Genomic resource development for non-model organisms is rapidly progressing, seeking to uncover molecular mechanisms and evolutionary adaptations enabling thriving in diverse environments. Limited genomic data for bat species hinder insights into their evolutionary processes, particularly within the diverse Myotis genus of the Vespertilionidae family. In Mexico, 15 Myotis species exist, with three-M. vivesi, M. findleyi, and M. planiceps-being endemic and of conservation concern. Methods: We obtained samples of Myotis vivesi, M. findleyi, and M. planiceps for genomic analysis. Each of three genomic DNA was extracted, sequenced, and assembled. The scaffolding was carried out utilizing the M. yumanensis genome via a genome-referenced approach within the ntJoin program. GapCloser was employed to fill gaps. Repeat elements were characterized, and gene prediction was done via ab initio and homology methods with MAKER pipeline. Functional annotation involved InterproScan, BLASTp, and KEGG. Non-coding RNAs were annotated with INFERNAL, and tRNAscan-SE. Orthologous genes were clustered using Orthofinder, and a phylogenomic tree was reconstructed using IQ-TREE. Results: We present genome assemblies of these endemic species using Illumina NovaSeq 6000, each exceeding 2.0 Gb, with over 90% representing single-copy genes according to BUSCO analyses. Transposable elements, including LINEs and SINEs, constitute over 30% of each genome. Helitrons, consistent with Vespertilionids, were identified. Values around 20,000 genes from each of the three assemblies were derived from gene annotation and their correlation with specific functions. Comparative analysis of orthologs among eight Myotis species revealed 20,820 groups, with 4,789 being single copy orthogroups. Non-coding RNA elements were annotated. Phylogenomic tree analysis supported evolutionary chiropterans' relationships. These resources contribute significantly to understanding gene evolution, diversification patterns, and aiding conservation efforts for these endangered bat species.

Assuntos

RESUMO

BACKGROUND: Neltuma pallida is a tree that grows in arid soils in northwestern Peru. As a predominant species of the Equatorial Dry Forest ecoregion, it holds significant economic and ecological value for both people and environment. Despite this, the species is severely threatened and there is a lack of genetic and genomic research, hindering the proposal of evidence-based conservation strategies. RESULTS: In this work, we conducted the assembly, annotation, analysis and comparison of the chloroplast genome of a N. pallida specimen with those of related species. The assembled chloroplast genome has a length of 162,381 bp with a typical quadripartite structure (LSC-IRA-SSC-IRB). The calculated GC content was 35.97%. However, this is variable between regions, with a higher GC content observed in the IRs. A total of 132 genes were annotated, of which 19 were duplicates and 22 contained at least one intron in their sequence. A substantial number of repetitive sequences of different types were identified in the assembled genome, predominantly tandem repeats (> 300). In particular, 142 microsatellites (SSR) markers were identified. The phylogenetic reconstruction showed that N. pallida grouped with the other Neltuma species and with Prosopis cineraria. The analysis of sequence divergence between the chloroplast genome sequences of N. pallida, N. juliflora, P. farcta and Strombocarpa tamarugo revealed a high degree of similarity. CONCLUSIONS: The N. pallida chloroplast genome was found to be similar to those of closely related species. With a size of 162,831 bp, it had the classical chloroplast quadripartite structure and GC content of 35.97%. Most of the 132 identified genes were protein-coding genes. Additionally, over 800 repetitive sequences were identified, including 142 SSR markers. In the phylogenetic analysis, N. pallida grouped with other Neltuma spp. and P. cineraria. Furthermore, N. pallida chloroplast was highly conserved when compared with genomes of closely related species. These findings can be of great potential for further diversity studies and genetic improvement of N. pallida.

Assuntos

RESUMO

The house sparrow (Passer domesticus) is a valuable avian model for studying evolutionary genetics, development, neurobiology, physiology, behavior, and ecology, both in laboratory and field-based settings. The current annotation of the P. domesticus genome available at the Ensembl Rapid Release site is primarily focused on gene set building and lacks functional information. In this study, we present the first comprehensive functional reannotation of the P. domesticus genome using intestinal Illumina RNA sequencing (RNA-Seq) libraries. Our revised annotation provides an expanded view of the genome, encompassing 38592 transcripts compared to the current 23574 transcripts in Ensembl. We also predicted 14717 protein-coding genes, achieving 96.4% completeness for Passeriformes lineage BUSCOs. A substantial improvement in this reannotation is the accurate delineation of untranslated region (UTR) sequences. We identified 82.7% and 93.8% of the transcripts containing 5'- and 3'-UTRs, respectively. These UTR annotations are crucial for understanding post-transcriptional regulatory processes. Our findings underscore the advantages of incorporating additional specific RNA-Seq data into genome annotation, particularly when leveraging fast and efficient data processing capabilities. This functional reannotation enhances our understanding of the P. domesticus genome, providing valuable resources for future investigations in various research fields.

RESUMO

Four large cryptic plasmids were identified in the salmon pathogen Piscirickettsia salmonis reference strain LF-89. These plasmids appeared highly novel, with less than 7% nucleotidic identity to the nr plasmid database. Plasmid copy number analysis revealed that they are harbored in chromosome equivalent ratios. In addition to plasmid-related genes (plasmidial autonomous replication, partitioning, maintenance, and mobilization genes), mobile genetic elements such as transposases, integrases, and prophage sequences were also identified in P. salmonis plasmids. However, bacterial lysis was not observed upon the induction of prophages. A total of twelve putative virulence factors (VFs) were identified, in addition to two global transcriptional regulators, the widely conserved CsrA protein and the regulator Crp/Fnr. Eleven of the putative VFs were overexpressed during infection in two salmon-derived cellular infection models, supporting their role as VFs. The ubiquity of these plasmids was also confirmed by sequence similarity in the genomes of other P. salmonis strains. The ontology of P. salmonis plasmids suggests a role in bacterial fitness and adaptation to the environment as they encode proteins related to mobilization, nutrient transport and utilization, and bacterial virulence. Further functional characterization of P. salmonis plasmids may improve our knowledge regarding virulence and mobile elements in this intracellular pathogen.

RESUMO

BACKGROUND: Elephant grass [Cenchrus purpureus (Schumach.) Morrone] is used for bioenergy and animal feed. In order to identify candidate genes that could be exploited for marker-assisted selection in elephant grass, this study aimed to investigate changes in predictive accuracy using genomic relationship information and simple sequence repeats for eight traits (height, green biomass, dry biomass, acid and neutral detergent fiber, lignin content, biomass digestibility, and dry matter concentration) linked to bioenergetics and animal feeding. RESULTS: We used single-step, genome-based best linear unbiased prediction and genome association methods to investigate changes in predictive accuracy and find candidate genes using genomic relationship information. Genetic variability (p < 0.05) was detected for most of the traits evaluated. In general, the overall means for the traits varied widely over the cuttings, which was corroborated by a significant genotype by cutting interaction. Knowing the genomic relationships increased the predictive accuracy of the biomass quality traits. We found that one marker (M28_161) was significantly associated with high values of biomass digestibility. The marker had moderate linkage disequilibrium with another marker (M35_202) that, in general, was detected in genotypes with low values of biomass digestibility. In silico analysis revealed that both markers have orthologous regions in other C4 grasses such as Setaria viridis, Panicum hallii, and Panicum virgatum, and these regions are located close to candidate genes involved in the biosynthesis of cell wall molecules (xyloglucan and lignin), which support their association with biomass digestibility. CONCLUSIONS: The markers and candidate genes identified here are useful for breeding programs aimed at changing biomass digestibility in elephant grass. These markers can be used in marker-assisted selection to grow elephant grass cultivars for different uses, e.g., bioenergy production, bio-based products, co-products, bioactive compounds, and animal feed.

Assuntos

RESUMO

BACKGROUND: Although animal mitochondrial DNA sequences are known to evolve rapidly, their gene arrangements often remain unchanged over long periods of evolutionary time. Therefore, comparisons of mitochondrial genomes may result in significant insights into the evolution both of organisms and of genomes. Mammalian mitochondrial genomes recently published in the GenBank database of NCBI show numerous rearrangements in various regions of the genome, from which it may be inferred that the mammalian mitochondrial genome is more dynamic than expected. However, it is alternatively possible that these are errors of annotation and, if so, are misleading our interpretations. In order to verify these possible errors of annotation, we performed a comparative genomic analysis of mammalian mitochondrial genomes available in the NCBI database. RESULTS: Using a combination of bioinformatics methods to carefully examine the mitochondrial gene arrangements in 304 mammalian species, we determined that there are only two sets of gene arrangements, one that is shared by all of the marsupials and another that is shared by all of the monotremes and eutherians, with these two arrangements differing only by the positions of tRNA genes in the region commonly designated as "WANCY" for the genes it comprises. All of the 68 other cases of reported gene rearrangements are errors. We note that there are also numerous errors of impossibly short, incorrect gene annotations, cases where genomes that are reported as complete are actually missing portions of the sequence, and genes that are clearly present but were not annotated in these records. CONCLUSIONS: We judge that the application of simple bioinformatic tools in the verification of gene annotation, particularly for organelle genomes, would be a very useful enhancement for the curation of genome sequences submitted to GenBank.

Assuntos

RESUMO

Leishmania braziliensis is the etiological agent of American mucosal leishmaniasis, one of the most severe clinical forms of leishmaniasis. Here, we report the assembly of the L. braziliensis (M2904) genome into 35 continuous chromosomes. Also, the annotation of 8395 genes is provided. The public availability of this information will contribute to a better knowledge of this pathogen and help in the search for vaccines and novel drug targets aimed to control the disease caused by this Leishmania species.

Assuntos

RESUMO

Background: Cinnamomum longepaniculatum is an important commercial crop and the main source of volatile terpenoids. The biosynthesis of key bioactive metabolites of C. longepaniculatum is not well understood because of the lack of available genomic and transcriptomic information. To address this issue, we performed transcriptome sequencing of C. longepaniculatum leaves to identify factors involved in terpenoid metabolite biosynthesis. Results: Transcriptome sequencing of C. longepaniculatum leaves generated over 56 million raw reads. The transcriptome was assembled using the Trinity software and yielded 82,061 unigenes with an average length of 879.43 bp and N50 value of 1387 bp. Furthermore, Benchmarking Universal Single-Copy Orthologs analysis indicated that our assembly is 91% complete. The unigenes were used to query the nonredundant database depending on sequence similarity; 42,809 unigenes were homologous to known genes in different species, with an annotation rate of 42.87%. The transcript abundance and Gene Ontology analyses revealed that numerous unigenes were associated with metabolism, while others were annotated in functional categories including transcription, signal transduction, and secondary metabolism. The Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that 19,260 unigenes were involved in 385 metabolic pathways, with 233 unigenes found to be involved in terpenoid metabolism. Moreover, 23,463 simple sequence repeats were identified using the microsatellite identification tool. Conclusion: This is the first detailed transcriptome analysis of C. longepaniculatum. The findings provide insights into the molecular basis of terpenoid biosynthesis and a reference for future studies on the genetics and breeding of C. longepaniculatum.

Assuntos

RESUMO

Background: Marker-assisted introgression currently represents the most widely spread application of DNA markers as an aid to selection in plant breeding. New barley germplasm should be supplemented by genes that facilitate growth and development under stressful conditions. The homology search against known genes is a fundamental approach to identify genes among the generated sequences. This procedure can be utilized for SNP search in genes of predicted function of interest and associated gene ontology (GO). Results: Backcross breeding enhanced by marker selection may become a powerful method to transfer one or a few genes controlling a specific trait. In the study, the integrated approach of combining phenotypic selection with marker assisted backcross breeding for introgression of LTP2 gene, in the background of semi-dwarf spring barley cultivar, was employed. This study discusses the efficiency of molecular marker application in backcrossing targeted on the selected gene. Conclusions: BC6 lines developed in this study can serve as a unique and adequate plant material to dissect the role of LTP2 gene. Due to its role in lipid transfer, the LTP2 may be crucial in lipidome modification in response to abiotic stress.

Assuntos

RESUMO

Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffea eugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffea arabica together with Coffea canephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next-generation sequencing and to analyze specific genes that were highly expressed in leaves and fruits with potential exploratory characteristics for breeding and understanding the evolutionary biology of coffee. A de novo assembly generated 36,935 contigs that were annotated using eight databases. We observed a total of ~5000 differentially expressed genes between leaves and fruits. Several genes exclusively expressed in fruits did not exhibit similarities with sequences in any database. We selected ten differentially expressed unigenes in leaves and fruits to evaluate transcriptional profiles using qPCR. Our study provides the first gene catalog for C. eugenioides and enhances the knowledge concerning the mechanisms involved in the C. arabica homeologous. Furthermore, this work will open new avenues for studies into specific genes and pathways in this species, especially related to fruit, and our data have potential value in assisted breeding applications.

Assuntos

RESUMO

CONTEXT: Paracoccidioides brasiliensis, a dimorphic fungus is the causative agent of paracoccidioidomycosis, a disease globally affecting millions of people. The haloacid dehalogenase (HAD) superfamily hydrolases enzyme in the fungi, in particular, is known to be responsible in the pathogenesis by adhering to the tissue. Hence, identification of novel drug targets is essential. AIMS: In-silico based identification of co-expressed genes along with HAD superfamily hydrolase in P. brasiliensis during the morphogenesis from mycelium to yeast to identify possible genes as drug targets. MATERIALS AND METHODS: In total, four datasets were retrieved from the NCBI-gene expression omnibus (GEO) database, each containing 4340 genes, followed by gene filtration expression of the data set. Further co-expression (CE) study was performed individually and then a combination these genes were visualized in the Cytoscape 2. 8.3. STATISTICAL ANALYSIS USED: Mean and standard deviation value of the HAD superfamily hydrolase gene was obtained from the expression data and this value was subsequently used for the CE calculation purpose by selecting specific correlation power and filtering threshold. RESULTS: The 23 genes that were thus obtained are common with respect to the HAD superfamily hydrolase gene. A significant network was selected from the Cytoscape network visualization that contains total 7 genes out of which 5 genes, which do not have significant protein hits, obtained from gene annotation of the expressed sequence tags by BLAST X. For all the protein PSI-BLAST was performed against human genome to find the homology. CONCLUSIONS: The gene co-expression network was obtained with respect to HAD superfamily dehalogenase gene in P. Brasiliensis.

RESUMO

Statistical Inference of Function Through Evolutionary Relationships (SIFTER) is a powerful computational platform for probabilistic protein domain annotation. Nevertheless, SIFTER is not widely used, likely due to usability and scalability issues. Here we present SIFTER-T (SIFTER Throughput-optimized), a substantial improvement over SIFTER's original proof-of-principle implementation. SIFTER-T is optimized for better performance, allowing it to be used at the genome-wide scale. Compared to SIFTER 2.0, SIFTER-T achieved an 87-fold performance improvement using published test data sets for the known annotations recovering module and a 72.3% speed increase for the gene tree generation module in quad-core machines, as well as a major decrease in memory usage during the realignment phase. Memory optimization allowed an expanded set of proteins to be handled by SIFTER's probabilistic method. The improvement in performance and automation that we achieved allowed us to build a web server to bring the power of Bayesian phylogenomic inference to the genomics community. SIFTER-T and its online interface are freely available under GNU license at http://labpib.fmrp.usp.br/methods/SIFTER-t/ and https://github.com/dcasbioinfo/SIFTER-t.

Assuntos