The advent of NGS (Next Generation Sequencing) technologies has resulted in an exponential increase in the number of complete genomes available in biological databases. This advance has allowed the development of several computational tools enabling analyses of large amounts of data in each of the various steps, from processing and quality filtering to gap filling and manual curation. The tools developed for gap closure are very useful as they result in more complete genomes, which will influence downstream analyses of genomic plasticity and comparative genomics. However, the gap filling step remains a challenge for genome assembly, often requiring manual intervention. Here, we present GapBlaster, a graphical application to evaluate and close gaps. GapBlaster was developed via Java programming language. The software uses contigs obtained in the assembly of the genome to perform an alignment against a draft of the genome/scaffold, using BLAST or Mummer to close gaps. Then, all identified alignments of contigs that extend through the gaps in the draft sequence are presented to the user for further evaluation via the GapBlaster graphical interface. GapBlaster presents significant results compared to other similar software and has the advantage of offering a graphical interface for manual curation of the gaps. GapBlaster program, the user guide and the test datasets are freely available at https://sourceforge.net/projects/gapblaster2015/. It requires Sun JDK 8 and Blast or Mummer.

This work reports on the whole-genome sequencing of Leishmania infantum chagasi from Honduras (Central America) and Brazil (South America).

Herein, we present the draft genome of Trametes villosa isolate CCMB561, a wood-decaying Basidiomycota commonly found in tropical semiarid climate. The genome assembly was 57.98 Mb in size with an L50 of 691. A total of 16,711 putative protein-encoding genes was predicted, including 590 genes coding for carbohydrate-active enzymes (CAZy), directly involved in the decomposition of lignocellulosic materials. This is the first genome of this species of high interest in bioenergy research. The draft genome of Trametes villosa isolate CCMB561 will provide an important resource for future investigations in biofuel production, bioremediation and other green technologies.

High-throughput sequencing technologies are a milestone in molecular biology for facilitating great advances in genomics by enabling the deposit of large volumes of biological data to public databases. The availability of such data has made possible the comparative genomic analysis through pipelines, using the entire gene repertoire of genomes. However, a large number of unfinished genomes exist in public databases; their number is approximately 16-fold higher than the number of complete genomes, which creates bias during comparative analyses. Therefore, the present work proposes a new tool called Pan4Drafts, an automated pipeline for pan-genomic analysis of draft prokaryotic genomes to maximize the representation and accuracy of the gene repertoire of unfinished genomes by using reads from sequencing data. Pan4Draft allows to perform comparative analyses using different methodologies such as combining complete and draft genomes, using only draft genomes or only complete genomes. Pan4Draft is available at http://www.computationalbiology.ufpa.br/pan4drafts and the test dataset is available at https://sourceforge.net/projects/pan4drafts.

No abstract

Corynebacterium pseudotuberculosis is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic markers known as microsatellites, or simple sequence repeats (SSRs), that can be used to characterize the genome, to study possible polymorphisms existing among strains, and to verify the effects of such polymorphic markers in coding regions and regions associated with VFs. In this study, several SSRs were identified within coding regions throughout the 54 genomes of this species, revealing possible polymorphisms associated with coding regions that could be used as strain-specific or serotype-specific identifiers of C. pseudotuberculosis. The similarities associated with SSRs amongst the different serum variants of C. pseudotuberculosis, biovars equi and ovis, were also evaluated, and it was possible to identify SSRs located in coding regions responsible for a VF enrolled in pathogenesis known to mediate bacterial adherence (SpaH-type pili virulence factor). Phylogenetic analyses revealed that strains sharing SSR patterns, including the possible polymorphisms identified in the same position of gene-coding regions, were displayed by strains with a common ancestor, corroborating with the Genome Tree Report of the NCBI. Statistical analysis showed that the microsatellite

Background: Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the issue when compared to marine viruses. The microbiological interactions that occur in these environments are still poorly known, especially between bacteriophages and their host bacteria, as well as between cyanophages and cyanobacteria. Lake Bologna, from Belém, capital of the Brazilian State of Pará, is a source of water that supplies the city and its metropolitan region, yet it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work's main aim is to clarify in terms of taxonomic diversity the species of DNA viruses that are present in this lake, especially bacteriophages and cyanophages, since they can act both as transducers of resistance genes and reporters of water quality for human consumption. Results: For this work, we used the metagenomic sequencing data generated by Alves et al. (2020), and we analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs assembly of viruses. The results observed in this work suggest the existence of a widely diverse viral community and an established microbial phage regulated dynamics in the Lake Bolonha. Conclusions: This work is the first-ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.

No abstract