Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021.

Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia, and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1,534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

Correction: Ten simple rules for organizing a bioinformatics training course in low- and middle-income countries.

[This corrects the article DOI: 10.1371/journal.pcbi.1009218.].

Colombia, an unknown genetic diversity in the era of Big Data.

BACKGROUND: Latin America harbors some of the most biodiverse countries in the world, including Colombia. Despite the increasing use of cutting-edge technologies in genomics and bioinformatics in several biological science fields around the world, the region has fallen behind in the inclusion of these approaches in biodiversity studies. In this study, we used data mining methods to search in four main public databases of genetic sequences such as: NCBI Nucleotide and BioProject, Pathosystems Resource Integration Center, and Barcode of Life Data Systems databases. We aimed to determine how much of the Colombian biodiversity is contained in genetic data stored in these public databases and how much of this information has been generated by national institutions. Additionally, we compared this data for Colombia with other countries of high biodiversity in Latin America, such as Brazil, Argentina, Costa Rica, Mexico, and Peru. RESULTS: In Nucleotide, we found that 66.84% of total records for Colombia have been published at the national level, and this data represents less than 5% of the total number of species reported for the country. In BioProject, 70.46% of records were generated by national institutions and the great majority of them is represented by microorganisms. In BOLD Systems, 26% of records have been submitted by national institutions, representing 258 species for Colombia. This number of species reported for Colombia span approximately 0.46% of the total biodiversity reported for the country (56,343 species). Finally, in PATRIC database, 13.25% of the reported sequences were contributed by national institutions. Colombia has a better biodiversity representation in public databases in comparison to other Latin American countries, like Costa Rica and Peru. Mexico and Argentina have the highest representation of species at the national level, despite Brazil and Colombia, which actually hold the first and second places in biodiversity worldwide. CONCLUSIONS: Our findings show gaps in the representation of the Colombian biodiversity at the molecular and genetic levels in widely consulted public databases. National funding for high-throughput molecular research, NGS technologies costs, and access to genetic resources are limiting factors. This fact should be taken as an opportunity to foster the development of collaborative projects between research groups in the Latin American region to study the vast biodiversity of these countries using 'omics' technologies.

The differential expression of Chironomus spp genes as useful tools in the search for pollution biomarkers in freshwater ecosystems.

Insects of the Chironomidae family are characterized by a wide ecological diversity in freshwater ecosystems. The larvae have the physiological potential to tolerate environmental stress even when there is a low concentration of oxygen, the presence of toxic substances or when there are changes in temperature and salinity. On the other hand, it is important to consider that at a cellular level, when individual insects are exposed to environmental changes, it induces responses of groups of genes that govern the molecular mechanisms related to such tolerance. In this review, using fourth instar larvae of Chironomus spp. in natural conditions and of Chironomus columbiensis under controlled conditions, we will discuss the genetic expression of a group of genes that respond to detoxification and also the biological functions involved and impacted on by mining stressors. The study of macroinvertebrate bioindicator species and their gene expression as a result of mining activity opens a window on the search for genetic biomarkers that could be used in environmental pollution assessments in freshwater ecosystems.

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.

Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.

Transcriptome analysis of the entomopathogenic fungus Beauveria bassiana grown on cuticular extracts of the coffee berry borer (Hypothenemus hampei).

The coffee berry borer (CBB; Hypothenemus hampei) is a major pest of coffee responsible for significant crop losses worldwide. The entomopathogenic fungus Beauveria bassiana represents a natural means of controlling this insect pest; however, little is known concerning the molecular determinants that contribute to the virulence of the fungus towards the CBB. In order to examine genes involved in insect virulence, two expressed sequence tag (EST) libraries, representing germinating conidia and growing hyphae/mycelia of B. bassiana cells grown on cuticular extracts of the CBB were constructed and analysed. In total, 4186 cDNA transcripts were obtained, which included 2141 from the cuticle-germinated conidia and 2045 from the cuticle-grown mycelium libraries, respectively. The average sequence length obtained was 470 bp and transcript assembly resulted in a set of 1271 and 1305 unique gene sequences for the conidial and mycelia libraries, respectively. Around 50 % of the sequences in each library could be annotated by gene ontology terms. An analysis of the two generated libraries as well as a previously reported EST library of B. bassiana grown on chitin was performed. Between the cuticle-germinated conidia and the cuticle-grown mycelia libraries, 322 unique gene sequences were shared, of which 90 % could be annotated, leaving 949 unique cuticle-germinated conidial genes and 983 unique growing hyphae/mycelia genes of which around 65 % were annotated. ESTs shared between the libraries indicated a basic response pattern for B. bassiana against H. hampei, which included genes implicated in pathogenicity. The expression profiles of four genes were evaluated with a cyclophilin, an alkaline-like serine protease and a mitogen-activated protein kinase (MAPK), showing elevated expression during initial phases of infection, i.e. conidia germinating on insect extracts. These data provide clues and gene candidates for further exploration concerning the biology and molecular mechanisms of entomopathogenicity by this fungus.

Necesidad de un centro nacional de bioinformática y biología computacional para Colombia / The need for a Colombian bioinformatics and computational biology centre

Los principales y más revolucionarios avances de la biología en este siglo se han derivado de la información proveniente de genomas completos de diferentes organismos. Los descubrimientos que se derivan de la genómica están generando un nuevo paradigma en la biología, sustituyendo la era de la biología centrada en los genes por aquella centrada en los genomas. Este nuevo concepto es base para desarrollos de gran potencial e impacto social en diferentes áreas como la medicina, la agricultura y la industria. El éxito en el desarrollo de métodos de última generación para la secuenciación de genomas, la proteómica y todas las “omicas”, ha contribuido al surgimiento de nuevas posibilidades para el análisis de la enorme cantidad de datos que se están generando mediante el uso de herramientas computacionales, dando origen a una nueva rama de estudio conocida como bioinformática o biología computacional.Este trabajo hace una revisión general del desarrollo de la bioinformática y la biología computacional en Colombia. Inicialmente, a modo de comparación, describimos el desarrollo de esta ciencia en otros países latinoamericanos que son reconocidos en el área. Finalmente, se discuten los principales aspectos que van a jugar un papel importante en el futuro de esta ciencia en nuestro país, y que además justifican la necesidad de crear un centro nacional de bioinformática y biología computacional.

The main, most revolutionary advances in biology during this century have arisen from information being provided from revealing different organisms’ complete genomes. The discoveries deriving from genomics are leading to a new paradigm in biology, the era of gene-centred biology being substituted for that centred on genomes. Such new concepts represent the basis for developments with great potential and social impact in different areas such as medicine, agriculture and industry. The successful development of latestgeneration methods for genome sequencing, proteomics and all the other “-omics” has contributed towards an enormous amount of genetic data being produced that needs to be analyzed using computational tools. This has led to the development of a new area called bioinformatics or computational biology.The present work gives a general overview of the development of bioinformatics and computational biology in Colombia. The justification for the establishment of a National ioinformatics and computational biology centre is discussed, as well as some aspects that will be crucial for developing this science in Colombia.