Search

Argania spinosa is one of the most important endemic species in Morocco and the only representative of the tropical family of Sapotaceae. It provides great ecological, pharmaceutical, and socioeconomic benefits for a dense human population in an arid zone located in the mid-western part of Morocco. This multipurpose species is experiencing degradation at an alarming rate; hence studying its genetic diversity is a must to save this national heritage. As part of this strategy, the complete mitochondrial (mt) genome of A. spinosa was sequenced, assembled, annotated, and compared to those of other Ericales members. The assembly generated a mitochondrial genome with a size of 707,441 bp and a GC% of 43.7%. The annotation predicted the presence of 34 genes

Verbascum thapsus is a biennial plant native to Europe, northern Africa, and Asia and introduced in the Americas and Australia. We present the whole genome sequence of this species. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR18183247) and assembled genome (JAOXOC000000000).

Chrysina resplendens is a scarab beetle endemic to Central America. We present the whole genome sequence of this species. Illumina sequencing was performed on a genetic sample from a single captive individual. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR5170512) and Assembly (JAADJY000000000).

Allotetraploid cotton ( Gossypium ) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD) 6 , Ge ] and Gossypium stephensii [(AD) 7 , Gs ], and one early form of domesticated Gossypium hirsutum , race punctatum [(AD) 1 , Ghp ]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs , Ge , and domesticated G. hirsutum . We describe genomic structural variation that arose during Gossypium evolution and describe its correlates—including phenotypic differentiation, genetic isolation, and genetic convergence—that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.

COVID-19 is a pandemic infection of the respiratory system caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral ribonucleic acid (RNA) was found in many parts of the COVID-19 patients including the stool, suggesting a potential interaction with the host’s gut microbiome. The gut microbiome also plays major roles in immunity and inflammation. It also impacts pulmonary functions through the gut-lung axis. There have been recent reports of the importance of the host microbiome in infection and pathogenicity. The understanding of the gut and lung microbiomes would open the gate to new therapeutic approaches.

Background: The Argane tree (Argania spinosa L. Skeels) is an endemic tree of southwestern Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.2 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3% of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological purposes., This work was supported by the Iridian Genome Foundation (MD, USA). H.G. is supported by a Grant from the NIH (MD, USA) for H3ABioNet/H3Africa (grant numbers U41HG006941 and U24 HG006941). O.B. and B.C. are Fulbright JSD (USA) grant recipients. This work also benefited from support of Midterm Research Program of INRA-Morocco through the use of its bioinformatics platform.

Trabajo presentado en el VII Workshop Probióticos, Prebióticos y Salud: Evidencia Científica, celebrado en Sevilla (España) el 28 y 29 de enero de 2016, El cáncer colorectal (CCR) es el tercero más común en el mundo y la segunda causa de muerte por cáncer en Estados Unidos (EU) y España. En los últimos años se han llevado a cabo diversos estudios del microbioma intestinal en esta patología, en la mayor parte de los casos con muestras de heces. Se ha observado alteraciones en la microbiota o disbiosis asociada al CRC y se ha propuesto un modelo microbiano para el desarrollo de inflamación crónica en la que estaría involucrada la microbiota intestinal. En este trabajo se presenta la comparación del microbioma, (composición microbiana y función inferida) determinado mediante secuenciación masiva y análisis bioinformático de amplicones del ARNr 16S, de tejido intestinal (sano y tumoral) obtenido durante recesiones de colon en pacientes con CRC en EU y España. En cuanto a la comparación entre tejido tumoral y adyacente se observaron diferencias significativas en la diversidad bacteriana para los individuos de un mismo país, con una menor riqueza de especies en los tumores. La comparación entre ambos tipos de tejido en cada cohorte identificó posibles patógenos, como Eikenella, sobrerrepresentados en los tumores de EU, mientras que Fusobacterium, y Campylobacter fueron significativamente más relevantes en los tumores españoles. La predicción funcional reveló perfiles funcionales parecidos pero con rutas metabólicas y enzimas diferencialmente representados en los tejidos tumorales. En general los datos mostraron diferencias composicionales entre ambas cohortes de estudio que deben de tenerse en cuenta previamente a abordar cualquier estudio del microbioma de CRC.

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.

Runs summary with detailed cluster configuration, mean size, coverage, splitting strategy (chr: chromosome, RG: read-group), total runtime, total cost, average runtime and average cost. (PDF 61Â kb)

Comparison with previous benchmarks for specific 1000Â g exomes/genomes. (PDF 26Â kb)

Input datasets per run. (PDF 215Â kb)

Trabajo presentado en el 5th International Human Microbiome Congress, IHMC, celebrado en Luxemburgo del 31 de marzo al 2 de abril de 2015, Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer deaths in the US and Spain. The molecular mechanisms involved in the etiology of CRC are not yet elucidated due in part to the complexity of the human gut microbiota. In this study, we compared the microbiome composition of 102 tumor and matching adjacent normal tissue (normal) from cohorts from the US and Spain by 16S rRNA amplicon sequencing in order to determine the impact of the geographic origin on the CRC microbiome. Data showed a significantly (P < 0.05) higher Phylogenetic Diversity (PD) for the US (PD Normal = 26.3 ± 5.3, PD Tumor = 23.3 ± 6.2) compared to the Spanish cohort (PD Normal = 18.9 ± 5.9, PD Tumor = 18.7 ± 6.6) while no significant differences in bacterial diversity were observed between tumor and normal tissues for individuals from the same country. Normal tissues from the Spanish cohort were enriched in Firmicutes (43.9% and 22.2%, P = 0.0001) and Actinobacteria (1.6% and 0.5%, P = 0.0018) compared to US normal tissues, while normal tissues from the US had significantly higher abundances of Fusobacteria (8.1% and 1.5%, P = 0.0023) and Sinergistetes (0.3% and 0.1%, P = 0.0097). Comparison of tumor and normal tissues in each cohort identified the genus Eikenella significantly over represented in US tumors (0.024% and 0%, P = 0.03), and the genera Fusobacterium (10.4% and 1.5%, P = < 0.0001), Bulleida (0.36% and 0.09%, P = 0.02), Gemella (1.46% and 0.19%, P = 0.03), Parvimonas (3.14% and 0.86%, P = 0.03), Campylobacter (0.15% and 0.008%, P = 0.047), and Streptococcus (2.84% and 2.19%, P = 0.05) significantly over represented in Spanish tumors. Our study suggests that microbiome compositional dissimilarities by geographic location should be taken in consideration when approaching CRC therapeutic options.

Comparison with existing implementations of the GATK best practices, features. (PDF 19Â kb)

FastQC quality control table. (PDF 302Â kb)