Evaluating the diversity of Neotropical anurans using DNA barcodes

This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4–19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11–39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study

High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly

Ramos RTJ, Carneiro AR, de Castro Soares S, et al. High efficiency application of a mate-paired library from next-generation sequencing to postlight sequencing: Corynebacterium pseudotuberculosis as a case study for microbial de novo genome assembly. Journal of microbiological methods. 2013;95(3):441-447.With the advent of high-throughput DNA sequencing platforms, there has been a reduction in the cost and time of sequencing. With these advantages, new challenges have emerged, such as the handling of large amounts of data, quality assessment, and the assembly of short reads. Currently, benchtop high-throughput sequencers enable the genomes of prokaryotic organisms to be sequenced within two hours with a reduction in coverage compared with the SOLiD, Illumina and 454 FLX Titanium platforms, making it necessary to evaluate the efficiency of less expensive benchtop instruments for prokaryotic genomics. In the present work, we evaluate and propose a methodology for the use of the Ion Torrent PGM platform for decoding the gram-positive bacterium Corynebacterium pseudotuberculosis, for which 15 complete genome sequences have already been deposited based on fragment and mate-paired libraries with a 3-kb insert size. Despite the low coverage, a single sequencing run using a mate-paired library generated 39 scaffolds after de novo assembly without data curation. This result is superior to that obtained by sequencing using libraries generated from fragments marketed by the equipment's manufacturer, as well as that observed for mate-pairs sequenced by SOLiD. The generated sequence added an extra 91kb to the genome available at NCBI

High-throughput sequencing of a South American Amerindian.

The emergence of next-generation sequencing technologies allowed access to the vast amounts of information that are contained in the human genome. This information has contributed to the understanding of individual and population-based variability and improved the understanding of the evolutionary history of different human groups. However, the genome of a representative of the Amerindian populations had not been previously sequenced. Thus, the genome of an individual from a South American tribe was completely sequenced to further the understanding of the genetic variability of Amerindians. A total of 36.8 giga base pairs (Gbp) were sequenced and aligned with the human genome. These Gbp corresponded to 95.92% of the human genome with an estimated miscall rate of 0.0035 per sequenced bp. The data obtained from the alignment were used for SNP (single-nucleotide) and INDEL (insertion-deletion) calling, which resulted in the identification of 502,017 polymorphisms, of which 32,275 were potentially new high-confidence SNPs and 33,795 new INDELs, specific of South Native American populations. The authenticity of the sample as a member of the South Native American populations was confirmed through the analysis of the uniparental (maternal and paternal) lineages. The autosomal comparison distinguished the investigated sample from others continental populations and revealed a close relation to the Eastern Asian populations and Aboriginal Australian. Although, the findings did not discard the classical model of America settlement; it brought new insides to the understanding of the human population history. The present study indicates a remarkable genetic variability in human populations that must still be identified and contributes to the understanding of the genetic variability of South Native American populations and of the human populations history

CDH1 mutations in gastric cancer patients from northern Brazil identified by Next- Generation Sequencing (NGS)

Gastric cancer is considered to be the fifth highest incident tumor worldwide and the third leading cause of cancer deaths. Developing regions report a higher number of sporadic cases, but there are only a few local studies related to hereditary cases of gastric cancer in Brazil to confirm this fact. CDH1 germline mutations have been described both in familial and sporadic cases, but there is only one recent molecular description of individuals from Brazil. In this study we performed Next Generation Sequencing (NGS) to assess CDH1 germline mutations in individuals who match the clinical criteria for Hereditary Diffuse Gastric Cancer (HDGC), or who exhibit very early diagnosis of gastric cancer. Among five probands we detected CDH1 germline mutations in two cases (40%). The mutation c.1023T > G was found in a HDGC family and the mutation c.1849G > A, which is nearly exclusive to African populations, was found in an early-onset case of gastric adenocarcinoma. The mutations described highlight the existence of gastric cancer cases caused by CDH1 germline mutations in northern Brazil, although such information is frequently ignored due to the existence of a large number of environmental factors locally. Our report represent the first CDH1 mutations in HDGC described from Brazil by an NGS platform

Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina

In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis PAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium

Complete Genome Sequence of Corynebacterium pseudotuberculosis I19, a Strain Isolated from a Cow in Israel with Bovine Mastitis

Silva A, Schneider MPC, Cerdeira L, et al. Complete Genome Sequence of Corynebacterium pseudotuberculosis I19, a Strain Isolated from a Cow in Israel with Bovine Mastitis. Journal of Bacteriology. 2011;193(1):323-324.This work reports the completion and annotation of the genome sequence of Corynebacterium pseudotuberculosis I19, isolated from an Israeli dairy cow with severe clinical mastitis. To present the whole-genome sequence, a de novo assembly approach using 33 million short (25-bp) mate-paired SOLiD reads only was applied. Furthermore, the automatic, functional, and manual annotations were attained with the use of several algorithms in a multistep process

Genome Sequence of Exiguobacterium antarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica

Exiguobacterium antarcticum is a psychotropic bacterium isolated for the first time from microbial mats of Lake Fryxell in Antarctica. Many organisms of the genus Exiguobacterium are extremophiles and have properties of biotechnological interest, e. g., the capacity to adapt to cold, which make this genus a target for discovering new enzymes, such as lipases and proteases, in addition to improving our understanding of the mechanisms of adaptation and survival at low temperatures. This study presents the genome of E. antarcticum B7, isolated from a biofilm sample of Ginger Lake on King George Island, Antarctic peninsula.National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Cientifico e TecnologicoCNPq)National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico-CNPq)Brazilian Federal Agency for the Support and Evaluation of Graduate Education (Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior-CAPES)Brazilian Federal Agency for the Support and Evaluation of Graduate Education (Coordenacao de Aperfeicoamento de Pessoal de Nivel SuperiorCAPES)Paraense Amazonia Foundation (Fundacao Amazonia ParaenseFAPESPA)Paraense Amazonia Foundation (Fundacao Amazonia Paraense-FAPESPA)Amazon Center of Excellence in Genomics of Microorganisms (Nucleo Amazonico de Excelencia em Genomica de Microorganismos)Centers of Excellence Support Program (Programa de apoio a Nucleo de Excelencia) Pronex/CNPq/FAPESPAAmazon Center of Excellence in Genomics of Microorganisms (Nucleo Amazonico de Excelencia em Genomica de Microorganismos)-Centers of Excellence Support Program (Programa de apoio a Nucleo de Excelencia) Pronex/CNPq/FAPESPANational Program for Academic Cooperation (Programa Nacional de Cooperacao Academica) PROCAD/CAPESNational Program for Academic Cooperation (Programa Nacional de Cooperacao Academica) PROCAD/CAPESStudies and Projects Funding Agency (Financiadora de Estudos e ProjetosFINEP)Studies and Projects Funding Agency (Financiadora de Estudos e Projetos-FINEP)Minas Gerais Research Fund (Fundacao de Amparo a Pesquisa do estado de Minas Gerais-FAPEMIG)Minas Gerais Research Fund (Fundacao de Amparo a Pesquisa do estado de Minas GeraisFAPEMIG

Comparative population-based genetic analysis of the Amerindian with the populations in the HapMap database.

<p>The Amerindian sample (IND) was compared to 20 randomly selected samples from the following populations in the HapMap database: JPT (Japanese in Tokyo, Japan), CHD (Chinese in metropolitan Denver, Colorado, USA), CHB (Han Chinese in Beijing, China), CEU (residents of Utah, Nevada, USA with Northern and Western European ancestry from the CEPH collection), TSI (Tuscans in Italy), GIH (Gujarati Indians in Houston, Texas, USA), YRI (Yoruba in Ibadan, Nigeria), ASW (individuals with African ancestry in Southwest USA), LWK (Luhya in Webuye, Kenya), MKK (Maasai in Kinyawa, Kenya), and MEX (individuals with Mexican ancestry in Los Angeles, California, USA). The populations were clustered according to their geographic origin as follows: East-Asia (JPT, CHB, and CHD), Europe (CEU and TSI), South-West Asia (SWA, formed by the GIH population), Africa (YRI, ASW, LWK, and MKK) and North America (NA, formed by the MEX population). A) Diagram of the genetic contribution of the models for a value of K in the range of four to seven. The x-axis represents the different samples that were clustered according to the population and the geographic area of origin. B) Principal Component Analysis (PCA) of the Amerindian sample (indicated with the arrow) and the samples extracted from the HapMap database. The abscissa represents the 1^st component, and the ordinate represents the 2^nd component. C) Heat map of the FST index between the investigated populations and the Amerindian sample.</p

High-quality polymorphisms identified and not identified in the dbSNP build 135 database.

<p>*These percentages correspond to the column total.</p

Population genetic structure analysis of 1,000 genomes project's, Aboriginal Australian and Native South American genotype dataset.

<p>The diagram of genetic contribution was obtained using Structure software for models of 4 to 6 subpopulations. The populations were grouped labeled as follow, according to their major continental ancestry: IND (Native South American individual, this work); ABO (Aboriginal Australian individual, Rasmussen et al. 2011); Eastern Asian (CHS, CHB and JPT); Europeans (CEU, IBS, TSI, FIN and GBR); African (ASW, LWK, MKK and YRI); and New Americans (CLM, PUR and MXL). The plot represents the rate of contribution from each subpopulation (colors) to the samples (x axis).</p