Draft genome of Thermomonospora sp. CIT 1 (Thermomonosporaceae) and in silico evidence of its functional role in filter cake biomass deconstruction
Abstract The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome ...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant
We report on the nearly complete genome sequence of Clostridium beijerinckii strain Br21, formerly isolated from a sugarcarne vinasse wastewater treatment plant. The resulting genome is ca. 5.9 Mbp in length and resembles the size of previously published C. beijerinckii genomes. We annotated the genome sequence and predicted a total of 5323 genes. Strain Br21 has a genetic toolkit that allows it to exploit diverse sugars that are often found after lignocellulosic biomass pretreatment to yield products of commercial interest. Besides the whole set of genes encoding for enzymes underlying hydrogen production, the genome of t...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
The complete chloroplast genome sequences of three Spondias species reveal close relationship among the species
This study reports the complete chloroplast sequences of three Spondias species. The genome sequences were obtained for Spondias tuberosa, Spondias bahienses, and Spondias mombin using the Illumina sequencing technology by a combination of de novo methods and a reference-guided assembly using Sapindus mukorossi as reference. The genomes of S. tuberosa, S. bahiensis, and S. mombin had 162,036, 162,218, and 162,302 bp, respectively. The coding regions exhibited 130 genes, including 34 – 35 tRNAs and 4 rRNAs. The results revealed synteny among the genomes, with high conservation in the gene order and content and CG content....
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
A re-annotation of the Anopheles darlingi mobilome
Abstract The mobilome, portion of the genome composed of transposable elements (TEs), of Anopheles darlingi was described together with the genome of this species. Here, this mobilome was revised using similarity and de novo search approaches. A total of 5.6% of the A. darlingi genome is derived of TEs. Class I gypsy and copia were the most abundant superfamilies, corresponding to 22.36% of the mobilome. Non-LTR elements of the R1 and Jockey superfamilies account for 11% of the TEs. Among Class II TEs, the mariner superfamily is the most abundant (16.01%). Approximately 87% of the A. darlingi mobilome consist of short, tru...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Science and evolution
Abstract Evolution is both a fact and a theory. Evolution is widely observable in laboratory and natural populations as they change over time. The fact that we need annual flu vaccines is one example of observable evolution. At the same time, evolutionary theory explains more than observations, as the succession on the fossil record. Hence, evolution is also the scientific theory that embodies biology, including all organisms and their characteristics. In this paper, we emphasize why evolution is the most important theory in biology. Evolution explains every biological detail, similar to how history explains many aspects o...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Genetic diversity and population structure of naturally rare Calibrachoa species with small distribution in southern Brazil
Abstract Calibrachoa is a South-American genus comprising 27 species, several considered endemic or rare; few were subjects in genetic studies. We attempted to generate new data about the phylogenetically related and rare species C. eglandulata, C. sendtneriana, C. serrulata, and C. spathulata concerning their genetic diversity and population structure, which, coupled with their known restricted distribution, could help access their conservation status and contribute to the study of the Brazilian biodiversity. We sequenced 88 individuals for plastid intergenic spacers and genotyped 186 individuals for five microsatellite l...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
In silico characterization of microRNAs-like sequences in the genome of Paracoccidioides brasiliensis
Abstract Eukaryotic cells have different mechanisms of post-transcriptional regulation. Among these mechanisms, microRNAs promote regulation of targets by cleavage or degradation of the mRNA. Fungi of the Paracoccidioides complex are the etiological agents of the main systemic mycosis of Latin America. These fungi present a plasticity to adapt and survive in different conditions, and the presence of microRNAs-like molecules could be part of the mechanisms that provide such plasticity. MicroRNAs produced by the host influence the progression of this mycosis in the lungs besides regulating targets involved in apoptosis in ma...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Cross-genera SSR transferability in cacti revealed by a case study using Cereus (Cereeae, Cactaceae)
Abstract The study of transferability of simple sequence repeats (SSR) among closely related species is a well-known strategy in population genetics, however transferability among distinct genera is less common. We tested cross-genera SSR amplification in the family Cactaceae using a total of 20 heterologous primers previously developed for the genera Ariocarpus, Echinocactus, Polaskia and Pilosocereus, in four taxa of the genus Cereus: C. fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, C. jamacaru and C. insularis. Nine microsatellite loci were amplified in Cereus resulting in 35.2% of success in...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Overexpression of salt-induced protein (salT) delays leaf senescence in rice
Abstract Senescence, a highly programmed process, largely determines yield and quality of crops. However, knowledge about the onset and progression of leaf senescence in crop plants is still limited. Here, we report that salt-induced protein (salT), a new gene, may be involved in leaf senescence. Overexpressing salT could prolong the duration of leaves with higher concentrations of chlorophyll compared with the wild type. Moreover, overexpression of salT could delay the senescence of rice leaves though the inhibition of senescence associated genes (SAGs). Overall, the characterization of salT suggested that it is a new gen...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Development and characterization of 20 polymorphic microsatellite markers for Epinephelus marginatus (Lowe, 1834) (Perciformes: Epinephelidae) using 454 pyrosequencing
This study provides the first set of species-specific microsatellite loci for E. marginatus that can be applied when assessing both intra- and interpopulation genetic variation. Twenty microsatellite loci were isolated and characterized for the dusky grouper by genotyping 20 individuals obtained from the North Eastern Atlantic Ocean (n = 4) and from the South Western Atlantic Ocean (n = 16). The number of alleles per locus varied from 2 to 11, while the observed and expected heterozygosities ranged from 0.25 to 0.94 and 0.34 to 0.89, respectively. The polymorphic information content varied from moderately to highly informa...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
In silico identification and characterization of novel microsatellite loci for the Blue-and-yellow Macaw Ara ararauna (Linnaeus, 1758) (Psittaciformes, Psittacidae)
This study aimed to identify and characterize novel microsatellite loci for population and parentage analysis of A. ararauna. Scaffold sequences of Ara macao available in the NCBI database were used for microsatellite searches using MsatCommander software. We tested a total of 28 loci, from which 25 were polymorphic, one was monomorphic, and two did not generated amplification products. For polymorphic loci, the mean number of alleles was 8.24 (4 – 15 alleles per locus), the observed heterozygosity ranged from 0.333 to 0.917, and the expected heterozygosity from 0.353 to 0.890. The paternity exclusion probability and id...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Polymorphism of Sooty-fronted Spinetail (Synallaxis frontalis Aves: Furnariidae): Evidence of chromosomal rearrangements by pericentric inversion in autosomal macrochromosomes
Abstract The Passeriformes is the most diverse and cytogenetically well-known clade of birds, comprising approximately 5,000 species. The sooty-fronted spinetail (Synallaxis frontalis Aves: Furnariidae) species, which belongs to the order Passeriformes, is typically found in South America, where it is widely distributed. Polymorphisms provide genetic variability, important for several evolutionary processes, including speciation and adaptation to the environment. The aim of this work was to analyze the possible cytotypes and systemic events involved in the species polymorphism. Of the sampled 19 individuals, two thirds wer...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Linkage disequilibrium and past effective population size in native Tunisian cattle
Abstract To carry out effective genome-wide association studies, information about linkage disequilibrium (LD) is essential. Here, we used medium-density SNP chips to provide estimates of LD in native Tunisian cattle. The two measures of LD that were used, mean r2 and D ’ , decreased from 0.26 to 0.05 and from 0.73 to 0.40, respectively, when the distance between markers increased from less than 20 Kb to 200 Kb. The decay in LD over physical distance occurred at a faster rate than that reported for European and other indigenous breeds, and reached background levels at less than 500 Kb distance. This is consistent with th...
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
GJB2 c.235delC variant associated with autosomal recessive nonsyndromic hearing loss and auditory neuropathy spectrum disorder
This study shows that the association of homozygosity of the GJB2 c.235delC variant with ARNSHL and ANSD in a patient. (Source: Genetics and Molecular Biology)
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
Increased expression levels of Syntaxin 1A and Synaptobrevin 2/Vesicle-Associated Membrane Protein-2 are associated with the progression of bladder cancer
In this study, we analyzed the relative expression of the STX1A and VAMP2 (SYB2) for their possible association in the progression and metastasis of bladder cancer. The profiling of the genes showed a significant increase in STX1A and VAMP2 expression (p< 0.001) in high-grade tumor cells compared to normal and low-grade tumors. These findings suggest that elevated expression of STX1A and VAMP2 might have caused the abnormal progression and invasion of cancer cells leading to the transformation of cells into high-grade tumor in bladder cancer. (Source: Genetics and Molecular Biology)
Source: Genetics and Molecular Biology - March 19, 2019 Category: Genetics & Stem Cells Source Type: research
