Metagenomic exploration of microbial community in mine tailings of Malanjkhand copper project, India
This study was designed to understand microbial community composition and potential for acid generation using samples from mine tailings of Malanjkhand copper project (MCP), India through 16S rRNA gene based amplicon sequencing approach (targeting V4 region). Three tailings samples (T1, T2 and T3) with varied physiochemical properties selected for the study revealed distinct microbial assemblages. Sample (T3) with most extreme nature (pH<2.0) harbored Proteobacteria, Actinobacteria, Chloroflexi while the samples (T1 and T3) with slightly moderate nature (pH<4.0 and >3.0) exhibited abundance of Proteoba...
Source: Genomics Data - February 3, 2017 Category: Genetics & Stem Cells Source Type: research
Genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia
Publication date: Available online 28 January 2017 Source:Genomics Data Author(s): Anastasiia Kovaliova, Vitaly V. Kadnikov, Dmitrii V. Antsiferov, Alexey V. Beletsky, Ehrzena V. Danilova, Marat R. Avakyan, Andrey V. Mardanov, Olga V. Karnachuk Here we report the draft genome sequence of the acid-tolerant Desulfovibrio sp. DV isolated from the sediments of a Pb-Zn mine tailings dam in the Chita region, Russia. The draft genome has a size of 4.9Mb and encodes multiple K+-transporters and proton-consuming decarboxylases. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain DV clus...
Source: Genomics Data - January 27, 2017 Category: Genetics & Stem Cells Source Type: research
Dynamic transcriptome landscape of sesame (Sesamum indicum L.) under progressive drought and after rewatering
Publication date: Available online 27 January 2017 Source:Genomics Data Author(s): Komivi Dossa, Donghua Li, Linhai Wang, Xiaomin Zheng, Jingyin Yu, Xin Wei, Daniel Fonceka, Diaga Diouf, Liao Boshou, Ndiaga Cisse, Xiurong Zhang Drought is one of the most important abiotic stresses that impair sesame (Sesamum indicum L.) productivity mainly when it occurs at flowering stage. However up to now, very few studies have attempted to investigate the molecular responses of sesame to drought stress. In this experiment, two genotypes having contrasting responses to drought (tolerant and sensitive) were submitted to prog...
Source: Genomics Data - January 26, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of Sugiyamaella xylanicola UFMG-CM-Y1884T, a xylan-degrading yeast species isolated from rotting wood samples in Brazil
We present the draft genome sequence of the type strain of the yeast Sugiyamaella xylanicola UFMG-CM-Y1884T (=UFMG-CA-32.1T =CBS 12683T), a xylan-degrading species capable of fermenting d-xylose to ethanol. The assembled genome has a size of ~13.7Mb and a GC content of 33.8% and contains 5971 protein-coding genes. We identified 15 genes with significant similarity to the d-xylose reductase gene from several other fungal species. The draft genome assembled from whole-genome shotgun sequencing of the yeast Sugiyamaella xylanicola UFMG-CM-Y1884T (=UFMG-CA-32.1T =CBS 12683T) has been deposited at DDBJ/ENA/GenBank under the acc...
Source: Genomics Data - January 26, 2017 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of heavy metal tolerant Silene dioica
Publication date: Available online 26 January 2017 Source:Genomics Data Author(s): Radim Cegan, Vojtech Hudzieczek, Roman Hobza Silene dioica is a dioecious plant of the family Caryophyllaceae. In the present study, we used Illumina sequencing technology (MiSeq) to sequence, de novo assembly and annotate the transcriptomes of male and female copper tolerant S. dioica individuals. We sequenced the normalized mRNA of roots, shoots, flower buds and flowers for each sex. Raw reads of the transcriptome assembly project for S. dioica male and female individual have been deposited in NCBI's Sequence Read Archive (SRA) databa...
Source: Genomics Data - January 25, 2017 Category: Genetics & Stem Cells Source Type: research
Genome sequence of Ochrobactrum anthropi strain SUBG007, a plant pathogen and potential xenobiotic compounds degradation bacterium
Publication date: Available online 4 January 2017 Source:Genomics Data Author(s): Kiran S. Chudasama, Vrinda S. Thaker Ochrobactrum anthropi SUBG007 was isolated from the fruit of Prunus dulcis in Rajkot (22.30°N, 70.78°E), Gujarat, India. Here we present the 4.37Mb genome sequence strain SUBG007, which may provide the genetic information for the application in environment pollution degradation and agriculture field. The strain also posses many genes cluster which involved in production of important secondary metabolites. The nucleotide sequence of this genome was deposited into NCBI GenBank under the accession LUAY0...
Source: Genomics Data - January 4, 2017 Category: Genetics & Stem Cells Source Type: research
Molecular characterization of endophytic fungi associated with the roots of Chenopodium quinoa inhabiting the Atacama Desert, Chile
This study focused on the Identification of the fungal endophytic community associated with the roots of quinoa plants (Chenopodium quinoa) growing near the salt lakes of the Atacama Desert, Chile. One hundred endophytic fungi were isolated from healthy quinoa roots, and the internal transcribed spacer (ITS) region was sequenced for phylogenetic and taxonomic analysis. The isolates were classified into eleven genera and 21 distinct operational taxonomic units (OTUs). Despite a relatively high diversity of root endophytic fungi associated with quinoa plants, the fungal community was dominated by only the Ascomycota phyla. I...
Source: Genomics Data - January 4, 2017 Category: Genetics & Stem Cells Source Type: research
Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom)
Publication date: Available online 31 December 2016 Source:Genomics Data Author(s): F. Nadiya, N. Anjali, Jinu Thomas, A. Gangaprasad, K.K. Sabu Elettaria cardamomum (L.) Maton, known as ‘queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,9...
Source: Genomics Data - December 31, 2016 Category: Genetics & Stem Cells Source Type: research
Genome sequence of the copper resistant and acid-tolerant Desulfosporosinus sp. BG isolated from the tailings of a molybdenum-tungsten mine in the Transbaikal area
Publication date: Available online 29 December 2016 Source:Genomics Data Author(s): Olga V. Karnachuk, Vitalii V. Kadnikov, Inna A. Panova, Andrey V. Mardanov, Alexey V. Beletsky, Erzhena V. Danilova, Marat R. Avakyan, Nikolai V. Ravin Here, we report on the draft genome of a copper-resistant and acidophilic Desulfosporosinus sp. BG, isolated from the tailings of a molybdenum-tungsten mine in Transbaikal area. The draft genome has a size of 4.52Mb and encodes transporters of heavy metals. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain BG clusters together with the other ac...
Source: Genomics Data - December 29, 2016 Category: Genetics & Stem Cells Source Type: research
Genome sequencing and annotation of Geobacillus sp. 1017, a hydrocarbon-oxidizing thermophilic bacterium isolated from a heavy oil reservoir (China)
Publication date: Available online 29 December 2016 Source:Genomics Data Author(s): Vitaly V. Kadnikov, Andrey V. Mardanov, Andrey B. Poltaraus, Diyana S. Sokolova, Ekaterina M. Semenova, Nikolay V. Ravin, Tatiyana P. Tourova, Tamara N. Nazina The draft genome sequence of Geobacillus sp. strain 1017, a thermophilic aerobic oil-oxidizing bacterium isolated from formation water of the Dagang high-temperature oilfield, China, is presented here. The genome comprised 3.6Mbp, with the G+C content of 51.74%. The strain had a number of genes responsible for numerous metabolic and transport systems, exopolysaccharide bios...
Source: Genomics Data - December 29, 2016 Category: Genetics & Stem Cells Source Type: research
Complete genome sequence of Luteibacter rhizovicinus strain LJ96T, isolated from the rhizosphere of barley (Hordeum vulgare L.) in Denmark
We present the complete genome sequence of Luteibacter rhizovicinus type strain LJ96T, a yellow-pigmented gammaproteobacterium isolated from the rhizosphere of barley (Hordeum vulgare) [1], a species with numerous potential applications. The genome sequence was deposited to NCBI GenBank with the accession number CP017480. (Source: Genomics Data)
Source: Genomics Data - December 27, 2016 Category: Genetics & Stem Cells Source Type: research
Unraveling the microbial and functional diversity of Coamo thermal spring in Puerto Rico using metagenomic library generation and shotgun sequencing
Publication date: Available online 23 December 2016 Source:Genomics Data Author(s): Ricky Padilla-Del Valle, Carlos Rios-Velazquez In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo have never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Esch...
Source: Genomics Data - December 23, 2016 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly of shrimp Palaemon serratus
In this study, we used Illumina sequencing technology (HiSeq 2000) to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The tr...
Source: Genomics Data - December 22, 2016 Category: Genetics & Stem Cells Source Type: research
Topoisomerase I inhibition leads to length-dependent gene expression changes in human primary astrocytes
Publication date: Available online 23 December 2016 Source:Genomics Data Author(s): Akira Gokoolparsadh, Zhiming Fang, Nady Braidy, Irina Voineagu Topoisomerase I is required for the proper expression of long genes (>100 kb) in mouse and human cortical neurons, including many candidate genes for autism spectrum disorder (ASD) [1]. Given the important role of astrocytes in brain development [2], we investigated whether long genes, including autism susceptibility genes, also require topoisomerase I expression in human primary astrocytes. We carried genome-wide expression profiling of cultured human primary astro...
Source: Genomics Data - December 22, 2016 Category: Genetics & Stem Cells Source Type: research
Draft genome of the strain RCAM1026 Rhizobium leguminosarum bv. viciae
Publication date: March 2017 Source:Genomics Data, Volume 11 Author(s): Alexey Afonin, Anton Sulima, Aleksandr Zhernakov, Vladimir Zhukov Rhizobium leguminosarum bv. viciae RCAM1026 is a strain first isolated in 1964 from nodules of “Ramensky 77” cultivar of garden pea (Pisum sativum L.) now routinely used as a model strain in inoculation experiments on pea. Assembly with SPAdes yielded 133 contigs longer then 200bp (N50=202,321, GC%=60.84). Resulting annotated genome is 7,248,686 bp encoding 6792 genes. (Source: Genomics Data)
Source: Genomics Data - December 22, 2016 Category: Genetics & Stem Cells Source Type: research
