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Genomics Data

Vasanthakumar Ponesakki, Sayan Paul, Dinesh Kumar Sudalai Mani, Veeraragavan Rajendiran, Paulkumar Kanniah, Sudhakar Sivasubramaniam
In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al...
December 2017: Genomics Data
Lushun Yuan, Liang Chen, Kaiyu Qian, Guofeng Qian, Chin-Lee Wu, Xinghuan Wang, Yu Xiao
Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC ( n  = 97). Six hub genes ( CCNB2 , CDC20 , CEP55 , KIF20A , TOP2A and UBE2C ) were identified in both co-expression and protein-protein interaction (PPI) networks, which were highly correlated with pathologic stage. The significance of expression of the hub genes in ccRCC was ranked top 4 among all cancers and correlated with poor prognosis...
December 2017: Genomics Data
Yong Huang, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun
The Chinese giant salamander ( Andrias davidianus ) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively...
December 2017: Genomics Data
Yue Li, An Zeng, Xiao-Shuan Han, Ge Li, Yong-Qin Li, Bairong Shen, Qing Jing
Small noncoding RNAs play a pivotal role in the regulation of gene expression, and are key regulators of animal development. Freshwater planarian exhibits an extraordinary ability to regenerate any missing body parts, representing an emerging model for studying mechanism underlying stem cell regulation and tissue regeneration. Here, we utilized next-generation sequencing (NGS) to identify small RNAs that are expressed in planarian adult stem cells, and are implicated in tissue regeneration. We profiled microRNAs (miRNAs), piwi-interacting RNA (piRNAs), small rDNA-derived RNAs (srRNAs) and endogenous interfering RNAs ( endo -siRNAs) population from size 18-30 nt, measured the expression of 244 conserved miRNAs, and identified 41 novel miRNAs and 64 novel endo-siRNAs...
December 2017: Genomics Data
Jaeyoung Choi, Gir-Won Lee, Ki-Tae Kim, Jongbum Jeon, Nicolas Détry, Hsiao-Che Kuo, Hui Sun, Fred O Asiegbu, Yong-Hwan Lee
The causal agent of root and butt rot of conifer trees, Heterobasidion annosum , is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of H...
December 2017: Genomics Data
G Tandon, S Singh, S Kaur, Sarika, M A Iquebal, A Rai, D Kumar
Tomato ( Solanum lycopersicum ) is one of the major vegetable plant and a model system for fruit development. Its global importance is due to its lycopene pigment which has anti-oxidative and anti-cancerous properties. Though > 1.5 M biotic stress associated ESTs of tomato are available but cumulative analysis to predict genes is warranted. Availability of whole genome de novo assembly can advantageously be used to map them over different chromosome. Further, available 0.14 M catalogued markers can be used to introgress specific desirable genes in varietal improvement program...
December 2017: Genomics Data
Kuppusamy Sivasankaran, Pratheesh Mathew, Sekar Anand, Stanislaus Antony Ceasar, Soosaimanikam Mariapackiam, Savarimuthu Ignacimuthu
The complete mitochondrial genome of the fruit piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575 bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes ( rrnS and rrnL ), 22 transfer RNA (tRNA) genes and an A + T-rich region (D-loop). The nucleotide composition of the genome is highly A + T biased, accounting for 80.67% of nucleotides...
December 2017: Genomics Data
Balaji Veeraraghavan, Naveen Kumar Devanga Ragupathi, Sridhar Santhanam, Valsan Philip Verghese, Francis Yesurajan Inbanathan, Charles Livingston
Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS) isolates. Molecular data on clonality is lacking for GBS in India. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative genome studies of GBS isolates at global level. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers NHPL00000000 - NHPO00000000...
December 2017: Genomics Data
A Canaguier, J Grimplet, G Di Gaspero, S Scalabrin, E Duchêne, N Choisne, N Mohellibi, C Guichard, S Rombauts, I Le Clainche, A Bérard, A Chauveau, R Bounon, C Rustenholz, M Morgante, M-C Le Paslier, D Brunel, A-F Adam-Blondon
No abstract text is available yet for this article.
December 2017: Genomics Data
Sayak Ganguli, Sabdar Rahaman, Abhishek R Bera, Vineet Vishal, Shelvia Malik, K Roopalakshmi, Pankaj K Singh
This study reports the analyses of the rhizospheric microbiome of the terrestrial mangrove fern Acrostichum aureum Linn. from the Indian Sunderbans. Samples were collected using standard protocols and 16S rRNA gene V3-V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere. A total of 1,931,252 quality checked reads were assembled into 204,818 contigs and were analysed using QIIME to reveal the abundance of Proteobacteria, Acidobacteria and Planctomycetes...
December 2017: Genomics Data
Grant C O'Connell, Paul D Chantler, Taura L Barr
Our group recently employed genome-wide transcriptional profiling in tandem with machine-learning based analysis to identify a ten-gene pattern of differential expression in peripheral blood which may have utility for detection of stroke. The objective of this study was to assess the diagnostic capacity and temporal stability of this stroke-associated transcriptional signature in an independent patient population. Publicly available whole blood microarray data generated from 23 ischemic stroke patients at 3, 5, and 24 h post-symptom onset, as well from 23 cardiovascular disease controls, were obtained via the National Center for Biotechnology Information Gene Expression Omnibus...
December 2017: Genomics Data
Emmanuel Haruna, Noraziah M Zin, Jonathan M Adams
Here we report the draft genome sequence of an endophytic Paenibacillus tyrfis strain isolated from the Universiti Kebangsaan Malaysia reserve forest, Malaysia. The genome size was approximately 8.04 Mb, and the assembly consisted of 107 scaffolds with 168 contigs, and had a G + C content of 53%. Phylogenetic analysis of strain SUK123 using the 16S rRNA gene revealed that it belonged to the family Paenibacillaceae with the highest similarity to Paenibacillus elgii SD(T) (99%). Whole genome comparison of SUK123 with related species using average nucleotide identity (ANI) analysis revealed a similarity of 98% to Paenibacillus tyrfis Mst1(T), 94% to Paenibacillus elgii B69(T), 91% to Paenibacillus ehimensis A2(T), 68% to Paenibacillus polymyxa SC2(T) and 69% to Paenibacillus alvei DMS29(T)...
December 2017: Genomics Data
Rupa Iyer, Brian Iken, Ashish Damania
P. nitroreducens DF05 is a Gram negative, motile, aerobic, rod-shaped and psychrotrophic bacterium that was isolated from contaminated San Jacinto River sediment near River Terrace Park in Channelview, Texas. The draft genome of strain DF05 consists of a total of 192 contigs assembled at the scaffold level totaling 6,487,527 bp and encoding for 5862 functional proteins, 1116 of which are annotated as hypothetical proteins. The bacterial chromosome has a GC content of 65.15% and contains 22 rRNA and 70 tRNA loci...
December 2017: Genomics Data
Hengyou Zhang, Bao-Hua Song
Soybean [Glycine max (L.) Merr.] is an important crop rich in vegetable protein and oil, and is a staple food for human and animals worldwide. However, soybean plants have been challenged by soybean cyst nematode (SCN, Heterodera glycines), one of the most damaging pests found in soybean fields. Applying SCN-resistant cultivars is the most efficient and environmentally friendly strategy to manage SCN. Currently, soybean breeding and further improvement in soybean agriculture are hindered by severely limited genetic diversity in cultivated soybeans...
December 2017: Genomics Data
Gang Gao, Heping Xiong, Kunmei Chen, Jikang Chen, Ping Chen, Chunming Yu, Aiguo Zhu
Ramie (Boehmeria nivea (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems was grown in the soil or in a hydroponic water solution, and cultured in the same environmental conditions. Root samples of terrestrial ramie, and different developmental stages of hydroponic ramie (5 days, 30 days), were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000...
December 2017: Genomics Data
Ranu Sharma, Vimal Rawat, C G Suresh
The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other fabaceae species...
December 2017: Genomics Data
Jill Gaskell, Phil Kersten, Luis F Larrondo, Paulo Canessa, Diego Martinez, David Hibbett, Monika Schmoll, Christian P Kubicek, Angel T Martinez, Jagjit Yadav, Emma Master, Jon Karl Magnuson, Debbie Yaver, Randy Berka, Kathleen Lail, Cindy Chen, Kurt LaButti, Matt Nolan, Anna Lipzen, Andrea Aerts, Robert Riley, Kerrie Barry, Bernard Henrissat, Robert Blanchette, Igor V Grigoriev, Dan Cullen
No abstract text is available yet for this article.
December 2017: Genomics Data
Mingyeong Woo, Sun-Hee Park, Kyounghee Park, Min-Kyu Park, Ji-Yeon Kim, Han-Seung Lee, Jae Hak Sohn, Dong-Woo Lee, Gaewon Nam, Kee-Sun Shin, Sang-Jae Lee
The draft genome sequence of the halophilic bacterium Halobacillus mangrovi KTB 131, isolated from Topan salt of the Jeon-nam in Korea, was established. The genome comprises 4,151,649 bp, with a G + C content of 41.6%. The strain displays a high number of genes responsible for secondary metabolite biosynthesis, transport, and catabolism compared to other Halobacillus bacterial genus members. Numerous genes responsible for various transport systems, solute accumulation, and aromatic/sulfur decomposition were detected...
December 2017: Genomics Data
Apostolos Kalivas, Ioannis Ganopoulos, Fotis Psomopoulos, Ioannis Grigoriadis, Aliki Xanthopoulou, Evangelos Hatzigiannakis, Maslin Osathanunkul, Athanasios Tsaftaris, Panagiotis Madesis
Nutrients in the form of fertilizers and/or other additives such as amino acids, dramatically influence plant development and growth, plant nutrient composition and the level of soil pollution. Moreover, the treatment of soil microbiota is emerging as a new strategy in plant breeding to achieve desirable traits. Thus, integrated study of fertilizer application and soil microbiota might lead to a better understanding of soil-plant interactions and inform the design of novel ways to fertilize plants. Herein we report metagenomics data for soil microbiota in lettuce (Lactuca sativa) treated with fertilizer, amino acids or their combinations as follows: N-fertilizer + Amino16®, Amino16®, N-fertilizer and no treatment control...
December 2017: Genomics Data
Rupa Iyer, Ashish Damania, Brian Iken
The genus Microbacterium is composed of high GC content, Gram-positive bacteria of the phylum Acintobacteria known for their antibiotic production. Microbacterium species commonly colonize agricultural rhizospheres and more infrequently have been found to colonize and infect human tissues as well. Here we report the 3,696,310 bp draft genome (chromosome and plasmids) sequence assembled at the scaffold level from 232 contigs of Microbacterium sp. strain AISO3, isolated from polluted San Jacinto River sediment in Channelview, Texas...
December 2017: Genomics Data
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