Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea)
Publication date: December 2017 Source:Genomics Data, Volume 14 Author(s): 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 elucidate...
Source: Genomics Data - August 17, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12
Publication date: Available online 10 August 2017 Source:Genomics Data Author(s): 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 (Source: Genomics Data)
Source: Genomics Data - August 11, 2017 Category: Genetics & Stem Cells Source Type: research
RNA-seq data comparisons of wild soybean genotypes in response to soybean cyst nematode (Heterodera glycines)
In this study, transcriptomes of the resistant and susceptible genotypes of the wild soybean, Glycine soja Sieb & Zucc, were sequenced to examine the genetic basis of SCN resistance. Seedling roots were treated with infective second-stage juveniles (J2s) of the soybean cyst nematode (HG type 2.5.7) for 3, 5, 8days and pooled for library construction and RNA sequencing. The transcriptome sequencing generated approximately 245 million (M) high quality (Q>30) raw sequence reads (125bp in length) for twelve libraries. The raw sequence reads were deposited in NCBI sequence read archive (SRA) database, with the ac...
Source: Genomics Data - August 10, 2017 Category: Genetics & Stem Cells Source Type: research
Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16 ® application in lettuce
Publication date: Available online 2 August 2017 Source:Genomics Data Author(s): 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 ...
Source: Genomics Data - August 2, 2017 Category: Genetics & Stem Cells Source Type: research
Whole genome of Klebsiella aerogenes PX01 isolated from San Jacinto River sediment west of Baytown, Texas reveals the presence of multiple antibiotic resistance determinants and mobile genetic elements
Publication date: Available online 23 July 2017 Source:Genomics Data Author(s): Rupa Iyer, Brian Iken, Ashish Damania Klebsiella aerogenes is a Gram-negative bacterium of the family Enterobacteriaceae which is widely distributed in water, air and soil. It also forms part of the normal microbiota found in human and animal gastrointestinal tracts. Here we report the draft genome sequence (chromosome and 1 plasmid) of K. aerogenes strain PX01 compiled at the scaffold level from 97 contigs totaling 5,262,952bp. K. aerogenes PX01 was isolated from sediment along the northern face of Burnet Bay west of Baytown, Texas. The n...
Source: Genomics Data - July 24, 2017 Category: Genetics & Stem Cells Source Type: research
Draft genome sequence of the halophilic Halobacillus mangrovi KTB 131 isolated from Topan salt of the Jeon-nam in Korea
Publication date: Available online 23 July 2017 Source:Genomics Data Author(s): 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 4,151,649bp, 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 ...
Source: Genomics Data - July 24, 2017 Category: Genetics & Stem Cells Source Type: research
Whole genome sequencing of Microbacterium sp. AISO3 from polluted San Jacinto River sediment reveals high bacterial mobility, metabolic versatility and heavy metal resistance
Publication date: Available online 20 July 2017 Source:Genomics Data Author(s): 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 3,696,310bp 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 sed...
Source: Genomics Data - July 20, 2017 Category: Genetics & Stem Cells Source Type: research
RNA-seq data from different developmental stages of Rafflesia cantleyi floral buds
Publication date: Available online 18 July 2017 Source:Genomics Data Author(s): Safoora Amini, Halimah Alias, Mohd Afiq Aizat-Juhari, Mohd-Noor Mat-Isa, Jumaat Haji Adam, Hoe-Han Goh, Kiew-Lian Wan Rafflesia cantleyi, known as one of the world's largest flowers, is a specialised holoparasite due to dramatic morphological modifications. It possesses highly reduced vegetative structure and only appears as a flower for sexual reproduction. Moreover, it has an unusual life cycle in that its floral bud development takes up to nine months. In order to fully understand the highly modified floral organ structure and long ...
Source: Genomics Data - July 19, 2017 Category: Genetics & Stem Cells Source Type: research
A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts
Publication date: Available online 8 July 2017 Source:Genomics Data Author(s): Fanchang Zeng, Xin Lian, Guirong Zhang, Xiaoman Yu, Carl A. Bradley, Ray Ming Fungi are the causal agents of many of the world's most serious plant diseases causing disastrous consequences for large-scale agricultural production. Pathogenicity genomic basis is complex in fungi as multicellular eukaryotic pathogens. Here, we report the genome sequence of C. sojina, and comparative genome analysis with plant pathogen members of the genus Mycosphaerella (Zymoseptoria. tritici (synonyms M. graminicola), M. pini, M. populorum and M. fijiensis...
Source: Genomics Data - July 9, 2017 Category: Genetics & Stem Cells Source Type: research
Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F2 Duroc ×Pietrain pig resource population
Publication date: Available online 5 July 2017 Source:Genomics Data Author(s): Kaitlyn R. Daza, Juan P. Steibel, Deborah Velez-Irizarry, Nancy E. Raney, Ronald O. Bates, Catherine W. Ernst To elucidate the effects of microRNA (miRNA) regulation in skeletal muscle of adult pigs, miRNA expression profiling was performed with RNA extracted from longissimus dorsi (LD) muscle samples from 174 F2 pigs (~5.5months of age) from a Duroc×Pietrain resource population. Total RNA was extracted from LD samples, and libraries were sequenced on an Illumina HiSeq 2500 platform in 1×50bp format. After processing, 232,826,977 total...
Source: Genomics Data - July 6, 2017 Category: Genetics & Stem Cells Source Type: research
Cultivar-specific transcriptome prediction and annotation in Ficus carica L.
Publication date: Available online 5 July 2017 Source:Genomics Data Author(s): Liceth Solorzano Zambrano, Gabriele Usai, Alberto Vangelisti, Flavia Mascagni, Tommaso Giordani, Rodolfo Bernardi, Andrea Cavallini, Riccardo Gucci, Giovanni Caruso, Claudio D'Onofrio, Mike Frank Quartacci, Piero Picciarelli, Barbara Conti, Andrea Lucchi, Lucia Natali The availability of transcriptomic data sequence is a key step for functional genomics studies. Recently, a repertoire of predicted genes of a Japanese cultivar of fig (Ficus carica L.) was released. Because of the great phenotypic variability that can be found in ...
Source: Genomics Data - July 6, 2017 Category: Genetics & Stem Cells Source Type: research
Genome-wide miRNA, gene and methylation analysis of triple negative breast cancer to identify changes associated with lymph node metastases
Publication date: Available online 6 July 2017 Source:Genomics Data Author(s): Kelly A. Avery-Kiejda, Andrea Mathe, Rodney J. Scott Triple negative breast cancer (TNBC) is a particularly important breast cancer subtype with an aggressive clinical phenotype that is associated with a higher likelihood of metastasis. This subtype is characterized by an absence of the estrogen (ER) and progesterone (PR) receptors, as well as the human epidermal growth factor receptor 2 (HER2/HER neu). The absence of the three receptors significantly reduces targeted treatment options for patients with TNBC and as such, there is an urgent ...
Source: Genomics Data - July 6, 2017 Category: Genetics & Stem Cells Source Type: research
De novo transcriptome assembly for the lung of the ornamented pygmy frog (Microhyla fissipes)
This study provides the transcriptome and functional annotation of genes in M. fissipes lung development, which will be useful for comparative transcriptome analyses and promote research into mechanism of lung development in anuran. (Source: Genomics Data)
Source: Genomics Data - July 5, 2017 Category: Genetics & Stem Cells Source Type: research
Genome sequence of the type strain CLIB 1764T (=CBS 14374T) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough
Publication date: Available online 4 July 2017 Source:Genomics Data Author(s): Véronique Sarilar, Lieven Sterck, Saki Matsumoto, Noémie Jacques, Cécile Neuvéglise, Colin R. Tinsley, Delphine Sicard, Serge Casaregola Kazachstania saulgeensis is a recently described species isolated from French organic sourdough. Here, we report the high quality genome sequence of a monosporic segregant of the type strain of this species, CLIB 1764T (=CBS 14374T). The genome has a total length of 12.9Mb and contains 5326 putative protein-coding genes, excluding pseudogenes and transposons. The nucleotide sequences were deposite...
Source: Genomics Data - July 5, 2017 Category: Genetics & Stem Cells Source Type: research
Erratum to “RNA-seq detects pharmacological inhibition of Epstein-Barr virus late transcription during spontaneous reactivation” [Genomics Data 13 (2017) 5–6]
Publication date: Available online 5 July 2017 Source:Genomics Data Author(s): An T. Phan, Delsy M. Martinez, J.J.L. Miranda (Source: Genomics Data)
Source: Genomics Data - July 5, 2017 Category: Genetics & Stem Cells Source Type: research
