Abstract：
:Pseudomonas aeruginosa PGPR2 is a mung bean rhizosphere strain that produces secondary metabolites and hydrolytic enzymes contributing to excellent antifungal activity against Macrophomina phaseolina, one of the prevalent fungal pathogens of mung bean. Genome sequencing was performed using the Ion Torrent Personal Genome Machine generating 1,354,732 reads (6,772,433 sequenced bases) achieving ~25-fold coverage of the genome. Reference genome assembly using MIRA 3.4.0 yielded 198 contigs. The draft genome of PGPR2 encoded 6803 open reading frames, of which 5314 were genes with predicted functions, 1489 were genes of known functions, and 80 were RNA-coding genes. Strain specific and core genes of P. aeruginosa PGPR2 that are relevant to rhizospheric habitat were identified by pangenome analysis. Genes involved in plant growth promoting function such as synthesis of ACC deaminase, indole-3-acetic acid, trehalose, mineral scavenging siderophores, hydrogen cyanide, chitinases, acyl homoserine lactones, acetoin, 2,3-butanediol, and phytases were identified. In addition, niche-specific genes such as phosphate solubilising 3-phytase, adhesins, pathway-specific transcriptional regulators, a diguanylate cyclase involved in cellulose synthesis, a receptor for ferrienterochelin, a DEAD/DEAH-box helicase involved in stress tolerance, chemotaxis/motility determinants, an HtpX protease, and enzymes involved in the production of a chromanone derivative with potent antifungal activity were identified.
journal_name
Int J Genomicsjournal_title
International journal of genomicsauthors
Illakkiam D,Shankar M,Ponraj P,Rajendhran J,Gunasekaran Pdoi
10.1155/2014/123058subject
Has Abstractpub_date
2014-01-01 00:00:00pages
123058eissn
2314-436Xissn
2314-4378journal_volume
2014pub_type
杂志文章abstract：:Arabidopsis thaliana (L.) Heynh. is a model organism of plant molecular biology. More than 1,700 whole genome sequences have been sequenced, but no Korean isolate genomes have been sequenced thus far despite the fact that many A. thaliana isolated in Japan and China have been sequenced. To understand the genetic backg...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2020/3236461
更新日期：2020-09-05 00:00:00
abstract：:Paeonia lactiflora is a herbaceous flower in the family Paeoniaceae with both hypocotyl and epicotyl dormant seeds. We used high-throughput transcriptome sequencing on two different developmental stages of P. lactiflora seeds to identify seed dormancy and germination-related genes. We performed de novo assembly and an...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2017/8027626
更新日期：2017-01-01 00:00:00
abstract：Purpose:Airway epithelium acts as a protective barrier against the particles from the inhaled air. Damage to the epithelium may result in loss of the barrier function. Epithelial repair in response to injury requires complex mechanisms, such as microRNA, small noncoding molecules, to regulate the processes involved in ...
journal_title：International journal of genomics
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doi：10.1155/2018/9093785
更新日期：2018-09-05 00:00:00
abstract：:Severe gastroenteritis and foodborne illness caused by Noroviruses (NoVs) during the winter are a worldwide phenomenon. Vulnerable populations including young children and elderly and immunocompromised people often require hospitalization and may die. However, no efficient vaccine for NoVs exists because of their vari...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2013/456356
更新日期：2013-01-01 00:00:00
abstract：:Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newb...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2014/267482
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abstract：:Background and Objectives. Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airflow limitation. Although airway inflammation and oxidative stress are known to be important in the pathogenesis of COPD, the mechanism underlying airflow obstruction is not fully understood. Gene expressio...
journal_title：International journal of genomics
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更新日期：2015-01-01 00:00:00
abstract：:Photobacterium damselae subsp. damselae (PDD) is a Gram-negative bacterium that can infect a variety of aquatic organisms and humans. Based on an epidemiological investigation conducted over the past 3 years, PDD is one of the most important pathogens causing septic skin ulcer in deep-sea cage-cultured Sebastes schleg...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2019/4242653
更新日期：2019-04-10 00:00:00
abstract：:In recent years the human microbiome has become a growing area of research and it is becoming clear that the microbiome of humans plays an important role for human health. Extensive research is now going into cataloging and annotating the functional role of the human microbiome. The ability to explore and describe the...
journal_title：International journal of genomics
pub_type： 杂志文章,评审
doi：10.1155/2016/5304028
更新日期：2016-01-01 00:00:00
abstract：:The purpose of this work was to study changes in the level of cell-free DNA (cfDNA) in the blood of young and old rats in the normal state and with induced benign prostatic hyperplasia (BPH). Male Wistar rats were divided into 4 groups-young (3 months), old (20 months), intact, or with testosterone-induced BPH. Groups...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2019/8173630
更新日期：2019-06-02 00:00:00
abstract：:To better understand the molecular functions of the master stress-response regulator AtfA in Aspergillus nidulans, transcriptomic analyses of the atfA null mutant and the appropriate control strains exposed to menadione sodium bisulfite- (MSB-), t-butylhydroperoxide- and diamide-induced oxidative stresses were perform...
journal_title：International journal of genomics
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更新日期：2017-01-01 00:00:00
abstract：:The Gene Ontology (GO) provides a resource for consistent annotation of genes and gene products that is extensively used by numerous large public repositories. The GO is constructed of three subontologies describing the cellular component of action, molecular function, and overall biological process of a gene or gene ...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2013/594528
更新日期：2013-01-01 00:00:00
abstract：:Goat plays a crucial role in human livelihoods, being a major source of meat, milk, fiber, and hides, particularly under adverse climatic conditions. The goat genomics related to the candidate gene approach is now being used to recognize molecular mechanisms that have different expressions of growth, reproductive, mil...
journal_title：International journal of genomics
pub_type： 杂志文章,评审
doi：10.1155/2020/5940205
更新日期：2020-08-18 00:00:00
abstract：:Taxol is one of the most potent and effective anticancer drugs and is originally isolated from Taxus species. To investigate the specific regulatory mechanisms of taxol synthesis in Taxus wallichiana var. mairei, RNA-seq was conducted to reveal the differences in transcriptional levels between wild type (WT) and "Jinx...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2019/1596895
更新日期：2019-05-02 00:00:00
abstract：:Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. In order to understand the genetic components of grain appearance traits in paddy, brown, and head rice, 1...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2019/3160275
更新日期：2019-02-25 00:00:00
abstract：:A population of 146 RILs (Recombinant Inbred Line) was derived from the cross between a cold-sensitive cultivated Solanum lycopersicum L. XF98-7 and a cold-tolerant wild Solanum pimpinellifolium LA2184. Relative germination ratio (RGR) and chilling index (CI) were used to evaluate the cold tolerance of the parental li...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2016/3219276
更新日期：2016-01-01 00:00:00
abstract：:The threat of heat stress on crop production increased dramatically due to global warming leading to the rise on the demand of heat-tolerant crops and understanding their tolerance. The leguminous forage crop Guar [Cyamopsis tetragonoloba (L.) Taub] is a high-temperature tolerant plant with numerous works on its toler...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2020/3126592
更新日期：2020-06-19 00:00:00
abstract：:We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were perf...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2018/3505428
更新日期：2018-10-28 00:00:00
abstract：:The Chinese Kunming (KM) mouse is a widely used outbred mouse stock in China. However, its genetic structure remains unclear. In this study, we sequenced the genome of the C57BL/6J-Chr1KM (B6-Chr1KM) strain, the chromosome 1 (Chr 1) of which was derived from one KM mouse. With 36.6× average coverage of the entire geno...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2017/1712530
更新日期：2017-01-01 00:00:00
abstract：:The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus ...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2015/198560
更新日期：2015-01-01 00:00:00
abstract：Purpose:Next-generation sequencing (NGS) has become more accessible, leading to an increasing number of genetic studies of familial bradycardia being reported. However, most of the variants lack full evaluation. The relationship between genetic factors and bradycardia should be summarized and reevaluated. Methods:We s...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2020/2415850
更新日期：2020-02-25 00:00:00
abstract：Background:Chronic kidney disease (CKD) is characterized by progressive renal function loss, which may finally lead to end-stage renal disease (ESRD). The study is aimed at identifying crucial genes related to CKD progressive and constructing a disease prediction model to investigate risk factors. Methods:GSE97709 and...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2020/7524057
更新日期：2020-11-12 00:00:00
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journal_title：International journal of genomics
pub_type： 杂志文章,评审
doi：10.1155/2019/8458263
更新日期：2019-08-21 00:00:00
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journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2013/376454
更新日期：2013-01-01 00:00:00
abstract：:The expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may modify the affinit...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2015/260159
更新日期：2015-01-01 00:00:00
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journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2018/7658910
更新日期：2018-04-29 00:00:00
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journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2020/1426761
更新日期：2020-05-22 00:00:00
abstract：:Orobanche crenata is a parasitic weed that causes considerable yield losses on food legumes in Ethiopia and the Mediterranean region. Understanding the genetic diversity of Orobanche crenata using molecular techniques generate useful information in managing the weed through resistance breeding. This study aimed at ass...
journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2020/3202037
更新日期：2020-08-13 00:00:00
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journal_title：International journal of genomics
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更新日期：2018-02-11 00:00:00
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journal_title：International journal of genomics
pub_type： 杂志文章
doi：10.1155/2017/8753498
更新日期：2017-01-01 00:00:00
abstract：:Cancer is a multistep process characterized by various and different genetic lesions which cause the transformation of normal cells into tumor cells. To preserve the genomic integrity, eukaryotic cells need a complex DNA damage/repair response network of signaling pathways, involving many proteins, able to induce cell...
journal_title：International journal of genomics
pub_type： 杂志文章,评审
doi：10.1155/2014/820248
更新日期：2014-01-01 00:00:00
