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International Journal of Genomics

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https://www.readbyqxmd.com/read/27872842/transcriptome-based-analysis-of-dof-family-transcription-factors-and-their-responses-to-abiotic-stress-in-tea-plant-camellia-sinensis
#1
Hui Li, Wei Huang, Zhi-Wei Liu, Yong-Xin Wang, Jing Zhuang
Tea plant (Camellia sinensis (L.) O. Kuntze) is affected by abiotic stress during its growth and development. DNA-binding with one finger (Dof) transcription factors (TFs) play important roles in abiotic stress tolerance of plants. In this study, a total of 29 putative Dof TFs were identified based on transcriptome of tea plant, and the conserved domains and common motifs of these CsDof TFs were predicted and analyzed. The 29 CsDof proteins were divided into 7 groups (A, B1, B2, C1, C2.1, C2.2, and D2), and the interaction networks of Dof proteins in C...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27872841/novel-graphical-analyses-of-runs-of-homozygosity-among-species-and-livestock-breeds
#2
Laura Iacolina, Astrid V Stronen, Cino Pertoldi, Małgorzata Tokarska, Louise S Nørgaard, Joaquin Muñoz, Anders Kjærsgaard, Aritz Ruiz-Gonzalez, Stanisław Kamiński, Deirdre C Purfield
Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27868058/gpa-mds-a-visualization-approach-to-investigate-genetic-architecture-among-phenotypes-using-gwas-results
#3
Wei Wei, Paula S Ramos, Kelly J Hunt, Bethany J Wolf, Gary Hardiman, Dongjun Chung
Genome-wide association studies (GWAS) have identified tens of thousands of genetic variants associated with hundreds of phenotypes and diseases, which have provided clinical and medical benefits to patients with novel biomarkers and therapeutic targets. Recently, there has been accumulating evidence suggesting that different complex traits share a common risk basis, namely, pleiotropy. Previously, a statistical method, namely, GPA (Genetic analysis incorporating Pleiotropy and Annotation), was developed to improve identification of risk variants and to investigate pleiotropic structure through a joint analysis of multiple GWAS datasets...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27843935/differential-gene-expression-during-larval-metamorphic-development-in-the-pearl-oyster-pinctada-fucata-based-on-transcriptome-analysis
#4
Haimei Li, Bo Zhang, Guiju Huang, Baosuo Liu, Sigang Fan, Dongling Zhang, Dahui Yu
P. fucata experiences a series of transformations in appearance, from swimming larvae to sessile juveniles, during which significant changes in gene expression likely occur. Thus, P. fucata could be an ideal model in which to study the molecular mechanisms of larval metamorphosis during development in invertebrates. To study the molecular driving force behind metamorphic development in larvae of P. fucata, transcriptomes of five larval stages (trochophore, D-shape, umbonal, eyespots, and spats) were sequenced using an Illumina HiSeq™ 2000 system and assembled and characterized with the transcripts of six tissues...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27840818/proteome-analysis-of-date-palm-phoenix-dactylifera-l-under-severe-drought-and-salt-stress
#5
Haddad A El Rabey, Abdulrahman L Al-Malki, Khalid O Abulnaja
Date palm cultivars differently tolerate salinity and drought stress. This study was carried out to study the response of date palm to severe salinity and drought based on leaf proteome analysis. Eighteen-month-old date palm plants were subjected to severe salt (48 g/L NaCl) and drought (82.5 g/L PEG or no irrigation) conditions for one month. Using a protein 2D electrophoresis method, 55 protein spots were analyzed using mass spectrometry. ATP synthase CF1 alpha chains were significantly upregulated under all three stress conditions...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27822466/analysis-of-gene-expression-in-an-inbred-line-of-soft-shell-clams-mya-arenaria-displaying-growth-heterosis-regulation-of-structural-genes-and-the-nod2-pathway
#6
John J Wilson, Janelle Grendler, Azaline Dunlap-Smith, Brian F Beal, Shallee T Page
Mya arenaria is a bivalve mollusk of commercial and economic importance, currently impacted by ocean warming, acidification, and invasive species. In order to inform studies on the growth of M. arenaria, we selected and inbred a population of soft-shell clams for a fast-growth phenotype. This population displayed significantly faster growth (p < 0.0001), as measured by 35.4% greater shell size. To assess the biological basis of this growth heterosis, we characterized the complete transcriptomes of six individuals and identified differentially expressed genes by RNAseq...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27818993/molecular-cloning-characterization-and-mrna-expression-of-hemocyanin-subunit-in-oriental-river-prawn-macrobrachium-nipponense
#7
Youqin Kong, Liqiao Chen, Zhili Ding, Jianguang Qin, Shengming Sun, Ligai Wang, Jinyun Ye
Hemocyanin is a copper-containing protein with immune function against disease. In this study, a hemocyanin subunit named MnHc-1 was cloned from Macrobrachium nipponense. The full-length cDNA of MnHc-1 was 2,163 bp with a 2,028-bp open reading frame (ORF) encoding a polypeptide of 675 amino acids. The MnHc-1 mRNA was expressed in the hepatopancreas, gill, hemocytes, intestine, ovary, and stomach, with the highest level in the hepatopancreas. In the infection trial, the MnHc-1 mRNA transcripts in the hemocytes were significantly downregulated at 3 h after injection of Aeromonas hydrophila and then upregulated at 6 h and 12 h, followed by a gradual recovery from 24 to 48 h...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27818992/performance-characterization-and-validation-of-saliva-as-an-alternative-specimen-source-for-detecting-hereditary-breast-cancer-mutations-by-next-generation-sequencing
#8
Varsha Meghnani, Nadeem Mohammed, Christopher Giauque, Rahul Nahire, Thomas David
Identification of pathogenic germline mutations by next generation sequencing is a widely accepted tool for predicting the risk of hereditary cancer development. Blood is the most common source of DNA for such tests. However, blood as a sample type has many drawbacks, including the invasive collection method, poor sample stability, and a relatively high cost of collection. Therefore, in the current study we have assessed the suitability of saliva as an alternative source of genomic DNA for the identification of germline mutations in the BRCA1/2 genes by next generation sequencing (NGS)...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27774452/rna-sequencing-of-formalin-fixed-paraffin-embedded-specimens-for-gene-expression-quantification-and-data-mining
#9
Yan Guo, Jie Wu, Shilin Zhao, Fei Ye, Yinghao Su, Travis Clark, Quanhu Sheng, Brian Lehmann, Xiao-Ou Shu, Qiuyin Cai
Background. Proper rRNA depletion is crucial for the successful utilization of FFPE specimens when studying gene expression. We performed a study to evaluate two major rRNA depletion methods: Ribo-Zero and RNase H. RNAs extracted from 4 samples were treated with the two rRNA depletion methods in duplicate and sequenced (N = 16). We evaluated their reducibility, ability to detect RNA, and ability to molecularly subtype these triple negative breast cancer specimens. Results. Both rRNA depletion methods produced consistent data between the technical replicates...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27689071/embracing-integrative-multiomics-approaches
#10
REVIEW
Daniel M Rotroff, Alison A Motsinger-Reif
As "-omics" data technology advances and becomes more readily accessible to address complex biological questions, increasing amount of cross "-omics" dataset is inspiring the use and development of integrative bioinformatics analysis. In the current review, we discuss multiple options for integrating data across "-omes" for a range of study designs. We discuss established methods for such analysis and point the reader to in-depth discussions for the various topics. Additionally, we discuss challenges and new directions in the area...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27660755/genome-wide-characterization-and-expression-profiles-of-the-superoxide-dismutase-gene-family-in-gossypium
#11
Jingbo Zhang, Bo Li, Yang Yang, Wenran Hu, Fangyuan Chen, Lixia Xie, Ling Fan
Superoxide dismutase (SOD) as a group of significant and ubiquitous enzymes plays a critical function in plant growth and development. Previously this gene family has been investigated in Arabidopsis and rice; it has not yet been characterized in cotton. In our study, it was the first time for us to perform a genome-wide analysis of SOD gene family in cotton. Our results showed that 10 genes of SOD gene family were identified in Gossypium arboreum and Gossypium raimondii, including 6 Cu-Zn-SODs, 2 Fe-SODs, and 2 Mn-SODs...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27656648/clinical-application-of-a-modular-genomics-technique-in-systemic-lupus-erythematosus-progress-towards-precision-medicine
#12
Eric Zollars, Sean M Courtney, Bethany J Wolf, Norm Allaire, Ann Ranger, Gary Hardiman, Michelle Petri
Monitoring disease activity in a complex, heterogeneous disease such as lupus is difficult. Both over- and undertreatment lead to damage. Current standard of care serologies are unreliable. Better measures of disease activity are necessary as we move into the era of precision medicine. We show here the use of a data-driven, modular approach to genomic biomarker development within lupus-specifically lupus nephritis.
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27652256/transcriptome-analyses-reveal-lipid-metabolic-process-in-liver-related-to-the-difference-of-carcass-fat-content-in-rainbow-trout-oncorhynchus-mykiss
#13
Guo Hu, Wei Gu, Peng Sun, Qingli Bai, Bingqian Wang
Excessive accumulation of carcass fat in farm animals, including fish, has a significant impact on meat quality and on the cost of feeding. Similar to farmed animals and humans, the liver can be considered one of the most important organs involved in lipid metabolism in rainbow trout (Oncorhynchus mykiss). RNA-seq based whole transcriptome sequencing was performed to liver tissue of rainbow trout with high and low carcass fat content in this study. In total 1,694 differentially expressed transcripts were identified, including many genes involved in lipid metabolism, such as L-FABP, adiponectin, PPAR-α, PPAR-β, and IGFBP1a...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27652255/genetic-contribution-of-ningmai-9-wheat-to-its-derivatives-evaluated-by-using-snp-markers
#14
Peng Jiang, Ping-Ping Zhang, Xu Zhang, Hong-Xiang Ma
Founder parent usually plays an important role in wheat breeding. Ningmai 9 is a soft wheat variety with good performance in yield, quality, and resistance to wheat disease. Therefore it serves as an important commercial variety and founder parent in middle and lower Yangtze River of China. To date, 20 new cultivars have been developed from Ningmai 9 and released to wheat production in the last 10 years. In this study, the 90K iSELECT ILLUMINA chip was used to analyze the genotype of Ningmai 9 and its 17 derivatives...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27635394/genome-wide-analysis-of-genes-encoding-methionine-rich-proteins-in-arabidopsis-and-soybean-suggesting-their-roles-in-the-adaptation-of-plants-to-abiotic-stress
#15
Ha Duc Chu, Quynh Ngoc Le, Huy Quang Nguyen, Dung Tien Le
Oxidation and reduction of methionine (Met) play important roles in scavenging reactive oxygen species (ROS) and signaling in living organisms. To understand the impacts of Met oxidation and reduction in plants during stress, we surveyed the genomes of Arabidopsis and soybean (Glycine max L.) for genes encoding Met-rich proteins (MRPs). We found 121 and 213 genes encoding MRPs in Arabidopsis and soybean, respectively. Gene annotation indicated that those with known function are involved in vital cellular processes such as transcriptional control, calcium signaling, protein modification, and metal transport...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27610363/histological-and-molecular-characterization-of-grape-early-ripening-bud-mutant
#16
Da-Long Guo, Yi-He Yu, Fei-Fei Xi, Yan-Yan Shi, Guo-Hai Zhang
An early ripening bud mutant was analyzed based on the histological, SSR, and methylation-sensitive amplified polymorphism (MSAP) analysis and a layer-specific approach was used to investigate the differentiation between the bud mutant and its parent. The results showed that the thickness of leaf spongy tissue of mutant (MT) is larger than that of wild type (WT) and the differences are significant. The mean size of cell layer L2 was increased in the mutant and the difference is significant. The genetic background of bud mutant revealed by SSR analysis is highly uniform to its parent; just the variations from VVS2 SSR marker were detected in MT...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27525259/genetic-characterization-and-comparative-genome-analysis-of-brucella-melitensis-isolates-from-india
#17
Sarwar Azam, Sashi Bhushan Rao, Padmaja Jakka, Veera NarasimhaRao, Bindu Bhargavi, Vivek Kumar Gupta, Girish Radhakrishnan
Brucellosis is the most frequent zoonotic disease worldwide, with over 500,000 new human infections every year. Brucella melitensis, the most virulent species in humans, primarily affects goats and the zoonotic transmission occurs by ingestion of unpasteurized milk products or through direct contact with fetal tissues. Brucellosis is endemic in India but no information is available on population structure and genetic diversity of Brucella spp. in India. We performed multilocus sequence typing of four B. melitensis strains isolated from naturally infected goats from India...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27517040/ssr-mapping-of-qtls-conferring-cold-tolerance-in-an-interspecific-cross-of-tomato
#18
Yang Liu, Tengxia Zhou, Haiyan Ge, Wen Pang, Lijie Gao, Li Ren, Huoying Chen
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 lines and RILs. It was found that the RGR and CI were significantly different between S. lycopersicum XF98-7 and S. pimpinellifolium LA2184 under cold treatment, indicating that wild species was more adapted to chilling temperature...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27478823/accurate-identification-of-cancerlectins-through-hybrid-machine-learning-technology
#19
Jieru Zhang, Ying Ju, Huijuan Lu, Ping Xuan, Quan Zou
Cancerlectins are cancer-related proteins that function as lectins. They have been identified through computational identification techniques, but these techniques have sometimes failed to identify proteins because of sequence diversity among the cancerlectins. Advanced machine learning identification methods, such as support vector machine and basic sequence features (n-gram), have also been used to identify cancerlectins. In this study, various protein fingerprint features and advanced classifiers, including ensemble learning techniques, were utilized to identify this group of proteins...
2016: International Journal of Genomics
https://www.readbyqxmd.com/read/27446942/using-genome-wide-snp-discovery-and-genotyping-to-reveal-the-main-source-of-population-differentiation-in-nothofagus-dombeyi-mirb-oerst-in-chile
#20
Rodrigo Hasbún, Jorge González, Carolina Iturra, Glenda Fuentes, Diego Alarcón, Eduardo Ruiz
Within a woody plant species, environmental heterogeneity has the potential to influence the distribution of genetic variation among populations through several evolutionary processes. In some species, a relationship between environmental characteristics and the distribution of genotypes can be detected, showing the importance of natural selection as the main source of differentiation. Nothofagus dombeyi (Mirb.) Oerst. (Nothofagaceae) is an endemic tree species occurring both in Chile and in Argentina temperate forests...
2016: International Journal of Genomics
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