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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/28918562/crispr-cas9-genome-editing-in-wheat
#1
Dongjin Kim, Burcu Alptekin, Hikmet Budak
Genome editing has been a long-term challenge for molecular biology research, particularly for plants possess complex genome. The recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile tool for genome editing which enables editing of multiple genes based on the guidance of small RNAs. Even though the efficiency of CRISPR/Cas9 system has been shown with several studies from diploid plants, its application remains a challenge for plants with polyploid and complex genome...
September 16, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28900766/diversity-and-distribution-of-cyp-gene-family-in-bactrian-camel
#2
Surong Hasi, Jirimutu Yao, Siriguleng Yu, Yanan Tian
Cytochrome P450 (CYP) enzymes belong to a superfamily of monooxygenases which are phase I enzymes responsible for the first pass metabolism of about 90% of drugs in animals. However, these enzymes are often polymorphic and metabolism of the same drug in different species or different individuals is influenced by genetic and non-genetic factors. Bactrian camels are capable of survival in harsh living environments, being able to consume diets that are often toxic to other mammals and can tolerate extreme water and food deprivation...
September 12, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28856505/comparative-analysis-of-constitutive-proteome-between-resistant-and-susceptible-tomato-genotypes-regarding-to-late-blight
#3
Bruno Soares Laurindo, Renata Dias Freitas Laurindo, Patrícia Pereira Fontes, Camilo Elber Vital, Fábio Teixeira Delazari, Maria Cristina Baracat-Pereira, Derly José Henriques da Silva
Late blight is one of the most destructive diseases of the tomato, resulting in substantial economic losses. There is difficulty in controlling this disease, so the molecular characterization of tomato genotypes may help in the selection of higher resistance tomato plants against Phytophthora infestans, late blight's pathogen. The objective was to analyze the differences with regard to the constitutive proteome between the access Vegetable Germplasm Bank (BGH)-2127, resistant genotype, and Santa Clara-susceptible genotype to late blight...
August 30, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735352/long-noncoding-rna-expression-profiles-in-chondrogenic-and-hypertrophic-differentiation-of-mouse-mesenchymal-stem-cells
#4
Zhen Cao, Song Huang, Jianmei Li, Yun Bai, Ce Dou, Chuan Liu, Fei Kang, Xiaoshan Gong, Haibin Ding, Tianyong Hou, Shiwu Dong
Long noncoding RNAs (lncRNAs) are important regulators for a variety of biological processes. Chondrogenic differentiation of mesenchymal stem cells (MSCs) is a crucial stage in chondrogenesis while chondrocyte hypertrophy is related to endochondral ossification and osteoarthritis. However, the effects of lncRNAs on chondrogenic and hypertrophic differentiation of mouse MSCs are unclear. To explore the potential mechanisms of lncRNAs during chondrogenesis and chondrocyte hypertrophy, microarray was performed to investigate the expression profiles of lncRNA and mRNA in MSCs, pre-chondrocytes, and hypertrophic chondrocytes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735351/multiple-correlation-analyses-revealed-complex-relationship-between-dna-methylation-and-mrna-expression-in-human-peripheral-blood-mononuclear-cells
#5
Fang-Fei Xie, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28687892/transcriptome-and-metabolome-analysis-of-ferula-gummosa-boiss-to-reveal-major-biosynthetic-pathways-of-galbanum-compounds
#6
Ahmad Sobhani Najafabadi, Mohammad Reza Naghavi, Hamid Farahmand, Alireza Abbasi
Ferula gummosa Boiss. is an industrial and pharmaceutical plant that has been highly recognized for its valuable oleo-gum-resin, namely galbanum. Despite the fabulous value of galbanum, very little information on the genetic and biochemical mechanisms of its production existed. In the present study, the oleo-gum-resin and four organs (root, flower, stem, and leaf) of F. gummosa were assessed in terms of metabolic compositions and the expression of genes involved in their biosynthetic pathways. Results showed that the most accumulation of resin and essential oils were occurred in the roots (13...
July 7, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28674744/ectopic-expression-of-csd1-and-csd2-targeting-genes-of-mir398-in-grapevine-is-associated-with-oxidative-stress-tolerance
#7
XiangPeng Leng, Peipei Wang, Xudong Zhu, Xiaopeng Li, Ting Zheng, Lingfei Shangguan, Jinggui Fang
MicroRNAs (miRNAs) are endogenous small RNAs of -21 nucleotides that play an important role in diverse plant physiological processes at the post-transcriptional level by directing mRNA cleavage or translational inhibition. Previous studies have indicated that down-regulation of miR398 in response to oxidative stress allows up-regulation of the two target genes, cytosolic CSD1 and chloroplastic CSD2 (copper/zinc superoxide dismutase), resulting in protecting the plants to tolerate oxidative stress. In this study, we provide evidence that grapevine miR398 (Vv-miR398), by regulating the expression of its target genes, VvCSD1 and VvCSD2, mediates responses of grapevine to copper (Cu) stress which have been magnified due to increase in Cu-containing pesticide application...
July 3, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28470340/comprehensive-strategy-for-the-design-of-precision-drugs-and-identification-of-genetic-signature-behind-proneness-of-the-disease-a-pharmacogenomic-approach
#8
REVIEW
Preethi M Iyer, S Karthikeyan, P Sanjay Kumar, P K Krishnan Namboori
The proneness of diseases and susceptibility towards drugs vary from person to person. At present, there is a strong demand for the personalization of drugs. The genetic signature behind proneness of the disease has been studied through a comprehensive 'octopodial approach'. All the genetic variants included in the approach have been introduced. The breast cancer associated with BRCA1 mutation has been taken as the illustrative example to introduce all these factors. The genetic variants associated with the drug action of tamoxifen have been fully illustrated in the manuscript...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28190211/low-diversity-activity-and-density-of-transposable-elements-in-five-avian-genomes
#9
Bo Gao, Saisai Wang, Yali Wang, Dan Shen, Songlei Xue, Cai Chen, Hengmi Cui, Chengyi Song
In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes...
July 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28612136/identification-of-two-novel-chicken-gpr133-variants-and-their-expression-in-different-tissues
#10
Kai Tian, Qihai Xiao, Xueyou Zhang, Xi Lan, Xiaoling Zhao, Yan Wang, Diyan Li, Huadong Yin, Lin Ye, Qing Zhu
GPR133 (G protein-coupled receptor 133) plays significant roles in various physiological processes. Alternatively splicing (AS) variants of GPR133 in many species have been predicted in multiple databases, but there is no available information about the AS events of chicken GPR133 (cGPR133). In the present study, two chicken GPR133 variants, cGPR133-va and cGPR133-vb, were identified by a combination of reverse transcription PCR (RT-PCR) and rapid amplification of cDNA 5'-ends (5' RACE). Sequence analysis shows that cGPR133-va and cGPR133-vb are resulting from different AS modules and their sequences are predicted to encode two distinct putative proteins, respectively...
June 14, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28600722/genetic-dissection-of-plant-growth-habit-in-chickpea
#11
Hari D Upadhyaya, Deepak Bajaj, Rishi Srivastava, Anurag Daware, Udita Basu, Shailesh Tripathi, Chellapilla Bharadwaj, Akhilesh K Tyagi, Swarup K Parida
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs...
June 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28573536/exploring-the-heat-responsive-chaperones-and-microsatellite-markers-associated-with-terminal-heat-stress-tolerance-in-developing-wheat
#12
Ranjeet R Kumar, Suneha Goswami, Mohammad Shamim, Kavita Dubey, Khushboo Singh, Shweta Singh, Yugal K Kala, Ravi R K Niraj, Akshay Sakhrey, Gyanendra P Singh, Monendra Grover, Bhupinder Singh, Gyanendra K Rai, Anil K Rai, Viswanathan Chinnusamy, Shelly Praveen
Global warming is a major threat for agriculture and food security, and in many cases the negative impacts are already apparent. Wheat is one of the most important staple food crops and is highly sensitive to the heat stress (HS) during reproductive and grain-filling stages. Here, whole transcriptome analysis of thermotolerant wheat cv. HD2985 was carried out at the post-anthesis stage under control (22 ± 3 °C) and HS-treated (42 °C, 2 h) conditions using Illumina Hiseq and Roche GS-FLX 454 platforms...
June 1, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28550605/high-throughput-snp-genotyping-of-modern-and-wild-emmer-wheat-for-yield-and-root-morphology-using-a-combined-association-and-linkage-analysis
#13
Stuart J Lucas, Ayten Salantur, Selami Yazar, Hikmet Budak
Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T...
May 26, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28480497/expression-analysis-of-genes-encoding-double-b-box-zinc-finger-proteins-in-maize
#14
Wenlan Li, Jingchao Wang, Qi Sun, Wencai Li, Yanli Yu, Meng Zhao, Zhaodong Meng
The B-box proteins play key roles in plant development. The double B-box (DBB) family is one of the subfamily of the B-box family, with two B-box domains and without a CCT domain. In this study, 12 maize double B-box genes (ZmDBBs) were identified through a genome-wide survey. Phylogenetic analysis of DBB proteins from maize, rice, Sorghum bicolor, Arabidopsis, and poplar classified them into five major clades. Gene duplication analysis indicated that segmental duplications made a large contribution to the expansion of ZmDBBs...
May 8, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28477104/using-scale-and-feather-traits-for-module-construction-provides-a-functional-approach-to-chicken-epidermal-development
#15
Weier Bao, Matthew J Greenwold, Roger H Sawyer
Gene co-expression network analysis has been a research method widely used in systematically exploring gene function and interaction. Using the Weighted Gene Co-expression Network Analysis (WGCNA) approach to construct a gene co-expression network using data from a customized 44K microarray transcriptome of chicken epidermal embryogenesis, we have identified two distinct modules that are highly correlated with scale or feather development traits. Signaling pathways related to feather development were enriched in the traditional KEGG pathway analysis and functional terms relating specifically to embryonic epidermal development were also enriched in the Gene Ontology analysis...
May 5, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28386681/addition-to-special-issue-mirna-in-model-and-complex-organisms
#16
(no author information available yet)
No abstract text is available yet for this article.
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28220336/micrornas-in-model-and-complex-organisms
#17
EDITORIAL
Hikmet Budak, Baohong Zhang
Non-coding RNAs such as microRNAs (miRNAs) are very tiny ribonucleotides having an essential role in gene regulation at both post-transcriptional and translational levels. They are very conserved and expressed in worms, flies, plants, and mammals in a sequence-specific manner. Furthermore, it is now possible to clone miRNAs using the new genome editing tool CRISPR/cas9, which shows benefit in control of untargeted effect. In this special issue, we tried to cover researches associated with functional roles of miRNAs accross model and complex organisms...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28078489/identification-and-profiling-of-conserved-and-novel-micrornas-involved-in-oil-and-oleic-acid-production-during-embryogenesis-in-carya-cathayensis-sarg
#18
Zhengjia Wang, Ruiming Huang, Zhichao Sun, Tong Zhang, Jianqin Huang
MicroRNAs (miRNAs) are important regulators of plant development and fruit formation. Mature embryos of hickory (Carya cathayensis Sarg.) nuts contain more than 70% oil (comprising 90% unsaturated fatty acids), along with a substantial amount of oleic acid. To understand the roles of miRNAs involved in oil and oleic acid production during hickory embryogenesis, three small RNA libraries from different stages of embryogenesis were constructed. Deep sequencing of these three libraries identified 95 conserved miRNAs with 19 miRNA*s, 7 novel miRNAs (as well as their corresponding miRNA*s), and 26 potentially novel miRNAs...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28070736/genome-wide-analysis-of-mirnas-and-tasi-rnas-in-zea-mays-in-response-to-phosphate-deficiency
#19
Saurabh Gupta, Manju Kumari, Himansu Kumar, Pritish Kumar Varadwaj
Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28032247/a-systemic-identification-approach-for-primary-transcription-start-site-of-arabidopsis-mirnas-from-multidimensional-omics-data
#20
Qi You, Hengyu Yan, Yue Liu, Xin Yi, Kang Zhang, Wenying Xu, Zhen Su
The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts...
May 2017: Functional & Integrative Genomics
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