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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/28687892/transcriptome-and-metabolome-analysis-of-ferula-gummosa-boiss-to-reveal-major-biosynthetic-pathways-of-galbanum-compounds
#1
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
#2
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/28612136/identification-of-two-novel-chicken-gpr133-variants-and-their-expression-in-different-tissues
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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/28470340/comprehensive-strategy-for-the-design-of-precision-drugs-and-identification-of-genetic-signature-behind-proneness-of-the-disease-a-pharmacogenomic-approach
#9
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
#10
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/28386681/addition-to-special-issue-mirna-in-model-and-complex-organisms
#11
(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
#12
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
#13
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
#14
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
#15
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
https://www.readbyqxmd.com/read/27866284/a-syntenic-locus-on-buffalo-chromosome-20-novel-genomic-hotspot-for-mirnas-involved-in-follicular-luteal-transition
#16
Vijay Simha Baddela, Suneel Kumar Onteru, Dheer Singh
The developmental reorganization of ovarian follicular granulosa cells (GC) during follicular maturation, ovulation, and luteinization require a well-controlled regulation of dynamic gene expression profiles. Recently, microRNAs (miRNAs) were found to be key players of ovarian follicular dynamics. The current study aimed to understand the miRNA regulatory role in follicular-luteal transition by characterizing the miRNA profile through miRNA-seq at different follicular (small, medium, and large) and luteal (early, mid, and late) stages in Indian water buffaloes, mono-ovulatory animals like humans...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27858182/migration-of-endophytic-diazotroph-azorhizobium-caulinodans-ors571-inside-wheat-triticum-aestivum-l-and-its-effect-on-micrornas
#17
Li Qiu, Qiang Li, Junbiao Zhang, Yongchao Chen, Xiaojun Lin, Chao Sun, Weiling Wang, Huawei Liu, Baohong Zhang
Azorhizobium caulinodans ORS571, a novel rhizobium, forms endosymbionts with its nature host Sesbania rostrata, a semi-aquatic leguminous tree. Recent studies showed that A. caulinodans ORS571, as endophytic rhizobium, disseminated and colonized inside of cereal plants. However, how this rhizobium infects monocot plants and the regulatory mechanism remains unknown. MicroRNAs (miRNAs) are small, endogenous RNAs that regulate gene expression at the post-transcriptional levels. In this study, we employed laser scanning confocal microscope to monitor the pathway that rhizobium invade wheat; we also investigated the potential role of miRNAs during A...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27734229/micrornas-differentially-modulated-in-response-to-heat-and-drought-stress-in-durum-wheat-cultivars-with-contrasting-water-use-efficiency
#18
Lorenzo Giusti, Erica Mica, Edoardo Bertolini, Anna Maria De Leonardis, Primetta Faccioli, Luigi Cattivelli, Cristina Crosatti
Plant stress response is a complex molecular process based on transcriptional and posttranscriptional regulation of many stress-related genes. microRNAs are the best-studied class of small RNAs known to play key regulatory roles in plant response to stress, besides being involved in plant development and organogenesis. We analyzed the leaf miRNAome of two durum wheat cultivars (Cappelli and Ofanto) characterized by a contrasting water use efficiency, exposed to heat stress, and mild and severe drought stress...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27730426/drought-inducible-expression-of-hv-mir827-enhances-drought-tolerance-in-transgenic-barley
#19
Jannatul Ferdous, Ryan Whitford, Martin Nguyen, Chris Brien, Peter Langridge, Penny J Tricker
Drought is one of the major abiotic stresses reducing crop yield. Since the discovery of plant microRNAs (miRNAs), considerable progress has been made in clarifying their role in plant responses to abiotic stresses, including drought. miR827 was previously reported to confer drought tolerance in transgenic Arabidopsis. We examined barley (Hordeum vulgare L. 'Golden Promise') plants over-expressing miR827 for plant performance under drought. Transgenic plants constitutively expressing CaMV-35S::Ath-miR827 and drought-inducible Zm-Rab17::Hv-miR827 were phenotyped by non-destructive imaging for growth and whole plant water use efficiency (WUEwp)...
May 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27696076/characterization-of-mirnas-responsive-to-exogenous-ethylene-in-grapevine-berries-at-whole-genome-level
#20
Fanggui Zhao, Chen Wang, Jian Han, Xudong Zhu, Xiaopeng Li, Xicheng Wang, Jinggui Fang
MicroRNAs (miRNAs) are critical regulators of various biological and metabolic processes of plants. Numerous miRNAs and their functions have been identified and analyzed in many plants. However, till now, the involvement of miRNAs in the response of grapevine berries to ethylene has not been reported yet. Here, Solexa technology was employed to deeply sequence small RNA libraries constructed from grapevine berries treated with and without ethylene. A total of 124 known and 78 novel miRNAs were identified. Among these miRNAs, 162 miRNAs were clearly responsive to ethylene, with 55 downregulated, 59 upregulated, and 14 unchanged miRNAs detected only in the control...
May 2017: Functional & Integrative Genomics
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