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Functional & Integrative Genomics

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https://www.readbyqxmd.com/read/28321518/identification-and-characterization-of-durum-wheat-micrornas-in-leaf-and-root-tissues
#1
Veronica Fileccia, Edoardo Bertolini, Paolo Ruisi, Dario Giambalvo, Alfonso Salvatore Frenda, Gina Cannarozzi, Zerihun Tadele, Cristina Crosatti, Federico Martinelli
MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs...
March 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28293806/morpho-physiological-and-transcriptome-profiling-reveal-novel-zinc-deficiency-responsive-genes-in-rice
#2
Tirthankar Bandyopadhyay, Poonam Mehra, Suboot Hairat, Jitender Giri
Intensive farming has depleted the soil zinc (Zn) availability resulting in decreased crop productivity. Here, we attempt to understand the Zn deficiency response in rice through temporal transcriptome analysis. For this, rice seedlings were raised under Zn-deficient conditions up to 4 weeks followed by Zn re-supply for 3 days. Zn-deficient plants developed characteristic deficiency symptoms such as leaf bronzing, decrease in biomass, total chlorophyll, PSII efficiency, decreased carbonic anhydrase activity and increased ROS production...
March 14, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28285413/comprehensive-assessment-of-the-genes-involved-in-withanolide-biosynthesis-from-withania-somnifera-chemotype-specific-and-elicitor-responsive-expression
#3
Aditya Vikram Agarwal, Parul Gupta, Deeksha Singh, Yogeshwar Vikram Dhar, Deepak Chandra, Prabodh Kumar Trivedi
Withania somnifera (L.) Dunal (Family, Solanaceae), is among the most valuable medicinal plants used in Ayurveda owing to its rich reservoir of pharmaceutically active secondary metabolites known as withanolides. Withanolides are C28-steroidal lactones having a triterpenoidal metabolic origin synthesised via mevalonate (MVA) pathway and methyl-D-erythritol-4-phosphate (MEP) pathway involving metabolic intermediacy of 24-methylene (C30-terpenoid) cholesterol. Phytochemical studies suggest differences in the content and/or nature of withanolides in different tissues of different chemotypes...
March 11, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28251419/transcriptome-profile-of-the-human-placenta
#4
Marta Majewska, Aleksandra Lipka, Lukasz Paukszto, Jan Pawel Jastrzebski, Kamil Myszczynski, Marek Gowkielewicz, Marcin Jozwik, Mariusz Krzysztof Majewski
The human placenta is a particular organ that inseparably binds the mother and the fetus. The proper development and survival of the conceptus relies on the essential interplay between maternal and fetal factors involved in cooperation within the placenta. In our study, high-throughput sequencing (RNA-seq) was applied to analyze the global transcriptome of the human placenta during uncomplicated pregnancies. The RNA-seq was utilized to identify the global pattern of the gene expression in placentas (N = 4) from women in single and twin pregnancies...
March 1, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28247088/characterization-of-mir061-and-its-target-genes-in-grapevine-responding-to-exogenous-gibberellic-acid
#5
Mengqi Wang, Xin Sun, Chen Wang, Liwen Cui, Lide Chen, Chaobo Zhang, Lingfei Shangguan, Jinggui Fang
MicroRNAs (miRNAs), as an important growth regulator, are also involved in gibberellic acid (GA) signaling, revealing much relationship between miRNAs and GA in various plant responses. Grape is highly sensitive to GA3, which plays a significant regulatory role in regulation of flower development, berry expansion, berry set, berry ripening, and seedlessness induction; further, it was found that grapevine miR061 (VvmiR061) is a GA3 responsive miRNA. In this study, grapevine REV (VvREV) and HOX32 (VvHOX32), two target genes of VvmiR061, were predicted, verified, and cloned; homologous conservation was analyzed in various plants...
February 28, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28236275/gene-expression-profiles-predictive-of-cold-induced-sweetening-in-potato
#6
Jonathan Neilson, M Lagüe, S Thomson, F Aurousseau, A M Murphy, B Bizimungu, V Deveaux, Y Bègue, J M E Jacobs, H H Tai
Cold storage (2-4 °C) used in potato production to suppress diseases and sprouting during storage can result in cold-induced sweetening (CIS), where reducing sugars accumulate in tuber tissue leading to undesirable browning, production of bitter flavors, and increased levels of acrylamide with frying. Potato exhibits genetic and environmental variation in resistance to CIS. The current study profiles gene expression in post-harvest tubers before cold storage using transcriptome sequencing and identifies genes whose expression is predictive for CIS...
February 24, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28236274/comparative-pan-genome-analysis-of-oral-prevotella-species-implicated-in-periodontitis
#7
Maziya Ibrahim, Ahalyaa Subramanian, Sharmila Anishetty
Prevotella is part of the oral bacterial community implicated in periodontitis. Pan genome analyses of eight oral Prevotella species, P. dentalis, P. enoeca, P. fusca, P. melaninogenica, P. denticola, P. intermedia 17, P. intermedia 17-2 and P. sp. oral taxon 299 are presented in this study. Analysis of the Prevotella pan genome revealed features such as secretion systems, resistance to oxidative stress and clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems that enable the bacteria to adapt to the oral environment...
February 24, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28236273/developmental-processes-and-responses-to-hormonal-stimuli-in-tea-plant-camellia-sinensis-leaves-are-controlled-by-grf-and-gif-gene-families
#8
Zhi-Jun Wu, Wen-Li Wang, Jing Zhuang
Tea plant (Camellia sinensis (L.) O. Kuntze) is an important leaf-type woody crop used for producing of non-alcoholic beverages worldwide. The GROWTH-REGULATING FACTOR (GRF) transcription factors cooperated with GRF-INTERACTING FACTOR (GIF) transcriptional coactivators positively regulate leaf development. In the present study, six GRF and two GIF genes were identified and characterized in the leaf transcriptome of C. sinensis, respectively. The alignment results showed that the feature structures of the predicted homologous GRF and GIF proteins of C...
February 24, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28224250/abscisic-acid-sucrose-and-auxin-coordinately-regulate-berry-ripening-process-of-the-fujiminori-grape
#9
Haifeng Jia, Zhenqiang Xie, Chen Wang, Lingfei Shangguan, Ning Qian, Mengjie Cui, Zhongjie Liu, Ting Zheng, Mengqi Wang, Jinggui Fang
The aim of this study was to examine the effect of abscisic acid (ABA), sucrose, and auxin on grape fruit development and to assess the mechanism of these three factors on the grape fruit ripening process. Different concentrations of ABA, sucrose, and auxin were used to treat the grape fruit, and the ripening-related indices, such as physiological and molecular level parameters, were analyzed. The activity of BG protein activity was analyzed during the fruit development. Sucrose, ABA, and auxin influenced the grape fruit sugar accumulation in different ways, as well as the volatile compounds, anthocyanin content, and fruit firmness...
February 21, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28220336/micrornas-in-model-and-complex-organisms
#10
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...
February 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28213629/transcriptome-based-snp-discovery-by-gbs-and-the-construction-of-a-genetic-map-for-olive
#11
Ahmet İpek, Meryem İpek, Sezai Ercişli, Nesrin Aktepe Tangu
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique...
February 18, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28190211/low-diversity-activity-and-density-of-transposable-elements-in-five-avian-genomes
#12
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...
February 11, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28190210/identification-and-functional-characterization-of-four-novel-aldo-keto-reductases-in-anabaena-sp-pcc-7120-by-integrating-wet-lab-with-in-silico-approaches
#13
Chhavi Agrawal, Shivam Yadav, Shweta Rai, Antra Chatterjee, Sonia Sen, Ruchi Rai, L C Rai
Aldo/keto reductases (AKRs) constitute a multitasking protein family that catalyzes diverse metabolic transformations including detoxification of stress generated reactive aldehydes. Yet this important protein family is poorly understood particularly in cyanobacteria, the ecologically most diverse and significant group of micro-organisms. Present study is an attempt to characterize all putative AKRs of Anabaena sp. PCC 7120. In silico analysis, it revealed the presence of at least four putative AKRs in Anabaena PCC7120 genome...
February 11, 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
#14
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...
January 11, 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
#15
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...
January 9, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28058509/erratum-to-transcriptomics-analysis-of-hulless-barley-during-grain-development-with-a-focus-on-starch-biosynthesis
#16
Yawei Tang, Xingquan Zeng, Yulin Wang, Lijun Bai, Qijun Xu, Zexiu Wei, Hongjun Yuan, Tashi Nyima
No abstract text is available yet for this article.
January 5, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27913887/transcriptomics-analysis-of-hulless-barley-during-grain-development-with-a-focus-on-starch-biosynthesis
#17
Yawei Tang, Xingquan Zeng, Yulin Wang, Lijun Bai, Qijun Xu, Zexiu Wei, Hongjun Yuan, Tashi Nyima
Hulless barley, with its unique nutritional value and potential health benefits, has increasingly attracted attentions in recent years. However, the transcription dynamics during hulless barley grain development is not well understood. In the present study, we investigated the transcriptome changes during barley grain development using Illumina paired-end RNA-sequencing. Two datasets of the developing grain transcriptomes from two barley landraces with the differential seed starch synthesis traits were generated, and comparative transcriptome approach in both genotypes was performed...
January 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27900504/a-large-scale-chromosome-specific-snp-discovery-guideline
#18
Bala Ani Akpinar, Stuart Lucas, Hikmet Budak
Single-nucleotide polymorphisms (SNPs) are the most prevalent type of variation in genomes that are increasingly being used as molecular markers in diversity analyses, mapping and cloning of genes, and germplasm characterization. However, only a few studies reported large-scale SNP discovery in Aegilops tauschii, restricting their potential use as markers for the low-polymorphic D genome. Here, we report 68,592 SNPs found on the gene-related sequences of the 5D chromosome of Ae. tauschii genotype MvGB589 using genomic and transcriptomic sequences from seven Ae...
January 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27896456/dna-copy-number-profiling-in-microsatellite-stable-and-microsatellite-unstable-hereditary-non-polyposis-colorectal-cancers-by-targeted-cnv-array
#19
Weixiang Chen, Jun Ding, Long Jiang, Zebing Liu, Xiaoyan Zhou, Daren Shi
About half of hereditary non-polyposis colorectal cancers (HNPCCs) fulfilling the Amsterdam criteria (AC) do not display evidence of mismatch repair defects, and the difference between microsatellite-stable (MSS) and microsatellite-unstable HNPCC remains poorly understood. The study was to compare overall copy number variation (CNV) and loss of heterozygosity (LOH) of the entire genome in HNPCCs with MSS and microsatellite-instability (MSI) using the Cytoscan HD Array. This was a study carried out in samples from 20 patients with MSS HNPCC and four patients with MSI HNPCC from the Fudan University Shanghai Cancer Center (China)...
January 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27885507/erratum-to-genomic-and-functional-features-of-the-biosurfactant-producing-bacillus-sp-am13
#20
Shraddha Shaligram, Shreyas V Kumbhare, Dhiraj P Dhotre, Manohar G Muddeshwar, Atya Kapley, Neetha Joseph, Hemant J Purohit, Yogesh S Shouche, Shrikant P Pawar
No abstract text is available yet for this article.
January 2017: Functional & Integrative Genomics
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