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BMC Genomics

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https://www.readbyqxmd.com/read/28228130/transcriptome-of-the-floral-transition-in-rosa-chinensis-old-blush
#1
Xuelian Guo, Chao Yu, Le Luo, Huihua Wan, Ni Zhen, Tingliang Xu, Jiongrui Tan, Huitang Pan, Qixiang Zhang
BACKGROUND: The floral transition plays a vital role in the life of ornamental plants. Despite progress in model plants, the molecular mechanisms of flowering regulation remain unknown in perennial plants. Rosa chinensis 'Old Blush' is a unique plant that can flower continuously year-round. In this study, gene expression profiles associated with the flowering transition were comprehensively analyzed during floral transition in the rose. RESULTS: According to the transcriptomic profiles, 85,663 unigenes and 1,637 differentially expressed genes (DEGs) were identified, among which 32 unigenes were involved in the circadian clock, sugar metabolism, hormone, and autonomous pathways...
February 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28228125/rna-seq-of-life-stages-of-the-oomycete-phytophthora-infestans-reveals-dynamic-changes-in-metabolic-signal-transduction-and-pathogenesis-genes-and-a-major-role-for-calcium-signaling-in-development
#2
Audrey M V Ah-Fong, Kyoung Su Kim, Howard S Judelson
BACKGROUND: The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS: RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P...
February 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28222695/evolution-and-expression-of-the-fructokinase-gene-family-in-saccharum
#3
Yihong Chen, Qing Zhang, Weichang Hu, Xingtan Zhang, Liming Wang, Xiuting Hua, Qingyi Yu, Ray Ming, Jisen Zhang
BACKGROUND: Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. RESULTS: In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S...
February 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219347/aquaculture-genomics-genetics-and-breeding-in-the-united-states-current-status-challenges-and-priorities-for-future-research
#4
EDITORIAL
Hisham Abdelrahman, Mohamed ElHady, Acacia Alcivar-Warren, Standish Allen, Rafet Al-Tobasei, Lisui Bao, Ben Beck, Harvey Blackburn, Brian Bosworth, John Buchanan, Jesse Chappell, William Daniels, Sheng Dong, Rex Dunham, Evan Durland, Ahmed Elaswad, Marta Gomez-Chiarri, Kamal Gosh, Ximing Guo, Perry Hackett, Terry Hanson, Dennis Hedgecock, Tiffany Howard, Leigh Holland, Molly Jackson, Yulin Jin, Karim Kahlil, Thomas Kocher, Tim Leeds, Ning Li, Lauren Lindsey, Shikai Liu, Zhanjiang Liu, Kyle Martin, Romi Novriadi, Ramjie Odin, Yniv Palti, Eric Peatman, Dina Proestou, Guyu Qin, Benjamin Reading, Caird Rexroad, Steven Roberts, Mohamed Salem, Andrew Severin, Huitong Shi, Craig Shoemaker, Sheila Stiles, Suxu Tan, Kathy F J Tang, Wilawan Thongda, Terrence Tiersch, Joseph Tomasso, Wendy Tri Prabowo, Roger Vallejo, Hein van der Steen, Khoi Vo, Geoff Waldbieser, Hanping Wang, Xiaozhu Wang, Jianhai Xiang, Yujia Yang, Roger Yant, Zihao Yuan, Qifan Zeng, Tao Zhou
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219344/origin-and-phylogenetic-status-of-the-local-ashanti-dwarf-pig-adp-of-ghana-based-on-genetic-analysis
#5
Richard Osei-Amponsah, Benjamin M Skinner, Dennis O Adjei, Julien Bauer, Greger Larson, Nabeel A Affara, Carole A Sargent
BACKGROUND: The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. RESULTS: The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219342/effects-of-exposure-to-streptococcus-iniae-on-microrna-expression-in-the-head-kidney-of-genetically-improved-farmed-tilapia-oreochromis-niloticus
#6
Jun Qiang, Fanyi Tao, Jie He, Lanyi Sun, Pao Xu, Wenjin Bao
BACKGROUND: Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219341/integrating-genetic-maps-in-bambara-groundnut-vigna-subterranea-l-verdc-and-their-syntenic-relationships-among-closely-related-legumes
#7
Wai Kuan Ho, Hui Hui Chai, Presidor Kendabie, Nariman Salih Ahmad, Jaeyres Jani, Festo Massawe, Andrzej Kilian, Sean Mayes
BACKGROUND: Bambara groundnut [Vigna subterranea (L) Verdc.] is an indigenous legume crop grown mainly in subsistence and small-scale agriculture in sub-Saharan Africa for its nutritious seeds and its tolerance to drought and poor soils. Given that the lack of ex ante sequence is often a bottleneck in marker-assisted crop breeding for minor and underutilised crops, we demonstrate the use of limited genetic information and resources developed within species, but linked to the well characterised common bean (Phaseolus vulgaris) genome sequence and the partially annotated closely related species; adzuki bean (Vigna angularis) and mung bean (Vigna radiata)...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219339/deep-illumina-sequencing-reveals-conserved-and-novel-micrornas-in-grass-carp-in-response-to-grass-carp-reovirus-infection
#8
Libo He, Aidi Zhang, Pengfei Chu, Yongming Li, Rong Huang, Lanjie Liao, Zuoyan Zhu, Yaping Wang
BACKGROUND: The grass carp hemorrhagic disease caused by the grass carp reovirus (GCRV) is a major disease that hampers the development of grass carp aquaculture. The mechanism underlying GCRV pathogenesis and hemorrhagic symptoms is still unknown. MicroRNAs (miRNAs) are key regulators involved in various biological processes. The aim of this study was to identify conserved and novel miRNAs in grass carp in response to GCRV infection, as well as attempt to reveal the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28219337/chronic-nicotine-differentially-affects-murine-transcriptome-profiling-in-isolated-cortical-interneurons-and-pyramidal-neurons
#9
Jie Yang, Ai-Yi Liu, Bo Tang, Dong Luo, Yu-Jie Lai, Bing-Lin Zhu, Xue-Feng Wang, Zhen Yan, Guo-Jun Chen
BACKGROUND: Nicotine is known to differentially regulate cortical interneuron and pyramidal neuron activities in the neocortex, while the underlying molecular mechanisms have not been well studied. In this study, RNA-sequencing was performed in acutely isolated cortical somatostatin (Sst)- positive interneurons and pyramidal neurons (Thy1) from mice treated with systemic nicotine for 14 days. We assessed the differentially expressed genes (DEGs) by nicotine in Sst- or Thy1- neurons, respectively, and then compared DEGs between Sst- and Thy1- neurons in the absence and presence of nicotine...
February 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212627/genome-wide-identification-of-direct-hbx-genomic-targets
#10
Francesca Guerrieri, Laura Belloni, Daniel D'Andrea, Natalia Pediconi, Loredana Le Pera, Barbara Testoni, Cecilia Scisciani, Oceane Floriot, Fabien Zoulim, Anna Tramontano, Massimo Levrero
BACKGROUND: The Hepatitis B Virus (HBV) HBx regulatory protein is required for HBV replication and involved in HBV-related carcinogenesis. HBx interacts with chromatin modifying enzymes and transcription factors to modulate histone post-translational modifications and to regulate viral cccDNA transcription and cellular gene expression. Aiming to identify genes and non-coding RNAs (ncRNAs) directly targeted by HBx, we performed a chromatin immunoprecipitation sequencing (ChIP-Seq) to analyse HBV recruitment on host cell chromatin in cells replicating HBV...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212626/a-global-characterization-of-the-translational-and-transcriptional-programs-induced-by-methionine-restriction-through-ribosome-profiling-and-rna-seq
#11
Ke Zou, Qi Ouyang, Hao Li, Jiashun Zheng
BACKGROUND: Among twenty amino acids, methionine has a special role as it is coded by the translation initiation codon and methionyl-tRNAi (Met-tRNAi) is required for the assembly of the translation initiation complex. Thus methionine may play a special role in global gene regulation. Methionine has also been known to play important roles in cell growth, development, cancer, and aging. In this work, we characterize the translational and transcriptional programs induced by methionine restriction (MetR) and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212624/understanding-the-response-to-endurance-exercise-using-a-systems-biology-approach-combining-blood-metabolomics-transcriptomics-and-mirnomics-in-horses
#12
Núria Mach, Yuliaxis Ramayo-Caldas, Allison Clark, Marco Moroldo, Céline Robert, Eric Barrey, Jesús Maria López, Laurence Le Moyec
BACKGROUND: Endurance exercise in horses requires adaptive processes involving physiological, biochemical, and cognitive-behavioral responses in an attempt to regain homeostasis. We hypothesized that the identification of the relationships between blood metabolome, transcriptome, and miRNome during endurance exercise in horses could provide significant insights into the molecular response to endurance exercise. For this reason, the serum metabolome and whole-blood transcriptome and miRNome data were obtained from ten horses before and after a 160 km endurance competition...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212614/transcriptomic-profiling-provides-molecular-insights-into-hydrogen-peroxide-induced-adventitious-rooting-in-mung-bean-seedlings
#13
Shi-Weng Li, Yan Leng, Rui-Fang Shi
BACKGROUND: Hydrogen peroxide (H2O2) has been known to function as a signalling molecule involved in the modulation of various physiological processes in plants. H2O2 has been shown to act as a promoter during adventitious root formation in hypocotyl cuttings. In this study, RNA-Seq was performed to reveal the molecular mechanisms underlying H2O2-induced adventitious rooting. RESULTS: RNA-Seq data revealed that H2O2 treatment greatly increased the numbers of clean reads and expressed genes and abundance of gene expression relative to the water treatment...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212611/impact-of-novel-snps-identified-in-cynara-cardunculus-genes-on-functionality-of-proteins-regulating-phenylpropanoid-pathway-and-their-association-with-biological-activities
#14
Ana Margarida Ferro, Patrícia Ramos, Olinda Guerreiro, Eliana Jerónimo, Inês Pires, Carmen Capel, Juan Capel, Rafael Lozano, Maria F Duarte, M Margarida Oliveira, Sónia Gonçalves
BACKGROUND: Cynara cardunculus L. offers a natural source of phenolic compounds with the predominant molecule being chlorogenic acid. Chlorogenic acid is gaining interest due to its involvement in various biological properties such as, antibacterial, antifungal, antioxidant, hepatoprotective, and anticarcinogenic activities. RESULTS: In this work we screened a Cynara cardunculus collection for new allelic variants in key genes involved in the chlorogenic acid biosynthesis pathway...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212609/exogenous-glutamate-rapidly-induces-the-expression-of-genes-involved-in-metabolism-and-defense-responses-in-rice-roots
#15
Chia-Cheng Kan, Tsui-Yun Chung, Hsin-Yu Wu, Yan-An Juo, Ming-Hsiun Hsieh
BACKGROUND: Glutamate is an active amino acid. In addition to protein synthesis and metabolism, increasing evidence indicates that glutamate may also function as a signaling molecule in plants. Still, little is known about the nutritional role of glutamate and genes that are directly regulated by glutamate in rice. RESULTS: Exogenous glutamate could serve as a nitrogen nutrient to support the growth of rice seedlings, but it was not as effective as ammonium nitrate or glutamine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212608/transcriptomic-dynamics-of-breast-cancer-progression-in-the-mmtv-pymt-mouse-model
#16
Ying Cai, Ruben Nogales-Cadenas, Quanwei Zhang, Jhih-Rong Lin, Wen Zhang, Kelly O'Brien, Cristina Montagna, Zhengdong D Zhang
BACKGROUND: Malignant breast cancer with complex molecular mechanisms of progression and metastasis remains a leading cause of death in women. To improve diagnosis and drug development, it is critical to identify panels of genes and molecular pathways involved in tumor progression and malignant transition. Using the PyMT mouse, a genetically engineered mouse model that has been widely used to study human breast cancer, we profiled and analyzed gene expression from four distinct stages of tumor progression (hyperplasia, adenoma/MIN, early carcinoma and late carcinoma) during which malignant transition occurs...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212602/happi-2-a-comprehensive-and-high-quality-map-of-human-annotated-and-predicted-protein-interactions
#17
Jake Y Chen, Ragini Pandey, Thanh M Nguyen
BACKGROUND: Human protein-protein interaction (PPI) data is essential to network and systems biology studies. PPI data can help biochemists hypothesize how proteins form complexes by binding to each other, how extracellular signals propagate through post-translational modification of de-activated signaling molecules, and how chemical reactions are coupled by enzymes involved in a complex biological process. Our capability to develop good public database resources for human PPI data has a direct impact on the quality of future research on genome biology and medicine...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28209181/de-novo-sequencing-and-comparative-transcriptome-analysis-of-adventitious-root-development-induced-by-exogenous-indole-3-butyric-acid-in-cuttings-of-tetraploid-black-locust
#18
Jine Quan, Seng Meng, Erhui Guo, Sheng Zhang, Zhong Zhao, Xitian Yang
BACKGROUND: Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28209138/using-whole-genome-sequencing-to-investigate-transmission-in-a-multi-host-system-bovine-tuberculosis-in-new-zealand
#19
Joseph Crispell, Ruth N Zadoks, Simon R Harris, Brent Paterson, Desmond M Collins, Geoffrey W de-Lisle, Paul Livingstone, Mark A Neill, Roman Biek, Samantha J Lycett, Rowland R Kao, Marian Price-Carter
BACKGROUND: Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28209133/house-spider-genome-uncovers-evolutionary-shifts-in-the-diversity-and-expression-of-black-widow-venom-proteins-associated-with-extreme-toxicity
#20
Kerry L Gendreau, Robert A Haney, Evelyn E Schwager, Torsten Wierschin, Mario Stanke, Stephen Richards, Jessica E Garb
BACKGROUND: Black widow spiders are infamous for their neurotoxic venom, which can cause extreme and long-lasting pain. This unusual venom is dominated by latrotoxins and latrodectins, two protein families virtually unknown outside of the black widow genus Latrodectus, that are difficult to study given the paucity of spider genomes. Using tissue-, sex- and stage-specific expression data, we analyzed the recently sequenced genome of the house spider (Parasteatoda tepidariorum), a close relative of black widows, to investigate latrotoxin and latrodectin diversity, expression and evolution...
February 16, 2017: BMC Genomics
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