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BMC Genomics

Peter A Noble, Alexander E Pozhitkov
BACKGROUND: Our previous study found that more than 500 transcripts significantly increased in abundance in the zebrafish and mouse several hours to days postmortem relative to live controls. The current literature suggests that most mRNAs are post-transcriptionally regulated in stressful conditions. We rationalized that the postmortem transcripts must contain sequence features (3- to 9- mers) that are unique from those in the rest of the transcriptome and that these features putatively serve as binding sites for proteins and/or non-coding RNAs involved in post-transcriptional regulation...
September 14, 2018: BMC Genomics
Wei Wei, Kai Chen, Wei Miao, Wentao Yang, Jie Xiong
BACKGROUND: Pseudocohnilembus persalinus, a unicellular ciliated protozoan, is one of commonest facultative pathogens. We sequenced the macronuclear genome of P. persalinus in 2015, which provided new insights into its pathogenicity. RESULTS: Here, we present the P. persalinus genome database (PPGD) ( ), the first genome database for the scuticociliatosis pathogens. PPGD integrates P. persalinus macronuclear genomic and transcriptomic data, including genome sequence, transcript, gene expression data, and gene annotation, as well as relevant information on its biology, morphology and taxonomy...
September 14, 2018: BMC Genomics
Hong-Ai Su, Xue Bai, Tian Zeng, Yong-Yue Lu, Yi-Xiang Qi
BACKGROUND: Members of the transient receptor potential (TRP) superfamily are proteins that are critical for insects to detect changes in environmental stimuli and also play key roles in their sensory physiology. Moreover, this family provides potential targets for the design of insecticides. In contrast to a large number of studies conducted on Drosophila melanogaster, molecular studies to characterize TRP channels in agricultural pests are lacking. RESULTS: In this study, we identified 15 TRP channel genes in the genome of a notorious agricultural pest, the oriental fruit fly (Bactrocera dorsalis)...
September 14, 2018: BMC Genomics
Paula Moolhuijzen, Pao Theen See, James K Hane, Gongjun Shi, Zhaohui Liu, Richard P Oliver, Caroline S Moffat
September 13, 2018: BMC Genomics
Linfeng Chen, Xianlong Ding, Hao Zhang, Tingting He, Yanwei Li, Tanliu Wang, Xiaoqiang Li, Ling Jin, Qijian Song, Shouping Yang, Junyi Gai
BACKGROUND: Cytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which play crucial roles in microRNAs (miRNAs) function and post-transcription control. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput deep sequencing coupled with RNase R enrichment strategy was conducted...
September 12, 2018: BMC Genomics
Zhenyi Wang, Kanglu Zhao, Yuxin Pan, Jinpeng Wang, Xiaoming Song, Weina Ge, Min Yuan, Tianyu Lei, Li Wang, Lan Zhang, Yuxian Li, Tao Liu, Wei Chen, Wenjing Meng, Changkai Sun, Xiaobo Cui, Yun Bai, Xiyin Wang
BACKGROUND: Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional domains. RESULTS: As to sequence divergence, TTF genes were previously divided into five subfamilies, I-V. We found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years' evolution...
September 12, 2018: BMC Genomics
Chongjing Xia, Meinan Wang, Chuntao Yin, Omar E Cornejo, Scot H Hulbert, Xianming Chen
BACKGROUND: Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, especially at the forma specialis level, remains unclear. RESULTS: We sequenced two isolates each representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), different formae speciales of the stripe rust fungus P...
September 12, 2018: BMC Genomics
Francesca Fanelli, Vania Cosma Liuzzi, Antonio Francesco Logrieco, Claudio Altomare
BACKGROUND: So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus Trichoderma, the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions...
September 11, 2018: BMC Genomics
Huiru Sun, Pengbo Hao, Qiang Ma, Meng Zhang, Yuan Qin, Hengling Wei, Junji Su, Hantao Wang, Lijiao Gu, Nuohan Wang, Guoyuan Liu, Shuxun Yu
BACKGROUND: Pectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC, a cell wall modification enzyme, degrades de-esterified pectin for cell wall loosening, remodeling and rearrangement. Nevertheless, there have been few studies on PEL genes and no comprehensive analysis of the PEL gene family in cotton. RESULTS: We identified 53, 42 and 83 putative PEL genes in Gossypium raimondii (D5), Gossypium arboreum (A2), and Gossypium hirsutum (AD1), respectively...
September 10, 2018: BMC Genomics
Yanan Cao, Xiaowei Gao, Yue Yang, Zhi Ye, E Wang, Zhitao Dong
BACKGROUND: To explore long non-coding RNA (lncRNA), mRNA and circular RNA (circRNA) expression profiles and their biological functions in the pathogenesis of kidney stones in ethylene glycol-induced urolithiasis rats. RESULTS: The expression of 1440 lncRNAs, 2455 mRNAs and 145 circRNAs was altered in the kidneys of urolithiasis rats. GO and KEGG biological pathway analysis were performed to predict the functions of differentially expressed lncRNAs, circRNAs and co-expressed potential targeting genes...
September 10, 2018: BMC Genomics
Alexessander Couto Alves, Craig A Glastonbury, Julia S El-Sayed Moustafa, Kerrin S Small
BACKGROUND: Intermittent fasting and time-restricted diets are associated with lower risk biomarkers for cardio-metabolic disease. The shared mechanisms underpinning the similar physiological response to these events is not established, but circadian rhythm could be involved. Here we investigated the transcriptional response to fasting in a large cross-sectional study of adipose and skin tissue from healthy volunteers (N = 625) controlling for confounders of circadian rhythm: time of day and season...
September 7, 2018: BMC Genomics
Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund, Goutam Sahana
BACKGROUND: Improving resistance to mastitis, one of the costliest diseases in dairy production, has become an important objective in dairy cattle breeding. However, mastitis resistance is influenced by many genes involved in multiple processes, including the response to infection, inflammation, and post-infection healing. Low genetic heritability, environmental variations, and farm management differences further complicate the identification of links between genetic variants and mastitis resistance...
September 6, 2018: BMC Genomics
Mario Tello, Felipe Avalos, Omar Orellana
BACKGROUND: Small RNAs (sRNAs) are key regulators of gene expression in bacteria. In addition to modulating translation initiation, sRNAs can interact with mRNA coding regions to regulate mRNA stability and translation efficiency, enhancing or impeding progression of the ribosome along the mRNA. Since most amino acids are decoded by more than one codon (synonymous) we asked as to whether there is a codon bias in the interaction of sRNAs with coding regions of mRNAs. Therefore, we explored whether there are differences in codon usage or tRNA availability according to whether an mRNA is regulated by sRNAs or not...
September 6, 2018: BMC Genomics
Nicole Liechti, Nadia Schürch, Rémy Bruggmann, Matthias Wittwer
BACKGROUND: Members of the genus Naegleria are free-living eukaryotes with the capability to transform from the amoeboid form into resting cysts or moving flagellates in response to environmental conditions. More than 40 species have been characterized, but only Naegleria fowleri (N. fowleri) is known as a human pathogen causing primary amoebic meningoencephalitis (PAM), a fast progressing and mostly fatal disease of the central nervous system. Several studies report an involvement of phospholipases and other molecular factors, but the mechanisms involved in pathogenesis are still poorly understood...
September 5, 2018: BMC Genomics
Lyudmila V Dergunova, Ivan B Filippenkov, Vasily V Stavchansky, Alina E Denisova, Vadim V Yuzhakov, Sergey A Mozerov, Leonid V Gubsky, Svetlana A Limborska
BACKGROUND: The transient middle cerebral artery occlusion (tMCAO) model is used for studying the molecular mechanisms of ischemic damage and neuroprotection. Numerous studies have demonstrated the role of individual genes and associated signaling pathways in the pathogenesis of ischemic stroke. Here, the tMCAO model was used to investigate the genome-wide response of the transcriptome of rat brain tissues to the damaging effect of ischemia and subsequent reperfusion. RESULTS: Magnetic resonance imaging and histological examination showed that the model of focal ischemia based on endovascular occlusion of the right middle cerebral artery for 90 min using a monofilament, followed by restoration of the blood flow, led to reproducible localization of ischemic damage in the subcortical structures of the brain...
September 5, 2018: BMC Genomics
Alina Ott, James C Schnable, Cheng-Ting Yeh, Linjiang Wu, Chao Liu, Heng-Cheng Hu, Clifton L Dalgard, Soumik Sarkar, Patrick S Schnable
BACKGROUND: Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for large, complex and polyploid genomes. The linked read strategy has the potential to enhance the value of short reads for genome assembly because all reads originating from a single long molecule of DNA share a common barcode. However, the majority of studies to date that have employed linked reads were focused on human haplotype phasing and genome assembly...
September 4, 2018: BMC Genomics
Seokhyun Yoon, Daeseung Kim, Keunsoo Kang, Woong June Park
BACKGROUND: The challenges when developing a good de novo transcriptome assembler include how to deal with read errors and sequence repeats. Almost all de novo assemblers utilize a de Bruijn graph, with which complexity grows linearly with data size while suffering from errors and repeats. Although one can correct the errors by inspecting the topological structure of the graph, this is not an easy task when there are too many branches. Two research directions are to improve either the graph reliability or the path search precision, and in this study, we focused on the former...
September 4, 2018: BMC Genomics
Vikas C Ghattargi, Meghana A Gaikwad, Bharati S Meti, Yogesh S Nimonkar, Kunal Dixit, Om Prakash, Yogesh S Shouche, Shrikant P Pawar, Dhiraj P Dhotre
BACKGROUND: Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. RESULTS: E...
September 4, 2018: BMC Genomics
Gulden Olgun, Ozgur Sahin, Oznur Tastan
BACKGROUND: Long non-coding RNAs (lncRNAs) can indirectly regulate mRNAs expression levels by sequestering microRNAs (miRNAs), and act as competing endogenous RNAs (ceRNAs) or as sponges. Previous studies identified lncRNA-mediated sponge interactions in various cancers including the breast cancer. However, breast cancer subtypes are quite distinct in terms of their molecular profiles; therefore, ceRNAs are expected to be subtype-specific as well. RESULTS: To find lncRNA-mediated ceRNA interactions in breast cancer subtypes, we develop an integrative approach...
September 4, 2018: BMC Genomics
Steven M Sanders, Zhiwei Ma, Julia M Hughes, Brooke M Riscoe, Gregory A Gibson, Alan M Watson, Hakima Flici, Uri Frank, Christine E Schnitzler, Andreas D Baxevanis, Matthew L Nicotra
BACKGROUND: Hydractinia symbiolongicarpus, a colonial cnidarian, is a tractable model system for many cnidarian-specific and general biological questions. Until recently, tests of gene function in Hydractinia have relied on laborious forward genetic approaches, randomly integrated transgenes, or transient knockdown of mRNAs. RESULTS: Here, we report the use of CRISPR/Cas9 genome editing to generate targeted genomic insertions in H. symbiolonigcarpus. We used CRISPR/Cas9 to promote homologous recombination of two fluorescent reporters, eGFP and tdTomato, into the Eukaryotic elongation factor 1 alpha (Eef1a) locus...
September 3, 2018: BMC Genomics
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