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Yu Liu, Pei-Dong Wu, Dai-Zhen Zhang, Hua-Bin Zhang, Bo-Ping Tang, Qiu-Ning Liu, Li-Shang Dai
The mitochondrial genome (mitogenome) can provide important information for understanding phylogenetic analysis and thus molecular evolution. Herein, we amplified the complete mitogenome sequence of Pelteobagrus fulvidraco. The mitogenome was 16,526 bp in length and included 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and a non-coding control region (D-loop). Both the organization and location of genes in the mitogenome were consistent with those from Siluriformes fishes previously published in GenBank...
August 14, 2018: Genomics
Jiao Gong, Tingcai Cheng, Yuqian Wu, Xi Yang, Qili Feng, Kazuei Mita
Spodoptera litura is a polyphagous pest and can feed on >100 species of plants, causing great damage to agricultural production. The SNP results showed that there were gene exchanges between different regions. To explore the variations of larger segments in S. litura genome, we used genome resequencing samples from 14 regions of China, India, and Japan to study the copy number variations (CNVs). We identified 3976 CNV events and 1581 unique copy number variation regions (CNVRs) occupying the 108.5 Mb genome of S...
August 13, 2018: Genomics
Jun Li, Yaqi Zhao, Ruirui Lin, Yaoyao Zhang, Kunjie Hu, Yan Li, Zhuoran Huang, Shuying Peng, Jianhua Ding, Xuexia Geng, Haijun Zhang, Xu Zhang
In this study, mitogenome of Somena scintillans (Lepidoptera: Erebidae) were sequenced and compared with other Noctuoidea species. The mitogenome is 15,410 base pairs in length. All 13 protein-coding genes (PCGs) are initiated by ATN codons except cox1 with CGA and all of PCGs terminate with TAA except nad4 with TAG. The codons ACG and CGC are absent. All the tRNA genes could be folded into the typical cloverleaf secondary structure except the trnS1 which not only lose dihydrouridine (DHU) arm but also mutate its anticodon into TCT...
August 12, 2018: Genomics
Huihui Xu, Malcolm Whiteway, Linghuo Jiang
Through a genetic screen we have identified 21 genes whose inactivation renders Candida albicans cells sensitive to high levels of extracellular calcium. These genes are involved in the tricarboxylic acid cycle, cell wall integrity pathway, cytokinesis, intracellular pH homeostasis, magnesium transport, as well as DNA damage response and repair processes. The calcium sensitivity due to inactivation of nine of these genes can be partially or completely suppressed by cyclosporine A, an inhibitor of calcineurin...
August 10, 2018: Genomics
Varun B Dwaraka, Jeramiah J Smith, M Ryan Woodcock, S Randal Voss
Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model - Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 h post amputation...
August 6, 2018: Genomics
Kai Cui, Wujiao Li, Jake George James, Changjun Peng, Jiazheng Jin, Chaochao Yan, Zhenxin Fan, Lianming Du, Megan Price, Yongjie Wu, Bisong Yue
The monal genus (Lophophorus) is a branch of Phasianidae and its species inhabit the high-altitude mountains of the Qinghai-Tibet Plateau. The Chinese monal, L. lhuysii, is a threatened endemic bird of China that possesses high-altitude adaptability, diversity of plumage color and potentially low reproductive life history. This is the first study to describe the monal genome using next generation sequencing technology. The Chinese monal genome size is 1.01 Gb, with 16,940 protein-coding genes. Gene annotation yielded 100...
July 29, 2018: Genomics
Md Siddiqur Rahman, Usma Aktar, Md Rafsan Jani, Swakkhar Shatabda
Sigma promoter sequences in bacterial genomes are important due to their role in transcription initiation. Sigma 70 is one of the most important and crucial sigma factors. In this paper, we address the problem of identification of σ70 promoter sequences in bacterial genome. We propose iPromoter-FSEn, a novel predictor for identification of σ70 promoter sequences. Our proposed method is based on a feature subspace based ensemble classifier. A large set of of features extracted from the sequence of nucleotides are divided into subsets and each subset is given to individual single classifiers to learn...
July 29, 2018: Genomics
Guoqing Liu, Guo-Jun Liu, Jiu-Xin Tan, Hao Lin
The nucleosome is the fundamental structural unit of eukaryotic chromatin and plays an essential role in the epigenetic regulation of cellular processes, such as DNA replication, recombination, and transcription. Hence, it is important to identify nucleosome positions in the genome. Our previous model based on DNA deformation energy, in which a set of DNA physical descriptors was used, performed well in predicting nucleosome dyad positions and occupancy. In this study, we established a machine-learning model for predicting nucleosome occupancy in order to further verify the physical descriptors...
July 26, 2018: Genomics
Jie Liu, Guoxian Yu, Yazhou Ren, Maozu Guo, Jun Wang
Single nucleotide polymorphism (SNP) interactions can explain the missing heritability of common complex diseases. Many interaction detection methods have been proposed in genome-wide association studies, and they can be divided into two types: population-based and family-based. Compared with population-based methods, family-based methods are robust vs. population stratification. Several family-based methods have been proposed, among which Multifactor Dimensionality Reduction (MDR)-based methods are popular and powerful...
July 25, 2018: Genomics
Yao Ming, Jianbo Jian, Fei Yu, Xueying Yu, Jingzhen Wang, Wenhua Liu
The Indo-Pacific humpback dolphin, Sousa chinensis, being a member of cetaceans, had fully adapted to inshore waters. As a threatened marine mammal, little molecular information available for understanding the genetic basis of ecological adaptation. We firstly sequenced and obtained the draft genome map of S. chinensis. Phylogenetic analysis in this study, based on the single copy orthologous genes of the draft genome, is consistent with traditional phylogenetic classification. The comparative genomic analysis indicated that S...
July 20, 2018: Genomics
Wei Shen, Hui Li, Ruimin Teng, Yongxin Wang, Wenli Wang, Jing Zhuang
Tea plant (Camellia sinensis (L.) O. Kuntze) is a perennial evergreen woody plant, and its leaves contain various beneficial ingredients and have healthy efficacy. HD-Zip (homeodomain-leucine zipper) transcription factors (TFs) are widely distributed in plants and play an important role in plant growth and environmental response. To date, knowledge on HD-Zip gene family in tea plant is still limited. In this study, 33 HD-Zip TFs were selected based on the genomic and transcriptomic databases of tea plant. The conserved domains and common motifs of these TFs were predicted and analyzed...
July 19, 2018: Genomics
Mirzakamol S Ayubov, Mukhammad H Mirzakhmedov, Venkateswara R Sripathi, Zabardast T Buriev, Khurshida A Ubaydullaeva, Dilshod E Usmonov, Risolat B Norboboyeva, Chandrakanth Emani, Siva Prasad Kumpatla, Ibrokhim Y Abdurakhmonov
Small RNAs (sRNAs) are short, non-coding, 17-24 nucleotides long RNA molecules that play vital roles in regulating gene expression in every known organism investigated to date including cotton (Gossypium ssp.). These tiny RNA molecules target diverse categories of genes from different bioliogical and metabolic processes and have been reported in the three domains of life. Small RNAs, including miRNAs, are involved in ovule and fiber development, biotic and abiotic stresses, fertility, and other biochemical processes in cotton species...
July 17, 2018: Genomics
Qi Zhang, Shiyuan Wang, Yi Pan, Dongqing Su, Qianzi Lu, Yongchun Zuo, Lei Yang
Knowing the comprehensive knowledge about the protein subcellular localization is an important step to understand the function of the proteins. Recent advances in system biology have allowed us to develop more accurate methods for characterizing the proteins at subcellular localization level. In this study, the analysis method was developed to characterize the topological properties and biological properties of the cytoplasmic proteins, inner membrane proteins, outer membrane proteins and periplasmic proteins in Escherichia coli (E...
July 17, 2018: Genomics
Zhongxue Chen, Qingzhong Liu, Kai Wang
Gene- and pathway-based variant association tests are important tools in finding genetic variants that are associated with phenotypes of interest. Although some methods have been proposed in the literature, powerful and robust statistical tests are still desirable in this area. In this study, we propose a statistical test based on decomposing the genotype data into orthogonal parts from which powerful and robust independent p-value combination approaches can be utilized. Through a comprehensive simulation study, we compare the proposed test with some existing popular ones...
July 16, 2018: Genomics
Yaqing Xu, Mengyun Wu, Qingzhao Zhang, Shuangge Ma
Gene-environment (G-E) interactions have important implications for the etiology and progression of many complex diseases. Compared to continuous markers and categorical disease status, prognosis has been less investigated, with the additional challenges brought by the unique characteristics of survival outcomes. Most of the existing G-E interaction approaches for prognosis data share the limitation that they cannot accommodate long-tailed or contaminated outcomes. In this study, for prognosis data, we develop a robust G-E interaction identification approach using the censored quantile partial correlation (CQPCorr) technique...
July 16, 2018: Genomics
Lu Bao, Yonghen Zhang, Xing Gu, Yuefang Gao, Youben Yu
Zygaenidae comprises >1036 species, including many folivorous pests in agriculture. In the present study, the complete mitochondrial genome (mitogenome) of a major pest of tea trees, Eterusia aedea was determined. The 15,196-bp circular genome contained the common set of 37 mitochondrial genes (including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and exhibited the similar genomic features to reported Zygaenidae mitogenome. Comparative analyses of Zygaenidae mitogenomes showed a typical evolutionary trend of lepidopteran mitogenomes...
July 12, 2018: Genomics
Usha R Dutta, Sudha N Rao, Vijaya Kumar Pidugu, Vineeth V S, Amrita Bhattacherjee, Aneek Das Bhowmik, Sathish K Ramaswamy, Kumar Gautam Singh, Ashwin Dalal
Disease associated chromosomal rearrangements often have break points located within disease causing genes or in their vicinity. The purpose of this study is to characterize a balanced reciprocal translocation in a girl with intellectual disability and seizures by positional cloning and whole genome sequencing. The translocation was identification by G- banding and confirmed by WCP FISH. Fine mapping using BAC clones and whole genome sequencing using Oxford nanopore long read sequencing technology for a 1.46 X coverage of the genome was done...
July 10, 2018: Genomics
Gowdham Manivel, Arun Meyyazhagan, Ruban Durairaj D, Shanmughavel Piramanayagam
Trypanosoma brucei brucei (T.b.brucei) is an extra-cellular parasite that causes Animal African Trypanosomiasis (AAT) disease in animals. Till day, this disease is more difficult to treat and control due to lack of efficient vaccines and early diagnosis of the parasite infection. T.b.brucei Excretory/Secretory (ES) proteins were involved in pathogenesis and key for understanding the host-parasite interactions. Functions of T.b.brucei's ES proteins were poorly investigated and experimental identification is expensive and time-consuming...
July 10, 2018: Genomics
Jung-A Kim, Neha Samir Roy, Inn-Hye Lee, Ah-Young Choi, Beom-Soon Choi, Yei-Soo Yu, Nam-Il Park, Kyong-Cheul Park, Soonok Kim, Hee-Sun Yang, Ik-Young Choi
High-throughput RNA sequencing has revolutionized transcriptome-based studies of candidate genes, key pathways and gene regulation in non-model organisms. We analyzed full-length cDNA sequences in Zanthoxylum planispinum (Z. planispinum), a medicinal herb in major parts of East Asia. The full-length mRNA derived from tissues of leaf, early fruit and maturing fruit stage were sequenced using PacBio RSII platform to identify isoform transcriptome. We obtained 51,402 unigenes, with average 1781 bp per gene in 82...
July 10, 2018: Genomics
Yu Lin, Lili Xiao, Yiyuan Zhang, Ping Li, Yinsheng Wu, Yanping Lin
BACKGROUND: Understanding of the molecular mechanisms of miRNAs involved in osteoblast differentiation is important for the treatment of bone-related diseases. METHODS: MC3T3-E1 cells were induced to osteogenic differentiation by culturing with bone morphogenetic protein 2 (BMP2). After transfected with miR-26b-3p mimics or inhibitors, the osteogenic differentiation of MC3T3-E1 cells was detected by ALP and ARS staining. Cell viability was analyzed by MTT. The expressions of miR-26b-3p and osteogenic related markers and signaling were examined by qPCR and western blot...
July 5, 2018: Genomics
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