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Guilherme de Jong, Andrezza Kellen Alves Pamplona, Renzo Garcia Von Pinho, Marcio Balestre
The identification of causal regions associated with resistance to Fusarium verticillioides can be useful to understand resistance mechanisms and further be used in breeding programs. In this study, a genome-wide association study (GWAS) was conducted to identify candidate markers associated with resistance to the ear rot caused by the fungus F. verticillioides. A total of 242 maize inbred lines were genotyped with 23,153 DArT-seq markers. A total of 12 DArTs were associated with ear rot resistance. Some DArTs were localized close to genes with functions directly related to ear rot resistance, such as a gene responsible for the innate immune response that belongs to the class of NBS-LRR receptors...
December 6, 2017: Genomics
Qing Song, Wei Xu, Wenzhi Li, Shaohua He, Jiankang Liu, Guangming Wang, Li Ma
Accurate data imputation requires ethnicity-matched reference panels. However, recent admixtures have created mosaic human genomes, different chromosomal segments have different ethnic backgrounds, so it is impossible for a single-ethnicity reference panel to be the matched for data imputation. In this study, we explored a novel strategy for imputation. We created individualized mosaic reference panel for each person according to his/her ethnic backgrounds at each genomic locus. We examined on datasets with 70% missing values on haplotypes and 50% missing values on genotypes...
November 30, 2017: Genomics
Kakali Biswas, Debarun Acharya, Soumita Podder, Tapash Chandra Ghosh
Integrating gene expression into protein-protein interaction network (PPIN) leads to the construction of tissue-specific (TS) and housekeeping (HK) sub-networks, with distinctive TS- and HK-hubs. All such hub proteins are divided into multi-interface (MI) hubs and single-interface (SI) hubs, where MI hubs evolve slower than SI hubs. Here we explored the evolutionary rate difference between MI and SI proteins within TS- and HK-PPIN and observed that this difference is present only in TS, but not in HK-class...
November 30, 2017: Genomics
Jong Seok Kim, Min Jee Kim, Jun Seong Jeong, Iksoo Kim
The complete mitochondrial genome (mitogenome) of Saturnia jonasii (Lepidoptera: Saturniidae) was sequenced and compared to those of 19 other bombycoid species. Furthermore, the mitogenome sequences were used to infer phylogenetic relationships among bombycoid species. The 15,261-bp Saturnia jonasii mitogenome contained the typical sets of genes and gene arrangements found in majority of Lepidoptera. All Bombycoidea species, including Saturnia jonasii, have a 15-33-bp spacer sequence at the trnS2-ND1 junction...
November 27, 2017: Genomics
Subhram Das, Tamal Deb, Nilanjan Dey, Amira S Ashour, D K Bhattacharya, D N Tibarewala
Several proteins and genes are members of families that share a public evolutionary. In order to outline the evolutionary relationships and to recognize conserved patterns, sequence comparison becomes an emerging process. The current work investigates critically the k-mer role in composition vector method for comparing genome sequences. Generally, composition vector methods using k-mer are applied under choice of different value of k to compare genome sequences. For some values of k, results are satisfactory, but for other values of k, results are unsatisfactory...
November 24, 2017: Genomics
Eric A Lewallen, Christopher G Salib, William H Trousdale, Charlotte E Berry, Gabrielle M Hanssen, Joseph X Robin, Meagan E Tibbo, Anthony Viste, Nicolas Reina, Mark E Morrey, Joaquin Sanchez-Sotelo, Arlen D Hanssen, Daniel J Berry, Andre J van Wijnen, Matthew P Abdel
Total knee arthroplasty (TKA) is a durable and reliable procedure to alleviate pain and improve joint function. However, failures related to flexion instability sometimes occur. The goal of this study was to define biological differences between tissues from patients with and without flexion instability of the knee after TKA. Human knee joint capsule tissues were collected at the time of primary or revision TKAs and analyzed by RT-qPCR and RNA-seq, revealing novel patterns of differential gene expression between the two groups...
November 22, 2017: Genomics
Gökhan Karakülah
In recent years, retrotransposons have gained increasing attention as a source of binding motifs for transcription factors (TFs). Despite the substantial roles of these mobile genetic elements in the regulation of gene expression, a comprehensive resource enabling the investigation of retrotransposon species that are bound by TFs is still lacking. Herein, I introduce for the first time a novel database called RTFAdb, which allows exploring computationally predicted associations between retrotransposons and TFs in diverse cell lines and tissues of human and mouse...
November 16, 2017: Genomics
Wang-Ren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Jian-Hua Jia, Kuo-Chen Chou
Lysine crotonylation (Kcr) is an evolution-conserved histone posttranslational modification (PTM), occurring in both human somatic and mouse male germ cell genomes. It is important for male germ cell differentiation. Information of Kcr sites in proteins is very useful for both basic research and drug development. But it is time-consuming and expensive to determine them by experiments alone. Here, we report a novel predictor called iKcr-PseEns that is established by incorporating five tiers of amino acid pairwise couplings into the general pseudo amino acid composition...
October 26, 2017: Genomics
Hu Tao, Qi Xiong, Feng Zhang, Nian Zhang, Yang Liu, Xiaojun Suo, Xiaofeng Li, Qianping Yang, Mingxin Chen
Circular RNAs (circRNAs) are a new class of non-coding RNAs in animals and are a novel target of non-coding RNA (ncRNA) regulation. The mechanism and function of circRNAs have been reported in some species and tissues. However, there is little available information on the functions of circRNAs in the goat reproductive system. In the present study, we deeply sequenced and analyzed circRNAs through bioinformatics to reveal the expression profiles, and predicted 13,950 circRNAs in the pre-ovulatory ovarian follicles of goats for the first time...
October 26, 2017: Genomics
Joanna Ciura, Magdalena Szeliga, Michalina Grzesik, Mirosław Tyrka
Changes in fenugreek transcriptome related to enhanced production of steroids were induced by methyl jasmonate, cholesterol and squalene, and recorded using RNA-seq. A total of 112,850 unigenes were obtained after de novo assembling of next generation sequencing data, and used for functional annotations. In steroidal saponins pathway, transcripts involved in mevalonate, terpenoid backbone and plant sterol synthesis were annotated. Overexpression of several transcripts from phytosterol biosynthesis pathway was confirmed by quantitative RT-PCR...
October 26, 2017: Genomics
Mafalda Faria, Nicola Bordin, Jana Kizina, Jens Harder, Damien Devos, Olga M Lage
Planctomycetes are bacteria with complex molecular and cellular biology. They have large genomes, some over 7Mb, and complex life cycles that include motile cells and sessile cells. Some live on the complex biofilm of macroalgae. Factors governing their life in this environment were investigated at the genomic level. We analyzed the genomes of three planctomycetes isolated from algal surfaces. The genomes were 6.6Mbp to 8.1Mbp large. Genes for outer-membrane proteins, peptidoglycan and lipopolysaccharide biosynthesis were present...
October 23, 2017: Genomics
Chetan K Rane, Misaal Patel, Li Cai, William Senapedis, Erkan Baloglu, Audrey Minden
The p-21 Activated Kinase 4 (PAK4) protein kinase is implicated in many cancers, including breast cancer. Overexpression of PAK4 is sufficient to cause mouse mammary epithelial cells (iMMECs) to become tumorigenic. To gain insight into the long-term gene expression changes that occur downstream to PAK4, we performed Next Generation Sequencing of RNA collected from PAK4 overexpressing iMMECs and wild-type iMMECs. We identified a list of genes whose expression levels were altered in response to PAK4 overexpression in iMMECs...
October 18, 2017: Genomics
Shweta Aggarwal, Arnab Nayek, Dibyabhaba Pradhan, Rashi Verma, Monika Yadav, Kalaiarasan Ponnusamy, Arun Kumar Jain
Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data...
October 12, 2017: Genomics
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Information of the proteins' subcellular localization is crucially important for revealing their biological functions in a cell, the basic unit of life. With the avalanche of protein sequences generated in the postgenomic age, it is highly desired to develop computational tools for timely identifying their subcellular locations based on the sequence information alone. The current study is focused on the Gram-negative bacterial proteins. Although considerable efforts have been made in protein subcellular prediction, the problem is far from being solved yet...
October 6, 2017: Genomics
Bo-Ping Tang, Yu Liu, Zhao-Zhe Xin, Dai-Zhen Zhang, Zheng-Fei Wang, Xiao-Yu Zhu, Ying Wang, Hua-Bin Zhang, Chun-Lin Zhou, Xin-Yue Chai, Qiu-Ning Liu
The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterised the mitogenome of the crab Helice wuana to better understand its molecular evolution and phylogeny. The 16,359bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and an A+T-rich control region. The genome composition is highly A+T biased 68.42%, and exhibits a negative AT-skew (-0...
October 2, 2017: Genomics
Shilin Zhao, David C Samuels, Ying-Yong Zhao, Yan Guo
The human mitochondrial genome has been extensively studied for its function and disease associations. Utilizing five types of high-throughput sequencing data on ten breast cancer patients (total N=50), we examined several aspects of the mitochondrial genome that have not been thoroughly studied, including the occurrence of tri-allelic heteroplasmy, the difference between DNA and RNA, and the variants association with polynucleotide tracts. We validated four previously reported and identified 23 additional tri-allelic positions...
September 29, 2017: Genomics
Chunliang Xie, Wenbing Gong, Zuohua Zhu, Li Yan, Zhenxiu Hu, Yuande Peng
Blue light is an important environmental factor which could induce mushroom primordium differentiation and fruiting body development. However, the mechanisms of Pleurotus eryngii primordium differentiation and development induced by blue light are still unclear. The CAZymes (carbohydrate-active enzymes) play important roles in degradation of renewable lignocelluloses to provide carbohydrates for fungal growth, development and reproduction. In the present research, the expression profiles of genes were measured by comparison between the Pleurotus eryngii at primordium differentiated into fruiting body stage after blue light stimulation and dark using high-throughput sequencing approach...
September 29, 2017: Genomics
Heshan Zhang, Hong Tian, Mingxin Chen, Junbo Xiong, Hua Cai, Yang Liu
White clover (Trifolium repens L.) has been cultivated for ornamental use because of its flowers, leaf marks and creeping habit. Although a mutation in flower color is very infrequent in this species, the red-flowered mutant of white clover was a novel germplasm for ornamental white clover breeding. The mechanism of flower pigmentation in white clover is still limited because of the rarity of mutation materials and the lack of genomic data. In this study, two cDNA libraries from red-flowered white clover mutant between sunlight-exposed plants and shade-treated plants, respectively, were used for transcriptome sequencing...
September 28, 2017: Genomics
Pingxian Wu, Qiang Yang, Kai Wang, Jie Zhou, Jideng Ma, Qianzhi Tang, Long Jin, Weihang Xiao, Anan Jiang, Yanzhi Jiang, Li Zhu, Xuewei Li, Guoqing Tang
In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level...
September 21, 2017: Genomics
Hai Ming Ni, Da Wei Qi, Hongbo Mu
Converting DNA sequence to image by using chaos game representation (CGR) is an effective genome sequence pretreatment technology, which provides the basis for further analysis between the different genes. In this paper, we have constructed 10 mammal species, 48 hepatitis E virus (HEV), and 10 kinds of bacteria genetic CGR images, respectively, to calculate the mean structural similarity (MSSIM) coefficient between every two CGR images. From our analysis, the MSSIM coefficient of gene CGR images can accurately reflect the similarity degrees between different genomes...
September 20, 2017: Genomics
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