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genomics,genome annotation,

Xuebin Qi, Qu Zhang, Yaoxi He, Lixin Yang, Xiaoming Zhang, Peng Shi, Linping Yang, Zhengheng Liu, Fuheng Zhang, Fengyun Liu, Shiming Liu, Tianyi Wu, Chaoying Cui, Ouzhuluobu, Caijuan Bai, Baimakangzhuo, Jianlin Han, Shengguo Zhao, Chunnian Liang, Bing Su
Yak is one of the largest native mammalian species at the Himalayas, the highest plateau area in the world with an average elevation of more than 4,000 meters above the sea level. Yak is well adapted to high altitude environment with a set of physiological features for a more efficient blood flow for oxygen delivery under hypobaric hypoxia. Yet, the genetic mechanism underlying its adaptation remains elusive. We conducted a cross-tissue, cross-altitude and cross-species study to characterize the transcriptomic landscape of domestic yaks...
December 4, 2018: Genome Biology and Evolution
Lingling Wang, Zhaoen Yang, Bin Zhang, Daoqian Yu, Ji Liu, Qian Gong, Ghulam Qanmber, Yi Li, Lili Lu, Yongjun Lin, Zuoren Yang, Fuguang Li
BACKGROUND: The glycogen synthase kinase 3/shaggy kinase (GSK3) is a serine/threonine kinase with important roles in animals. Although GSK3 genes have been studied for more than 30 years, plant GSK genes have been studied only since the last decade. Previous research has confirmed that plant GSK genes are involved in diverse processes, including floral development, brassinosteroid signaling, and responses to abiotic stresses. RESULT: In this study, 20, 15 (including 5 different transcripts) and 10 GSK genes were identified in G...
December 4, 2018: BMC Plant Biology
István Prazsák, Norbert Moldován, Zsolt Balázs, Dóra Tombácz, Klára Megyeri, Attila Szűcs, Zsolt Csabai, Zsolt Boldogkői
BACKGROUND: Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring a relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when used for structural characterization of transcript isoforms, even if supplemented with primer extension or other techniques. Among others, they are inefficient in distinguishing between embedded RNA molecules, transcript isoforms, including splice and length variants, as well as between alternative polycistronic transcripts...
December 4, 2018: BMC Genomics
Francesco Panara, Loredana Lopez, Loretta Daddiego, Elio Fantini, Paolo Facella, Gaetano Perrotta
BACKGROUND: Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential production of NR will contribute to elucidate which genes are involved in the synthesis, regulation and accumulation of this natural polymer and could help to develop Tks into a rubber crop. RESULTS: We measured rubber content in the latex of 90 individual Tks plants from 9 accessions, observing a high degree of variability...
December 4, 2018: BMC Genomics
Gregory A Taylor, Heather Kirk, Lauren Coombe, Shaun D Jackman, Justin Chu, Kane Tse, Dean Cheng, Eric Chuah, Pawan Pandoh, Rebecca Carlsen, Yongjun Zhao, Andrew J Mungall, Richard Moore, Inanc Birol, Maria Franke, Marco A Marra, Christopher Dutton, Steven J M Jones
The grizzly bear ( Ursus arctos ssp. horribilis ) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96...
November 30, 2018: Genes
Guillaume P Ramstein, Joseph Evans, Aruna Nandety, Malay C Saha, E Charles Brummer, Shawn M Kaeppler, C Robin Buell, Michael D Casler
Switchgrass ( L.) is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving simple additive marker effects and also interactions with genetic backgrounds (e.g., ecotypes) or synergies with other markers. We analyzed plant height, C content, N content, and mineral concentration in a diverse panel consisting of 512 genotypes of upland and lowland ecotypes...
November 2018: Plant Genome
William M Matern, Joel S Bader, Petros C Karakousis
Infection with Mycobacterium avium is a significant cause of morbidity and its treatment requires the use of multiple antibiotics for more than 12 months. In the current work, we provide the genome sequence, gene annotations, gene ontology annotations, and protein homology data for M. avium strain 109 (MAC109), which has been used extensively in preclinical studies. The de novo assembled genome consists of a circular chromosome of length 5,188,883 bp and two circular plasmids of sizes 147,100 bp and 16,516 bp...
December 4, 2018: Scientific Data
Hongyan Zhao, Kejian Tian, Qing Qiu, Yu Wang, Hongyan Zhang, Shuang Ma, Shenbao Jin, Hongliang Huo
We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4 Mbp with G + C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5...
2018: International Journal of Genomics
Maojun Wang, Lili Tu, Daojun Yuan, De Zhu, Chao Shen, Jianying Li, Fuyan Liu, Liuling Pei, Pengcheng Wang, Guannan Zhao, Zhengxiu Ye, Hui Huang, Feilin Yan, Yizan Ma, Lin Zhang, Min Liu, Jiaqi You, Yicheng Yang, Zhenping Liu, Fan Huang, Baoqi Li, Ping Qiu, Qinghua Zhang, Longfu Zhu, Shuangxia Jin, Xiyan Yang, Ling Min, Guoliang Li, Ling-Ling Chen, Hongkun Zheng, Keith Lindsey, Zhongxu Lin, Joshua A Udall, Xianlong Zhang
Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1-4 . Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3-79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-throughput chromosome conformation capture techniques...
December 3, 2018: Nature Genetics
Doug Speed, David J Balding
We present SumHer, software for estimating confounding bias, SNP heritability, enrichments of heritability and genetic correlations using summary statistics from genome-wide association studies. The key difference between SumHer and the existing software LD Score Regression (LDSC) is that SumHer allows the user to specify the heritability model. We apply SumHer to results from 24 large-scale association studies (average sample size 121,000) using our recommended heritability model. We show that these studies tended to substantially over-correct for confounding, and as a result the number of genome-wide significant loci was under-reported by about a quarter...
December 3, 2018: Nature Genetics
Cheng Cheng, Jing Lu, Xi Cao, Fang-Yuan Yang, Jing-Yi Liu, Li-Ni Song, Han Shen, Chang Liu, Xiao-Rong Zhu, Jian-Bo Zhou, Jin-Kui Yang
Regulatory Factor X-box binding transcriptional factor 6 (Rfx6) plays an important role in the differentiation and development of pancreas in mammals. However, the direct target genes of Rfx6 to regulate this process were largely unknown. The present study aimed to investigate the function of Rfx6 on regulating pancreatic differentiation and development in a physiologically-relevant context. We performed the chromatin immunoprecipitation followed by the next generation sequencing analysis (ChIP-seq) using whole pancreatic tissue harvested from C57/BL6 adult mice to find target genes of Rfx6...
November 30, 2018: Biochemical and Biophysical Research Communications
Kamil Myszczyński, Piotr Górski, Monika Ślipiko, Jakub Sawicki
BACKGROUND: Comparative analyses of chloroplast and mitochondrial genomes have shown that organelle genomes in bryophytes evolve slowly. However, in contrast to seed plants, the organellar genomes are yet poorly explored in bryophytes, especially among liverworts. Discovering another organellar genomes of liverwort species by sequencing provides new conclusions on evolution of bryophytes. RESULTS: In this work, the organellar genomes of Gymnomitrion concinnatum liverwort were sequenced, assembled and annotated for the first time...
December 3, 2018: BMC Plant Biology
L Pereira, V Ruggieri, S Pérez, K G Alexiou, M Fernández, T Jahrmann, M Pujol, J Garcia-Mas
BACKGROUND: Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. RESULTS: In order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: "Védrantais", from the cantalupensis group, and "Piel de Sapo", from the inodorus group...
December 4, 2018: BMC Plant Biology
Dingwei Zhang, Jia Huo, Ruilian Li, Yanfei Zhang, Zhenghui Wang, Xiaoli Li
Benign chronic familial pemphigus or Hailey-Hailey disease (HHD, OMIM 169600) is a rare, autosomal dominant blistering skin disorder characterized by suprabasal cell separation (acantholysis) of the epidermis. To date, the proteomic changes in skin lesions from HHD patients has not been reported yet. In this study, a sample of skin lesions from HHD patients was collected for isobaric tags for relative and absolute quantitation to analyze proteome changes compared with unaffected individuals. The 134 differentially expressed proteins were assigned to at least one Gene Ontology term, and 123 annotated proteins with significant matches were assigned to 187 known metabolic or signaling pathways listed in the Kyoto Encyclopedia of Genes and Genomes...
December 3, 2018: Journal of Cellular Biochemistry
Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira, Josefa González
Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome-wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing dataset, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations...
November 30, 2018: Molecular Ecology
Louis Bengyella
The Cochliobolus genus consist of over 55 species among which the 5 most devastating are Cochliobolus carbonum, Cochliobolus heterostrophus, Cochliobolus miyabeanus, Crocus sativus and Cochliobolus lunatus causing damages in sorghum, wheat, rice, maize, cassava and soybean estimated at over 10 billion USD per annum worldwide. The dynamic pathogenicity of Cochliobolus species and the plethora of infected hosts is determined by the evolution of virulence determinants such as the velvet-like B protein (VelB)...
December 1, 2018: World Journal of Microbiology & Biotechnology
Stephen John Bentley, Miebaka Jamabo, Aileen Boshoff
The etiological agent of the neglected tropical disease African trypanosomiasis, Trypanosoma brucei, possesses an expanded and diverse repertoire of heat shock proteins, which have been implicated in cytoprotection, differentiation, as well as progression and transmission of the disease. Hsp70 plays a crucial role in proteostasis, and inhibition of its interactions with co-chaperones is emerging as a potential therapeutic target for numerous diseases. In light of genome annotations and the release of the genome sequence of the human infective subspecies, an updated and current in silico overview of the Hsp70/J-protein machinery in both T...
December 1, 2018: Cell Stress & Chaperones
Eugenia Bifeld, Stephan Lorenzen, Katharina Bartsch, Juan-José Vasquez, T Nicolai Siegel, Joachim Clos
The 90-kDa heat shock protein (HSP90) of eukaryotes is a highly abundant and essential chaperone required for the maturation of regulatory and signal proteins. In the protozoan parasite Leishmania donovani, causative agent of the fatal visceral leishmaniasis, HSP90 activity is essential for cell proliferation and survival. Even more importantly, its inhibition causes life cycle progression from the insect stage to the pathogenic, mammalian stage. To unravel the molecular impact of HSP90 activity on the parasites' gene expression, we performed a ribosome profiling analysis of L...
November 2018: MSystems
Guillaume Bernard, Paul Greenfield, Mark A Ragan, Cheong Xin Chan
Microbial genomes have been shaped by parent-to-offspring (vertical) descent and lateral genetic transfer. These processes can be distinguished by alignment-based inference and comparison of phylogenetic trees for individual gene families, but this approach is not scalable to whole-genome sequences, and a tree-like structure does not adequately capture how these processes impact microbial physiology. Here we adopted alignment-free approaches based on k -mer statistics to infer phylogenomic networks involving 2,783 completely sequenced bacterial and archaeal genomes and compared the contributions of rRNA, protein-coding, and plasmid sequences to these networks...
November 2018: MSystems
Mohammad Reza Pourreza, Hannane Mohammadi, Ladan Sadeghian, Samira Asgharzadeh, Mohammadreza Sehhati, Mohammad Amin Tabatabaiefar
Background: Hearing loss (HL) is a highly prevalent heterogeneous deficiency of sensory-neural system with involvement of several dozen genes. Whole-exome sequencing (WES) is capable of discovering known and novel genes involved with HL. Materials and Methods: Two pedigrees with HL background from Khuzestan province of Iran were selected. Polymerase chain reaction-sequencing of GJB2 and homozygosity mapping of 16 DFNB loci were performed. One patient of the first and two affected individuals from the second pedigree were subjected to WES...
2018: Advanced Biomedical Research
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