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Gene annotation

Ksenia S Egorova, Yuriy A Knirel, Philip V Toukach
In 2017, we reported a new database on glycosyltransferase (GT) activities, CSDB_GT (, which was built at the platform of the Carbohydrate Structure Database (CSDB, and contained data on experimentally confirmed GT activities from Arabidopsis thaliana. All entries in CSDB_GT are curated manually upon the analysis of scientific publications, and the key features of the database are accurate structural, genetic, protein and bibliographic references and close-to-complete coverage on experimentally proven GT activities in selected species...
January 31, 2019: Glycobiology
Karla Saavedra-Rodriguez, Corey L Campbell, Audrey Lenhart, Patricia Penilla, Saul Lozano-Fuentes, William C Black
Aedes aegypti is the major vector of a number of arboviruses that cause disease in humans. Without vaccines or pharmaceuticals, pyrethroid insecticides remain the major tool for public health protection. Pyrethroid resistance is now widespread. Replacement substitutions in the voltage-gated sodium channel (vgsc) that reduce the stability of pyrethroid binding account for most of the resistance but metabolic mechanisms also inactivate pyrethroids. High-throughput sequencing and the Ae. aegypti L5 annotated physical map has allowed interrogation of the exome for genes and single nucleotide polymorphisms (SNPs) associated with pyrethroid resistance...
February 13, 2019: Insect Molecular Biology
Kausik Ganguly, Tania Saha, Arpan Saha, Tithi Dutta, Souradeep Banerjee, Debmalya Sengupta, Sreyashi Bhattacharya, Sampurna Ghosh, Mainak Sengupta
Skin pigmentation in human is a complex trait, which varies widely, both within and between human populations. The exact players governing the trait of skin pigmentation remain elusive till date. Various Genome Wide Association Studies (GWAS) have shown the association of different genomic variants with normal human skin pigmentation, often indicating genes with no direct implications in melanin biosynthesis or distribution. Little has been explained in terms of the functionality of the associated Single-Nucleotide Polymorphisms (SNPs) with respect to modulating the skin pigmentation phenotype...
February 13, 2019: Archives of Dermatological Research
Yasuhiro Kyono, Jacob O Kitzman, Stephen C J Parker
Variation in non-coding DNA, encompassing gene regulatory regions such as enhancers and promoters, contributes to risk for complex disorders, including type 2 diabetes. While genome-wide association studies have successfully identified hundreds of type 2 diabetes loci throughout the genome, the vast majority of these reside in non-coding DNA, which complicates the process of determining their functional significance and level of priority for further study. Here we review the methods used to experimentally annotate these non-coding variants, to nominate causal variants and to link them to diabetes pathophysiology...
February 12, 2019: Diabetologia
Rafael Fonseca Benevenuto, Tarald Seldal, Stein Joar Hegland, Cesar Rodriguez-Saona, Joseph Kawash, James Polashock
BACKGROUND: Bilberry (Vaccinium myrtillus L.) is one of the most abundant wild berries in the Northern European ecosystems. This species plays an important ecological role as a food source for many vertebrate and invertebrate herbivores. It is also well-recognized for its bioactive compounds, particularly substances involved in natural defenses against herbivory. These defenses are known to be initiated by leaf damage (e.g. chewing by insects) and mediated by activation of the jasmonic acid (JA) signaling pathway...
February 12, 2019: BMC Plant Biology
Changxu Tian, Zhiyuan Li, Zhongdian Dong, Yang Huang, Tao Du, Huapu Chen, Dongneng Jiang, Siping Deng, Yulei Zhang, Saetan Wanida, Hongjuan Shi, Tianli Wu, Chunhua Zhu, Guangli Li
Silver sillago ( Sillago sihama ) is an emerging commercial marine aquaculture species in China. To date, fundamental information on S. sihama , such as genomic information, is lacking, and no data are available on the gonad transcriptome of S. sihama . Here, the first gonadal transcriptomes of S. sihama have been constructed and genes potentially involved in gonadal development and reproduction identified. Illumina sequencing generated 60.18 million clean reads for the testis and 59.10 million for the ovary...
February 11, 2019: Genes
Ho Phin Chong, Kae Yi Tan, Nget Hong Tan, Choo Hock Tan
The equatorial spitting cobra, Naja sumatrana , is a distinct species of medically important venomous snakes, listed as WHO Category 1 in Southeast Asia. The diversity of its venom genes has not been comprehensively examined, although a few toxin sequences annotated to Naja sputatrix were reported previously through cloning studies. To investigate this species venom genes' diversity, de novo venom-gland transcriptomics of N. sumatrana from West Malaysia was conducted using next-generation sequencing technology...
February 11, 2019: Toxins
Lucía Casares-Crespo, Paula Fernández-Serrano, María P Viudes-de-Castro
The present study was conducted to characterise rabbit sperm proteins focusing on the influence of the genetic origin. Six samples were recovered during two months from five males from genotype A (New Zealand White origin) and five from genotype R (California origin). Sperm proteins were extracted and subjected to in-gel digestion nano LC-MS/MS and bioinformatics analysis. The resulting library included 487 identified proteins validated with ≥95% Confidence (unused Score ≥ 1.3). All the identified proteins belonged to Oryctolagus cuniculus taxonomy...
February 6, 2019: Theriogenology
Ramachandran Chelliah, Shuai Wei, Byung-Jae Park, Yong-Guo Jin, Momna Rubab, Eric Banan-Mwine Daliri, Kaliyan Barathi Kannan, Deog-Hwan Oh
BACKGROUND: Among the Bacillus cereus group, B. thuringiensis, is one of the most extensively used biological control agent. The present study reports the complete genome and four novel plasmid analysis of the type strain B. thuringiensis ATCC 10792. METHODS: Complete genome sequencing of Bacillus thuringiensis ATCC 10792, assembled using de-novo (v.3.2.0, assembly name MIRA3), Pac-Bio sequencers and Hierarchical Genome Assembly Process software (version 4.1) and real-time polymerase chain reaction (qPCR) is a consistent technique for quantifying gene expression based on specific biomarkers, in addition the efficiency of the primers were analyzed based on artificially spiked food samples on lettuce, kimbab and spinach with B...
February 9, 2019: Microbial Pathogenesis
Jim Clauwaert, Gerben Menschaert, Willem Waegeman
Annotation of gene expression in prokaryotes often finds itself corrected due to small variations of the annotated gene regions observed between different (sub)-species. It has become apparent that traditional sequence alignment algorithms, used for the curation of genomes, are not able to map the full complexity of the genomic landscape. We present DeepRibo, a novel neural network utilizing features extracted from ribosome profiling information and binding site sequence patterns that shows to be a precise tool for the delineation and annotation of expressed genes in prokaryotes...
February 8, 2019: Nucleic Acids Research
Stefan Ebmeyer, Erik Kristiansson, D G Joakim Larsson
Objectives: To investigate the origin of CMY-1/MOX-family β-lactamases. Methods: Publicly available genome assemblies were screened for CMY-1/MOX genes. The loci of CMY-1/MOX genes were compared with respect to synteny and nucleotide identity, and subjected to phylogenetic analysis. Results: The chromosomal ampC genes of several Aeromonas species were highly similar to known mobile CMY-1/MOX variants. Annotation and sequence comparison revealed nucleotide identities >98% and conserved syntenies between MOX-1-, MOX-2- and MOX-9-associated mobile sequences and the chromosomal Aeromonas sanarellii, Aeromonas caviae and Aeromonas media ampC loci...
February 7, 2019: Journal of Antimicrobial Chemotherapy
Shur-Jen Wang, Stanley J F Laulederkind, Yiqing Zhao, G Thomas Hayman, Jennifer R Smith, Monika Tutaj, Jyothi Thota, Marek A Tutaj, Matthew J Hoffman, Elizabeth R Bolton, Jeffrey De Pons, Melinda R Dwinell, Mary Shimoyama
Rats have been used as research models in biomedical research for over 150 years. These disease models arise from naturally occurring mutations, selective breeding and, more recently, genome manipulation. Through the innovation of genome-editing technologies, genome-modified rats provide precision models of disease by disrupting or complementing targeted genes. To facilitate the use of these data produced from rat disease models, the Rat Genome Database (RGD) organizes rat strains and annotates these strains with disease and qualitative phenotype terms as well as quantitative phenotype measurements...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Gabriel E Rech, María Bogaerts-Márquez, Maite G Barrón, Miriam Merenciano, José Luis Villanueva-Cañas, Vivien Horváth, Anna-Sophie Fiston-Lavier, Isabelle Luyten, Sandeep Venkataram, Hadi Quesneville, Dmitri A Petrov, Josefa González
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions annotated in the reference genome of Drosophila melanogaster, in 91 samples from 60 worldwide natural populations. We identified a set of 300 polymorphic TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high...
February 2019: PLoS Genetics
Tomás Masson, María Laura Fabre, María Leticia Ferrelli, Matías Luis Pidre, Víctor Romanowski
Within family Baculoviridae, members of the Betabaculovirus genus are employed as biocontrol agents against lepidopteran pests, either alone or in combination with selected members of the Alphabaculovirus genus. Epinotia aporema granulovirus (EpapGV) is a fast killing betabaculovirus that infects the bean shoot borer (E. aporema) and is a promising biopesticide. Because occlusion bodies (OBs) play a key role in baculovirus horizontal transmission, we investigated the composition of EpapGV OBs. Using mass spectrometry-based proteomics we could identify 56 proteins that are included in the OBs during the final stages of larval infection...
2019: PloS One
Ornella Affinito, Paolo Salerno, Alfonso Manuel D'Alessio, Mariella Cuomo, Ermanno Florio, Francesca Carlomagno, Agnese Proietti, Riccardo Giannini, Fulvio Basolo, Lorenzo Chiariotti, Sergio Cocozza, Massimo Santoro
Molecular differentiation between benign (follicular thyroid adenoma, FTA) and malignant (follicular thyroid carcinoma, FTC) thyroid neoplasms is challenging. Here, we explored the genome-wide DNA methylation profile of FTA (n.10) and FTC (n.11) compared to normal thyroid (NT) (n.7) tissues. FTC featured 3,564 differentially-methylated CpGs (DMCpG), most (84%) of them hypermethylated, with respect to normal controls. At the principal component analysis (PCA), the methylation profile of FTA occupied an intermediate position between FTC and normal tissue...
February 1, 2019: Endocrine-related Cancer
Zhuo Shang, Jaclyn M Winter, Christopher A Kauffman, Inho Yang, William Fenical
Analysis of the full genome of an environmentally-unique, halotolerant Streptomyces sp. strain GSL-6C, isolated from the Great Salt Lake, revealed a gene cluster encoding the biosynthesis of the salinipeptins, D-amino acid containing members of the rare linaridin subfamily of ribosomally synthesized and post-translationally modified peptides (RiPPs). The sequence organization of the unmodified amino acid residues in salinipeptins A-D (1-4) were suggested by genome annotation, and subsequently their sequence and post-translational modifications were defined using a range of spectroscopic techniques and chemical derivatization approaches...
February 12, 2019: ACS Chemical Biology
Yan Zhu, Jinxin Zhao, Mohd Hafidz Mahamad Maifiah, Tony Velkov, Falk Schreiber, Jian Li
Multidrug-resistant (MDR) Acinetobacter baumannii has emerged as a very problematic pathogen over the past decades, with a high incidence in nosocomial infections. Discovered in the late 1940s but abandoned in the 1970s, polymyxins (i.e., polymyxin B and colistin) have been revived as the last-line therapy against Gram-negative "superbugs," including MDR A. baumannii. Worryingly, resistance to polymyxins in A. baumannii has been increasingly reported, urging the development of novel antimicrobial therapies to rescue this last-line class of antibiotics...
January 2019: MSystems
Xiao-Xia Liu, Xiao-Fang Luo, Ke-Xin Luo, Ya-Lin Liu, Ting Pan, Zhi-Zhang Li, Gregory J Duns, Fu-Lin He, Zuo-Dong Qin
To obtain insight into the function of miRNAs in the synthesis and storage of important nutrients during the development of Camellia oleifera fruit, Illumina sequencing of flower and fruit small-RNA was conducted. The results revealed that 797 miRNAs were significantly differentially expressed between flower and fruit samples of Camellia oleifera . Through integrated GO and KEGG function annotations, it was determined that the miRNA target genes were mainly involved in metabolic pathways, plant hormone signal transduction, fruit development, mitosis and regulation of biosynthetic processes...
2019: International Journal of Biological Sciences
J Alfredo Blakeley-Ruiz, Alison R Erickson, Brandi L Cantarel, Weili Xiong, Rachel Adams, Janet K Jansson, Claire M Fraser, Robert L Hettich
BACKGROUND: The gut microbiome plays a fundamental role in the human host's overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn's disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues...
February 11, 2019: Microbiome
Joon Yoon, Heebal Kim
Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of lncRNA annotation database has increased the importance and proportion of mapped reads accordingly. Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue...
November 28, 2018: Asian-Australasian Journal of Animal Sciences
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