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Gene annotation

Yusuke Kuwahara, Daisuke Nakajima, Sayaka Shinpo, Michimi Nakamura, Noriaki Kawano, Nobuo Kawahara, Mami Yamazaki, Kazuki Saito, Hideyuki Suzuki, Hideki Hirakawa
Gleditsia sinensis is widely used as a medicinal plant in Asia, especially in China. Triterpenes, alkaloids, and sterols were isolated from Gleditsia species. Among them, triterpenoid saponins are very important metabolites owing to their various pharmacological activities. However, the triterpenoid saponin biosynthesis pathway has not been well characterized. In the present study, we performed de novo transcriptome assembly for 14.3 Gbps of clean reads sequenced from nine tissues of G. sinensis. The results showed that 81,511 unique transcripts (unitranscripts) (47,855 unigenes) were constructed, of which 31,717 unigenes were annotated with Gene Ontology and EC numbers by Blast2GO against the NCBI-nr protein database...
December 13, 2018: Journal of Natural Medicines
Frederick S Varn, Yue Wang, Chao Cheng
Immune checkpoint inhibitors have shown great potential in treating solid tumors, inducing durable remission and prolonged survival time in responders. Despite their promise, a large fraction of patients remains unresponsive to these treatments highlighting the need for biomarkers that can predict patient sensitivity. Pre-treatment gene expression profiles for patients receiving immune checkpoint inhibitors have recently become available, establishing a new medium by which to discover biomarkers that predict therapy response...
2019: Oncoimmunology
Yoji Nakamura
Horizontal gene transfer (HGT) is the process whereby an organism acquires exogenous genes (horizontally transferred genes or HT genes) that are not inherited from the parent, but are derived from another organism. In prokaryotes, HGT has been considered as one of the important driving forces of evolution. Previously, genome-wide analyses have been conducted for estimating the proportion of HT genes in prokaryotic genomes, but the number of species examined at the time was limited, and gene annotation was relatively poor...
2018: Evolutionary Bioinformatics Online
Yang Yang, Baihui Cui, Zhiwen Tan, Bingxue Song, Hounan Cao, Chengwen Zong
BACKGROUND: Vaccinium uliginosum (Ericaceae) is an important wild berry having high economic value. The white-fruited V. uliginosum variety found in the wild lacks anthocyanin and bears silvery white fruits. Hence, it is a good resource for investigating the mechanism of fruit color development. This study aimed to verify the differences in the expression levels of some structural genes and transcription factors affecting the anthocyanin biosynthesis pathway by conducting high-throughput transcriptome sequencing and real-time PCR analysis by using the ripening fruits of V...
December 13, 2018: BMC Genomics
Monica A Schmidt, Eliot M Herman
BACKGROUND: Soybean is a globally important oil seed crop. Both the high protein and oil content of soybean seeds make this crop a lucrative commodity. As in higher eukaryotic species with available genomes, the functional annotation of most of soybean's genes still remains to be investigated. A major hurdle in the functional genomics of soybean is a rapid method to test gene constructs before embarking on stable transformation experiments. RESULTS: In this paper we describe the morphology and composition of the persistent single-cell aleurone layer that derives from the endosperm of developing soybean seeds...
December 13, 2018: BMC Plant Biology
Ling Li, Weihua Zhao, Xuechao Feng, Lulu Chen, Lida Zhang, Lingxia Zhao
Fruit firmness is an important trait in tomato (Solanum lycopersicum), associated with shelf life and economic value; however, the precise mechanism determining fruit softening remains elusive. A yellow fruit tomato 1(yft1) mutant, harbors a genetic lesion in the YFT1 gene, and has significantly firmer fruit than those of the cv. M82 wild type at a red ripe stage, 54 dpa (days post anthesis). When softening was further dissected, it was found that the yft1 firm fruit phenotype correlated with a difference in cellulose, hemicellulose and pectin deposition in the primary cell wall (PCW) compared to cv...
December 13, 2018: Journal of Agricultural and Food Chemistry
Le Guan, Muhammad Salman Haider, Nadeem Khan, Maazullah Nasim, Songtao Jiu, Muhammad Fiaz, Xudong Zhu, Kekun Zhang, Jinggui Fang
Salinity is ubiquitous abiotic stress factor limiting viticulture productivity worldwide. However, the grapevine is vulnerable to salt stress, which severely affects growth and development of the vine. Hence, it is crucial to delve into the salt resistance mechanism and screen out salt-resistance prediction marker genes; we implicated RNA-sequence (RNA-seq) technology to compare the grapevine transcriptome profile to salt stress. Results showed 2472 differentially-expressed genes (DEGs) in total in salt-responsive grapevine leaves, including 1067 up-regulated and 1405 down-regulated DEGs...
December 12, 2018: International Journal of Molecular Sciences
Lisa K Johnson, Harriet Alexander, C Titus Brown
Background: De novo transcriptome assemblies are required prior to analyzing RNAseq data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines", on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short read data collected by the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP)...
December 13, 2018: GigaScience
Shun Matsuzawa, Masaharu Isobe, Nobuyuki Kurosawa
The guinea pig has been used as a model to study various human infectious diseases because of its similarity to humans regarding symptoms and immune response, but little is known about the humoral immune response. To better understand the mechanism underlying the generation of the antibody repertoire in guinea pigs, we performed deep sequencing of full-length immunoglobulin variable chains from naïve B and plasma cells. We gathered and analyzed nearly 16,000 full-length VH, Vκ and Vλ genes and analyzed V and J gene segment usage profiles and mutation statuses by annotating recently reported genome data of guinea pig immunoglobulin genes...
2018: PloS One
Kemal Eren, Steven Weaver, Robert Ketteringham, Morné Valentyn, Melissa Laird Smith, Venkatesh Kumar, Sanjay Mohan, Sergei L Kosakovsky Pond, Ben Murrell
Next generation sequencing of viral populations has advanced our understanding of viral population dynamics, the development of drug resistance, and escape from host immune responses. Many applications require complete gene sequences, which can be impossible to reconstruct from short reads. HIV env, the protein of interest for HIV vaccine studies, is exceptionally challenging for long-read sequencing and analysis due to its length, high substitution rate, and extensive indel variation. While long-read sequencing is attractive in this setting, the analysis of such data is not well handled by existing methods...
December 13, 2018: PLoS Computational Biology
Kathryn A O'Donnell, Yabin Guo, Shruthy Suresh, Barrett L Updegraff, Xiaorong Zhou
Transposon mutagenesis has emerged as a powerful methodology for functionally annotating cancer genomes. Although in vivo transposon-mediated forward genetic screens have proven to be valuable for cancer gene identification, they are also time consuming and resource intensive. To facilitate the rapid and cost-effective identification of genes that regulate tumor-promoting pathways, we developed a complementary ex vivo transposon mutagenesis approach wherein human or mouse cells growing in culture are mutagenized and screened for the acquisition of specific phenotypes in vitro or in vivo, such as growth factor independence or tumor-forming ability...
2019: Methods in Molecular Biology
Wenfei Zhang, Jianru Gong, Siyu Wu, Haoneng Yin, Yinghong Jin, Hongping Wu, Peng Li, Ruiping Wang
Acinetobacter tandoii SC36 was isolated from a mangrove wetland ecosystem in the Dongzhaigang Nature Reserve in Haikou, China. This bacterium was found to have a capacity for polyphosphate accumulation. To provide insight into its phosphorus metabolism and facilitate its application in phosphorus removal, we developed a draft genome of this strain. KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed three ppk genes and several phosphate metabolic related pathways in the genome of SC36. These genome data of Acinetobacter tandoii SC36 will facilitate elucidation of the mechanism of polyphosphate accumulation...
December 12, 2018: Current Microbiology
Tao Zhang, Jianrong Guo, Jian Gu, Zheng Wang, Guobin Wang, Huili Li, Jiliang Wang
Colorectal cancer (CRC) is one of the principal causes of cancer‑associated mortality worldwide. The high incidence of liver metastasis is the leading risk factor of mortality in patients with CRC, and the mechanisms of CRC liver metastasis are poorly understood. In the present study, 7 datasets, including 3 gene expression profile datasets and 4 microRNA (miRNA) expression profile datasets were downloaded from the NCBI Gene Expression Omnibus (GEO) database to identify potential key genes and miRNAs, which may be candidate biomarkers for CRC liver metastasis...
November 1, 2018: Oncology Reports
Xuelian Ma, Hansheng Zhao, Wenying Xu, Qi You, Hengyu Yan, Zhimin Gao, Zhen Su
Bamboo is one of the fastest-growing non-timber forest plants. Moso bamboo ( Phyllostachys edulis ) is the most economically valuable bamboo in Asia, especially in China. With the release of the whole-genome sequence of moso bamboo, there are increasing demands for refined annotation of bamboo genes. Recently, large amounts of bamboo transcriptome data have become available, including data on the multiple growth stages of tissues. It is now feasible for us to construct co-expression networks to improve bamboo gene annotation and reveal the relationships between gene expression and growth traits...
2018: Frontiers in Genetics
Dongjuan Dai, William J Rhoads, Marc A Edwards, Amy Pruden
Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry...
2018: Frontiers in Microbiology
Ruaidhrí Jackson, Lina Kroehling, Alexandra Khitun, Will Bailis, Abigail Jarret, Autumn G York, Omair M Khan, J Richard Brewer, Mathias H Skadow, Coco Duizer, Christian C D Harman, Lelina Chang, Piotr Bielecki, Angel G Solis, Holly R Steach, Sarah Slavoff, Richard A Flavell
The annotation of the mammalian protein-coding genome is incomplete. Arbitrary size restriction of open reading frames (ORFs) and the absolute requirement for a methionine codon as the sole initiator of translation have constrained the identification of potentially important transcripts with non-canonical protein-coding potential1,2 . Here, using unbiased transcriptomic approaches in macrophages that respond to bacterial infection, we show that ribosomes associate with a large number of RNAs that were previously annotated as 'non-protein coding'...
December 12, 2018: Nature
Gyorgy Petrovics, Douglas K Price, Hong Lou, Yongmei Chen, Lisa Garland, Sara Bass, Kristine Jones, Indu Kohaar, Amina Ali, Lakshmi Ravindranath, Denise Young, Jennifer Cullen, Tiffany H Dorsey, Isabell A Sesterhenn, Stephen A Brassell, Inger L Rosner, Doug Ross, William Dahut, Stefan Ambs, William Douglas Figg, Shiv Srivastava, Michael Dean
BACKGROUND: Germline mutations in BRCA2 have been linked to a higher risk of prostate cancer (PCa), and high frequency of BRCA1 and BRCA2 (BRCA1/2) gene alterations was recently reported in metastatic castration-resistant PCa specimens. Mutations in BRCA2 vary in racial and ethnic groups including African-American (AA) and Caucasian-American (CA) populations. METHODS: BRCA1 and BRCA2 genes were sequenced (Ion AmpliSeq targeted sequencing) in archived blood DNA specimens in 1240 PCa patients, including 30% AA patients, in three different cohorts: localized early stage (T2) PCa (N = 935); advanced PCa (50% T3-4) (N = 189); and metastatic PCa (N = 116)...
December 12, 2018: Prostate Cancer and Prostatic Diseases
Anthony P Neumann, Garret Suen
Members of the genus Fibrobacter are cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novel Fibrobacter strains against the type strains for the two formally described Fibrobacter species F...
December 12, 2018: MSphere
Tinghua Huang, Xiali Huang, Bomei Shi, Fangfang Wang, Wenzhao Feng, Min Yao
Peripheral blood transcriptome is an important intermediate data source for investigating the mechanism of Salmonella invasion, proliferation, and transmission. We challenged 4-week old piglets with Salmonella enterica serovar Typhimurium LT2 and investigated the peripheral blood gene expression profile before treatment (d0) and at 2 and 7 days post-inoculation (dpi) using deep sequencing. Regulator pathways were first predicted in silico and validated by wet-lab experiments. In total, 1255, 765, and 853 genes were differentially expressed between 2 dpi/d0, 7 dpi/d0, and 7 dpi/2 dpi, respectively...
December 12, 2018: Veterinary Research
Matthew D C Neville, Jihoon Choi, Jonathan Lieberman, Qing Ling Duan
BACKGROUND: Candidate gene and genome-wide association studies have identified hundreds of asthma risk loci. The majority of associated variants, however, are not known to have any biological function and are believed to represent markers rather than true causative mutations. We hypothesized that many of these associated markers are in linkage disequilibrium (LD) with the elusive causative variants. METHODS: We compiled a comprehensive list of 449 asthma-associated variants previously reported in candidate gene and genome-wide association studies...
December 12, 2018: Respiratory Research
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