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genomics,genome annotation,

Yunhai Shao, Jun Li, Yanxin Wang, Fengmei Yi, Yanan Zhang, Peiwu Cui, Weihong Zhong
A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. This mechanism requires exploration via molecular omics. Thus, the complete genome of XJLW was sequenced, and the transcriptome difference was also analyzed based on the RNA-seq data of strain XJLW cultivated with methanol and glucose, respectively...
February 20, 2019: Molecular omics
Sherif Farag, Rachel M Bleich, Elizabeth A Shank, Olexandr Isayev, Albert A Bowers, Alexander Tropsha
MOTIVATION: Non-ribosomal peptide synthetases (NRPSs) are modular enzymatic machines that catalyze the ribosome-independent production of structurally complex small peptides, many of which have important clinical applications as antibiotics, antifungals, and anti-cancer agents. Several groups have tried to expand natural product diversity by intermixing different NRPS modules to create synthetic peptides. This approach has not been as successful as anticipated, suggesting that these modules are not fully interchangeable...
February 20, 2019: Bioinformatics
Salah Fatouh Abou-Elwafa, Abu El-Eyuoon Abu Zied Amin, Tariq Shehzad
Decreasing freshwater supply has led to the consideration of treated wastewater as an alternative source for agricultural irrigation. However, the higher content of heavy metals restricts their use in agricultural purposes. In the current study, a set of 181 SSR markers were used to perform association mapping in a structured sorghum population consisting of 107 accessions evaluated under tap-water and heavy-metals-containing water irrigation conditions. Significant differences between optimal and stressed growing conditions were shown in all evaluated phenotypic traits...
February 19, 2019: Ecotoxicology and Environmental Safety
Maichun Fang, Zejiao Zhou, Xusheng Zhou, Huiyong Yang, Meiru Li, Hongqing Li
Flowering time control is critically important for the reproductive accomplishment of higher plants as floral transition can be affected by both environmental and endogenous signals. Flowering Locus T-like ( FTL ) genes are major genetic determinants of flowering in plants. In rice, 13 OsFTL genes have been annotated in the genome and amongst them, Hd3a ( OsFTL2 ) and RFT1 ( OsFTL3 ) have been studied extensively and their functions are confirmed as central florigens that control rice flowering under short day and long day environment, respectively...
2019: PeerJ
Ilias Lagkouvardos, Till R Lesker, Thomas C A Hitch, Eric J C Gálvez, Nathiana Smit, Klaus Neuhaus, Jun Wang, John F Baines, Birte Abt, Bärbel Stecher, Jörg Overmann, Till Strowig, Thomas Clavel
BACKGROUND: Bacteria within family S24-7 (phylum Bacteroidetes) are dominant in the mouse gut microbiota and detected in the intestine of other animals. Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation. METHODS: We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species...
February 19, 2019: Microbiome
Vibe Maria Jacobsen, Shuxia Li, Ancong Wang, Dongyi Zhu, Min Liu, Mads Thomassen, Torben Kruse, Qihua Tan
Polycystic ovarian syndrome (PCOS) is a complex disorder affecting up to 15-20% of reproductive women. PCOS has recently been investigated using genome-wide association studies revealing important mutations and DNA methylation sites associated with the syndrome. As a clinically highly heterogenous condition, studying the molecular basis of the differential manifestation of PCOS is both meaningful concerning individualized management and important for understanding the biology of PCOS. Using genome-wide DNA methylation data collected from PCOS patients, we performed a powerful region-based analysis to detect differentially methylated regions (DMR) by correlating DNA methylation pattern in a genomic region with the level of each PCOS clinical sub-phenotype...
February 19, 2019: Gynecological Endocrinology
Cancan Zhu, Fenghou Shi, Yu Chen, Min Wang, Yuqiang Zhao, Guomin Geng
Chinese chestnut ( Castanea mollissima Blume) can be infested by Dryocosmus kuriphilus Yasumatsu, resulting in gall formation and yield losses. Research on the control of gall wasps using genomics approaches is rarely reported. We used RNA-seq to investigate the dynamic changes in the genes of a chestnut species ( C. mollissima B.) during four gall-formation stages caused by D. kuriphilus . A total of 21,306 genes were annotated by BLAST in databases. Transcriptome comparison between different gall-formation stages revealed many genes that were differentially expressed compared to the control...
February 15, 2019: International Journal of Molecular Sciences
Xiaohui Yang, Jie Liu, Jianfei Xu, Shaoguang Duan, Qianru Wang, Guangcun Li, Liping Jin
Potato ( Solanum tuberosum L.) is one of the three most important food crops worldwide; however, it is strongly affected by drought stress. The precise molecular mechanisms of drought stress response in potato are not very well understood. The diploid potato genotype P3-198 has been verified to be highly resistant to drought stress. Here, a time-course experiment was performed to identify drought resistance response genes in P3-198 under polyethylene glycol (PEG)-induced stress using RNA-sequencing. A total of 1665 differentially expressed genes (DEGs) were specifically identified, and based on gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the transcription factor activity, protein kinase activity, and the plant hormone signal transduction process were significantly enriched...
February 15, 2019: International Journal of Molecular Sciences
Hsing-Fang Lu, Kuo-Sheng Hung, Hou-Wei Chu, Henry Sung-Ching Wong, Jihye Kim, Bo Youl Choi, Mi Kyung Kim, Yu-Ting Tai, Shiro Ikegawa, Er-Chieh Cho, Wei-Chiao Chang
The stiffness index (SI) from quantitative ultrasound measurements is a good indicator of bone-mineral density and may be used to predict risk of osteoporotic fracture. We conducted a genome-wide association study (GWAS) for SI using 7,742 individuals from the Taiwan Biobank, followed by a replication study in a Korean population (n = 2,955). Approximately 6.1 million SNPs were subjected to association analysis, and SI-associated variants were identified. We further conducted meta-analysis of Taiwan Biobank significant SNPs with a Korean population-based cohort...
February 19, 2019: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Da Wei Huang, Moez Dawood, Calvin A Johnson, Roland Schmitz
High-throughput mRNA sequencing (RNA-Seq) provides both qualitative and quantitative evaluation of the transcriptome. This method uses complementary DNA (cDNA) to generate several millions of short sequence reads that are aligned to a reference genome allowing the comprehensive characterization of the transcripts in a cell. RNA-Seq has a wide variety of applications which lead to a pervasive adoption of this method well beyond the genomics community and a deployment of this technique as a standard part of the toolkit applied in life sciences...
2019: Methods in Molecular Biology
Huimin Cai, Qiye Li, Xiaodong Fang, Ji Li, Nicholas E Curtis, Andreas Altenburger, Tomoko Shibata, Mingji Feng, Taro Maeda, Julie A Schwartz, Shuji Shigenobu, Nina Lundholm, Tomoaki Nishiyama, Huanming Yang, Mitsuyasu Hasebe, Shuaicheng Li, Sidney K Pierce, Jian Wang
Elysia chlorotica, a sacoglossan sea slug found off the East Coast of the United States, is well-known for its ability to sequester chloroplasts from its algal prey and survive by photosynthesis for up to 12 months in the absence of food supply. Here we present a draft genome assembly of E. chlorotica that was generated using a hybrid assembly strategy with Illumina short reads and PacBio long reads. The genome assembly comprised 9,989 scaffolds, with a total length of 557 Mb and a scaffold N50 of 442 kb...
February 19, 2019: Scientific Data
Xabier Agirre, Cem Meydan, Yanwen Jiang, Leire Garate, Ashley S Doane, Zhuoning Li, Akanksha Verma, Bruno Paiva, José I Martín-Subero, Olivier Elemento, Christopher E Mason, Felipe Prosper, Ari Melnick
lncRNAs make up a majority of the human transcriptome and have key regulatory functions. Here we perform unbiased de novo annotation of transcripts expressed during the human humoral immune response to find 30% of the human genome transcribed during this process, yet 58% of these transcripts manifest striking differential expression, indicating an lncRNA phylogenetic relationship among cell types that is more robust than that of coding genes. We provide an atlas of lncRNAs in naive and GC B-cells that indicates their partition into ten functionally categories based on chromatin features, DNase hypersensitivity and transcription factor localization, defining lncRNAs classes such as enhancer-RNAs (eRNA), bivalent-lncRNAs, and CTCF-associated, among others...
February 18, 2019: Nature Communications
Katherine T Nesbit, Travis Fleming, Grant Batzel, Amara Pouv, Hannah D Rosenblatt, Douglas A Pace, Amro Hamdoun, Deirdre C Lyons
Although sea urchins are one of the oldest and most widely used marine model systems, few species have been routinely kept in culture through multiple generations. The workhorse of the field is the purple urchin Strongylocentrotus purpuratus. However, one disadvantage of S. purpuratus is its long generation time, making it impractical as a model for generating and maintaining transgenic lines. In an effort to develop a sea urchin that is suitable for transgenerational experiments and the generation of transgenic lines, we have focused on development of updated culturing methods and genomic resources for the painted sea urchin, Lytechinus pictus...
2019: Methods in Cell Biology
Alper Akay, David Jordan, Isabela Cunha Navarro, Tomasz Wrzesinski, Chris P Ponting, Eric A Miska, Wilfried Haerty
BACKGROUND: Functional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20 years ago. The last decade of research has seen a tremendous increase in the number of non-coding RNAs identified in various organisms. While we have mechanistic understandings of small non-coding RNA pathways, long non-coding RNAs represent a diverse class of active transcripts whose function remains less well characterised. RESULTS: By analysing hundreds of published transcriptome datasets, we annotated 3392 potential lncRNAs including 143 multi-exonic loci that showed increased nucleotide conservation and GC content relative to other non-coding regions...
February 18, 2019: BMC Biology
Satnam Singh, Mridula Gupta, Suneet Pandher, Gurmeet Kaur, Neha Goel, Pankaj Rathore, Subba Reddy Palli
BACKGROUND: Thrips tabaci is a severe pest of onion and cotton. Due to lack of information on its genome or transcriptome, not much is known about this insect at the molecular level. To initiate molecular studies in this insect, RNA was sequenced; de novo transcriptome assembly and analysis were performed. The RNAseq data was used to identify reference and RNAi pathway genes in this insect. Additionally, feeding RNAi was demonstrated in T. tabaci for the first time. RESULTS: From the assembled transcriptome, 27,836 coding sequence (CDS) with an average size of 1236 bp per CDS were identified...
February 18, 2019: BMC Molecular Biology
Xilong Liang, Xue Hou, Jianying Li, Yiqiang Han, Yuxian Zhang, Naijie Feng, Jidao Du, Wenhui Zhang, Dianfeng Zheng, Shumei Fang
BACKGROUND: Continuous cropping stress involves such factors as biological barriers, allelopathic autotoxicity, deterioration of soil physicochemical properties, and soil fertility imbalance and is regarded as a kind of comprehensive stress limiting soybean yield and quality. Genomic DNA methylation is an important regulatory mechanism for plants to resist various environmental stresses. Therefore, it is especially worthwhile to reveal genomic methylation characteristics under stress and clarify the relationship between DNA methylation status and continuous cropping stress adaptability in soybean...
February 18, 2019: BMC Plant Biology
Liang Sun, Upinder S Gill, Raja Sekhar Nandety, Soonil Kwon, Perdeep Mehta, Rebecca Dickstein, Michael K Udvardi, Kirankumar S Mysore, Jiangqi Wen
From a single transgenic line harboring five Tnt1 transposon insertions, we generated a near-saturated insertion population in Medicago truncatula. Using thermal asymmetric interlaced (TAIL) PCR followed by sequencing, we recovered 388,888 flanking sequence tags (FSTs) from 21,741 insertion lines in this population. FST recovery from 14 Tnt1 lines using the whole genome sequencing and/or Tnt1-capture sequencing approaches suggests an average of 80 insertions per line, which is more than previous estimation of 25 insertions...
February 18, 2019: Plant Journal: for Cell and Molecular Biology
Zhijie Han, Weiwei Xue, Lin Tao, Feng Zhu
The pathogenesis of Alzheimer's disease (AD) is identified to be significantly regulated by long non-coding RNA (lncRNA) based on in vivo and clinical experiments. Single nucleotide polymorphisms (SNPs) can strongly impact expression and function of lncRNA in AD, and previous genome-wide associations studies (GWAS) have discovered substantial amount of risk SNPs associated with AD. However, current studies omit the important information about SNPs when identifying potential AD-related lncRNAs. In addition to single discovery approach and small-scale samples in these studies, the number of lncRNAs discovered as keys in AD is limited...
February 13, 2019: Journal of Alzheimer's Disease: JAD
Qun-Feng Lu, De-Min Cao, Li-Li Su, Song-Bo Li, Guang-Bin Ye, Xiao-Ying Zhu, Ju-Ping Wang
N. gonorrhoeae and N. meningitidis , the only two human pathogens of Neisseria , are closely related species. But the niches they survived in and their pathogenic characteristics are distinctly different. However, the genetic basis of these differences has not yet been fully elucidated. In this study, comparative genomics analysis was performed based on 15 N. gonorrhoeae , 75 N. meningitidis , and 7 nonpathogenic Neisseria genomes. Core-pangenome analysis found 1111 conserved gene families among them, and each of these species groups had opening pangenome...
2019: International Journal of Genomics
Ying Cao, Kun Zhang, Lirong Liu, Wei Li, Bin Zhu, Shuang Zhang, Ping Xu, Wenjun Liu, Jing Li
Background: Influenza A virus (IAV) belongs to the Orthomyxoviridae family. IAV causes a highly contagious respiratory disease in humans that exacts severe economic losses globally. The virus uses strategies developed to exploit and subvert cellular proteins and pathways to increase its own replication and to inhibit antiviral immune response. Results: A/bar-headed goose/Qinghai/1/2005 (A/QH) was able to infect A549 and 293 T cells, with a high infection rate for A549 cells...
2019: Hereditas
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