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https://www.readbyqxmd.com/read/29166127/bat-biology-genomes-and-the-bat1k-project-to-generate-chromosome-level-genomes-for-all-living-bat-species
#1
Emma Teeling, Sonja Vernes, Liliana M Davalos, David A Ray, M Thomas P Gilbert, Eugene Myers, Bat K Consortium
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene...
November 20, 2017: Annual Review of Animal Biosciences
https://www.readbyqxmd.com/read/29163600/plastome-rearrangements-in-the-adenocalymma-neojobertia-clade-bignonieae-bignoniaceae-and-its-phylogenetic-implications
#2
Luiz H M Fonseca, Lúcia G Lohmann
The chloroplast is one of the most important organelles of plants. This organelle has a circular DNA with approximately 130 genes. The use of plastid genomic data in phylogenetic and evolutionary studies became possible with high-throughput sequencing methods, which allowed us to rapidly obtain complete genomes at a reasonable cost. Here, we use high-throughput sequencing to study the "Adenocalymma-Neojobertia" clade (Bignonieae, Bignoniaceae). More specifically, we use Hi-Seq Illumina technology to sequence 10 complete plastid genomes...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163598/an-rna-sequencing-transcriptome-analysis-of-grasspea-lathyrus-sativus-l-and-development-of-ssr-and-kasp-markers
#3
Xiaopeng Hao, Tao Yang, Rong Liu, Jinguo Hu, Yang Yao, Marina Burlyaeva, Yan Wang, Guixing Ren, Hongyan Zhang, Dong Wang, Jianwu Chang, Xuxiao Zong
Grasspea (Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeq(TM) 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163571/setting-up-shop-the-formation-and-function-of-the-viral-factories-of-cauliflower-mosaic-virus
#4
REVIEW
James E Schoelz, Scott Leisner
Similar to cells, viruses often compartmentalize specific functions such as genome replication or particle assembly. Viral compartments may contain host organelle membranes or they may be mainly composed of viral proteins. These compartments are often termed: inclusion bodies (IBs), viroplasms or viral factories. The same virus may form more than one type of IB, each with different functions, as illustrated by the plant pararetrovirus, Cauliflower mosaic virus (CaMV). CaMV forms two distinct types of IBs in infected plant cells, those composed mainly of the viral proteins P2 (which are responsible for transmission of CaMV by insect vectors) and P6 (required for viral intra-and inter-cellular infection), respectively...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163564/non-replicative-integral-membrane-proteins-encoded-by-plant-alpha-like-viruses-emergence-of-diverse-orphan-orfs-and-movement-protein-genes
#5
Andrey G Solovyev, Sergey Y Morozov
Fast accumulation of sequencing data on plant virus genomes and plant transcriptomes demands periodic re-evaluation of current views on the genome evolution of viruses. Here, we substantiate and further detail our previously mostly speculative model on the origin and evolution of triple gene block (TGB) encoding plant virus movement proteins TGB1, TGB2, and TGB3. Recent experimental data on functional competence of transport gene modules consisting of two proteins related to TGB1 and TGB2, as well as sequence analysis data on similarity of TGB2 and TGB3 encoded by a viral genome and virus-like RNAs identified in a plant transcriptomes, suggest that TGB evolution involved events of gene duplication and gene transfer between viruses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163486/structure-and-diversity-of-the-rhesus-macaque-immunoglobulin-loci-through-multiple-de-novo-genome-assemblies
#6
Akshaya Ramesh, Sam Darko, Axin Hua, Glenn Overman, Amy Ransier, Joseph R Francica, Ashley Trama, Georgia D Tomaras, Barton F Haynes, Daniel C Douek, Thomas B Kepler
The rhesus macaque is a critically important animal model in biomedical research, most recently playing a key role in the development of vaccines against human immunodeficiency virus-1. Nevertheless, the immunoglobulin (Ig) loci of macaques are as yet incompletely determined and our understanding of differences between human and macaque humoral immunity remains deficient. We completed a high-coverage, high-quality whole genome sequencing and assembly project with a single rhesus macaque of Indian origin, and partial genome assemblies using genomic molecular targeting of the Ig loci in nine other rhesus macaques of Indian origin...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29163419/reconstruction-of-diverse-verrucomicrobial-genomes-from-metagenome-datasets-of-freshwater-reservoirs
#7
Pedro J Cabello-Yeves, Rohit Ghai, Maliheh Mehrshad, Antonio Picazo, Antonio Camacho, Francisco Rodriguez-Valera
The phylum Verrucomicrobia contains freshwater representatives which remain poorly studied at the genomic, taxonomic, and ecological levels. In this work we present eighteen new reconstructed verrucomicrobial genomes from two freshwater reservoirs located close to each other (Tous and Amadorio, Spain). These metagenome-assembled genomes (MAGs) display a remarkable taxonomic diversity inside the phylum and comprise wide ranges of estimated genome sizes (from 1.8 to 6 Mb). Among all Verrucomicrobia studied we found some of the smallest genomes of the Spartobacteria and Opitutae classes described so far...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163389/genome-replication-in-thermococcus-kodakarensis-independent-of-cdc6-and-an-origin-of-replication
#8
Alexandra M Gehring, David P Astling, Rie Matsumi, Brett W Burkhart, Zvi Kelman, John N Reeve, Kenneth L Jones, Thomas J Santangelo
The initiation of DNA replication is typically tightly regulated by proteins that form initiation complexes at specific sequences known as replication origins. In Archaea and Eukaryotes, Cdc6, a near-universally conserved protein binds and facilitates the origin-dependent assembly of the replicative apparatus. TK1901 encodes Cdc6 in Thermococcus kodakarensis but, as we report here, TK1901 and the presumed origin of replication can be deleted from the genome of this hyperthermophilic Archaeon without any detectable effects on growth, genetic competence or the ability to support autonomous plasmid replication...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29162056/synima-a-synteny-imaging-tool-for-annotated-genome-assemblies
#9
Rhys A Farrer
BACKGROUND: Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes. RESULTS: Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29162031/norgal-extraction-and-de-novo-assembly-of-mitochondrial-dna-from-whole-genome-sequencing-data
#10
Kosai Al-Nakeeb, Thomas Nordahl Petersen, Thomas Sicheritz-Pontén
BACKGROUND: Whole-genome sequencing (WGS) projects provide short read nucleotide sequences from nuclear and possibly organelle DNA depending on the source of origin. Mitochondrial DNA is present in animals and fungi, while plants contain DNA from both mitochondria and chloroplasts. Current techniques for separating organelle reads from nuclear reads in WGS data require full reference or partial seed sequences for assembling. RESULTS: Norgal (de Novo ORGAneLle extractor) avoids this requirement by identifying a high frequency subset of k-mers that are predominantly of mitochondrial origin and performing a de novo assembly on a subset of reads that contains these k-mers...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29161754/the-sorghum-bicolor-reference-genome-improved-assembly-gene-annotations-a-transcriptome-atlas-and-signatures-of-genome-organization
#11
Ryan F McCormick, Sandra K Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock D Weers, Brian McKinley, Ashley Mattison, Daryl T Morishige, Jane Grimwood, Jeremy Schmutz, John E Mullet
Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29160428/plasmid-mediated-mcr-1-in-carbapenem-susceptible-escherichia-coli-st156-causing-a-blood-infection-an-unnoticeable-spread-of-colistin-resistance-in-brazil
#12
Flavia Rossi, Raquel Girardello, Carlos Morais, Ana Paula Cury, Layla Farage Martins, Aline Maria da Silva, Edson Abdala, João Carlos Setubal, Alberto José da Silva Duarte
OBJECTIVE: We describe an IncX4 pHC891/16mcr plasmid carrying mcr-1 in a colistin-resistant and carbapenem-susceptible E. coli isolate (HC891/16), ST156, which caused a blood infection in a Brazilian patient with gallbladder adenocarcinoma. METHODS: Strain HC891/16 was subjected to whole genome sequencing using the MiSeq Platform (Illumina, Inc., USA). Assembly was performed using Mira and ABACAS. RESULTS: The isolates showed resistance only to ciprofloxacin, ampicillin and cefoxitin, and whole-genome sequencing revealed the presence of aac(6')Ib-cr and blaTEM1...
October 2017: Clinics
https://www.readbyqxmd.com/read/29159421/qtl-mapping-of-downy-and-powdery-mildew-resistances-in-pi-197088-cucumber-with-genotyping-by-sequencing-in-ril-population
#13
Yuhui Wang, Kyle VandenLangenberg, Changlong Wen, Todd C Wehner, Yiqun Weng
Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'...
November 20, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29159068/transcriptome-analysis-of-the-chinese-giant-salamander-andrias-davidianus-using-rna-sequencing
#14
Yong Huang, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/29158994/detection-of-bacterial-contaminants-and-hybrid-sequences-in-the-genome-of-the-kelp-saccharina-japonica-using-taxoblast
#15
Simon M Dittami, Erwan Corre
Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences...
2017: PeerJ
https://www.readbyqxmd.com/read/29158974/whole-genome-sequencing-of-rhodotorula-mucilaginosa-isolated-from-the-chewing-stick-distemonanthus-benthamianus-insights-into-rhodotorula-phylogeny-mitogenome-dynamics-and-carotenoid-biosynthesis
#16
Han Ming Gan, Bolaji N Thomas, Nicole T Cavanaugh, Grace H Morales, Ashley N Mayers, Michael A Savka, André O Hudson
In industry, the yeast Rhodotorula mucilaginosa is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus Rhodotorula is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production...
2017: PeerJ
https://www.readbyqxmd.com/read/29158639/mining-and-characterization-of-est-ssr-markers-for-zingiber-officinale-roscoe-with-transferability-to-other-species-of-zingiberaceae
#17
Praveen Awasthi, Ashish Singh, Gulfam Sheikh, Vidushi Mahajan, Ajai Prakash Gupta, Suphla Gupta, Yashbir S Bedi, Sumit G Gandhi
Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158627/development-of-transcriptome-based-web-genomic-resources-of-yellow-mosaic-disease-in-vigna-mungo
#18
Rahul Singh Jasrotia, Mir Asif Iquebal, Pramod Kumar Yadav, Neeraj Kumar, Sarika Jaiswal, U B Angadi, Anil Rai, Dinesh Kumar
Vigna mungo (Urdbean) is cultivated in the tropical and sub-tropical continental region of Asia. It is not only important source of dietary protein and nutritional elements, but also of immense value to human health due to medicinal properties. Yellow mosaic disease caused by Mungbean Yellow Mosaic India Virus is known to incur huge loss to crop, adversely affecting crop yield. Contrasting genotypes are ideal source for knowledge discovery of plant defence mechanism and associated candidate genes for varietal improvement...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158564/long-read-genome-sequence-assembly-provides-insight-into-ongoing-retroviral-invasion-of-the-koala-germline
#19
Matthew Hobbs, Andrew King, Ryan Salinas, Zhiliang Chen, Kyriakos Tsangaras, Alex D Greenwood, Rebecca N Johnson, Katherine Belov, Marc R Wilkins, Peter Timms
The koala retrovirus (KoRV) is implicated in several diseases affecting the koala (Phascolarctos cinereus). KoRV provirus can be present in the genome of koalas as an endogenous retrovirus (present in all cells via germline integration) or as exogenous retrovirus responsible for somatic integrations of proviral KoRV (present in a limited number of cells). This ongoing invasion of the koala germline by KoRV provides a powerful opportunity to assess the viral strategies used by KoRV in an individual. Analysis of a high-quality genome sequence of a single koala revealed 133 KoRV integration sites...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158546/the-aegilops-tauschii-genome-reveals-multiple-impacts-of-transposons
#20
Guangyao Zhao, Cheng Zou, Kui Li, Kai Wang, Tianbao Li, Lifeng Gao, Xiaoxia Zhang, Hongjin Wang, Zujun Yang, Xu Liu, Wenkai Jiang, Long Mao, Xiuying Kong, Yuannian Jiao, Jizeng Jia
Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes...
November 20, 2017: Nature Plants
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