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DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

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https://www.readbyqxmd.com/read/27803028/unveiling-dna-structural-features-of-promoters-associated-with-various-types-of-tsss-in-prokaryotic-transcriptomes-and-their-role-in-gene-expression
#1
Aditya Kumar, Manju Bansal
Next-generation sequencing studies have revealed that a variety of transcripts are present in the prokaryotic transcriptome and a significant fraction of them are functional, being involved in various regulatory activities apart from coding for proteins. Identification of promoters associated with different transcripts is necessary for characterization of the transcriptome. Promoter regions have been shown to have unique structural features as compared with their flanking region, in organisms covering all domains of life...
November 1, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27803027/quantum-changes-in-helicobacter-pylori-gene-expression-accompany-host-adaptation
#2
Eng-Guan Chua, Michael J Wise, Yalda Khosravi, Shih-Wee Seow, Arlaine A Amoyo, Sven Pettersson, Fanny Peters, Chin-Yen Tay, Timothy T Perkins, Mun-Fai Loke, Barry J Marshall, Jamuna Vadivelu
Helicobacter pylori is a highly successful gastric pathogen. High genomic plasticity allows its adaptation to changing host environments. Complete genomes of H. pylori clinical isolate UM032 and its mice-adapted serial derivatives 298 and 299, generated using both PacBio RS and Illumina MiSeq sequencing technologies, were compared to identify novel elements responsible for host-adaptation. The acquisition of a jhp0562-like allele, which encodes for a galactosyltransferase, was identified in the mice-adapted strains...
November 1, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27773878/a-genomic-view-of-food-related-and-probiotic-enterococcus-strains
#3
Julieta Bonacina, Nadia Suárez, Ricardo Hormigo, Silvina Fadda, Marcus Lechner, Lucila Saavedra
The study of enterococcal genomes has grown considerably in recent years. While special attention is paid to comparative genomic analysis among clinical relevant isolates, in this study we performed an exhaustive comparative analysis of enterococcal genomes of food origin and/or with potential to be used as probiotics. Beyond common genetic features, we especially aimed to identify those that are specific to enterococcal strains isolated from a certain food-related source as well as features present in a species-specific manner...
October 23, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27651094/genome-sequence-of-aspergillus-luchuensis-nbrc-4314
#4
Osamu Yamada, Masayuki Machida, Akira Hosoyama, Masatoshi Goto, Toru Takahashi, Taiki Futagami, Youhei Yamagata, Michio Takeuchi, Tetsuo Kobayashi, Hideaki Koike, Keietsu Abe, Kiyoshi Asai, Masanori Arita, Nobuyuki Fujita, Kazuro Fukuda, Ken-Ichi Higa, Hiroshi Horikawa, Takeaki Ishikawa, Koji Jinno, Yumiko Kato, Kohtaro Kirimura, Osamu Mizutani, Kaoru Nakasone, Motoaki Sano, Yohei Shiraishi, Masatoshi Tsukahara, Katsuya Gomi
Awamori is a traditional distilled beverage made from steamed Thai-Indica rice in Okinawa, Japan. For brewing the liquor, two microbes, local kuro (black) koji mold Aspergillus luchuensis and awamori yeast Saccharomyces cerevisiae are involved. In contrast, that yeasts are used for ethanol fermentation throughout the world, a characteristic of Japanese fermentation industries is the use of Aspergillus molds as a source of enzymes for the maceration and saccharification of raw materials. Here we report the draft genome of a kuro (black) koji mold, A...
September 20, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27581378/comparison-of-the-complete-genome-sequences-of-four-%C3%AE-hexachlorocyclohexane-degrading-bacterial-strains-insights-into-the-evolution-of-bacteria-able-to-degrade-a-recalcitrant-man-made-pesticide
#5
Michiro Tabata, Satoshi Ohhata, Yuki Nikawadori, Kouhei Kishida, Takuya Sato, Toru Kawasumi, Hiromi Kato, Yoshiyuki Ohtsubo, Masataka Tsuda, Yuji Nagata
γ-Hexachlorocyclohexane (γ-HCH) is a recalcitrant man-made chlorinated pesticide. Here, the complete genome sequences of four γ-HCH-degrading sphingomonad strains, which are most unlikely to have been derived from one ancestral γ-HCH degrader, were compared. Together with several experimental data, we showed that (i) all the four strains carry almost identical linA to linE genes for the conversion of γ-HCH to maleylacetate (designated "specific" lin genes), (ii) considerably different genes are used for the metabolism of maleylacetate in one of the four strains, and (iii) the linKLMN genes for the putative ABC transporter necessary for γ-HCH utilization exhibit structural divergence, which reflects the phylogenetic relationship of their hosts...
August 30, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27567261/draft-genome-sequence-of-cicer-reticulatum-l-the-wild-progenitor-of-chickpea-provides-a-resource-for-agronomic-trait-improvement
#6
Sonal Gupta, Kashif Nawaz, Sabiha Parween, Riti Roy, Kamlesh Sahu, Anil Kumar Pole, Hitaishi Khandal, Rishi Srivastava, Swarup Kumar Parida, Debasis Chattopadhyay
Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny...
August 26, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27559081/ultra-deep-sequencing-of-ribosome-associated-poly-adenylated-rna-in-early-drosophila-embryos-reveals-hundreds-of-conserved-translated-sorfs
#7
Hongmei Li, Chuansheng Hu, Ling Bai, Hua Li, Mingfa Li, Xiaodong Zhao, Daniel M Czajkowsky, Zhifeng Shao
There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already identified to play critical roles in growth, development, and disease. However, our understanding of their biological importance has been hindered owing to the significant technical challenges limiting their annotation. Here we combined ultra-deep sequencing of ribosome-associated poly-adenylated RNAs with rigorous conservation analysis to identify a comprehensive population of translated sORFs during early Drosophila embryogenesis...
August 24, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27501718/a-draft-genome-of-the-brown-alga-cladosiphon-okamuranus-s-strain-a-platform-for-future-studies-of-mozuku-biology
#8
Koki Nishitsuji, Asuka Arimoto, Kenji Iwai, Yusuke Sudo, Kanako Hisata, Manabu Fujie, Nana Arakaki, Tetsuo Kushiro, Teruko Konishi, Chuya Shinzato, Noriyuki Satoh, Eiichi Shoguchi
The brown alga, Cladosiphon okamuranus (Okinawa mozuku), is economically one of the most important edible seaweeds, and is cultivated for market primarily in Okinawa, Japan. C. okamuranus constitutes a significant source of fucoidan, which has various physiological and biological activities. To facilitate studies of seaweed biology, we decoded the draft genome of C. okamuranus S-strain. The genome size of C. okamuranus was estimated as ∼140 Mbp, smaller than genomes of two other brown algae, Ectocarpus siliculosus and Saccharina japonica Sequencing with ∼100× coverage yielded an assembly of 541 scaffolds with N50 = 416 kbp...
August 8, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27436340/toward-high-resolution-population-genomics-using-archaeological-samples
#9
Irina Morozova, Pavel Flegontov, Alexander S Mikheyev, Sergey Bruskin, Hosseinali Asgharian, Petr Ponomarenko, Vladimir Klyuchnikov, GaneshPrasad ArunKumar, Egor Prokhortchouk, Yuriy Gankin, Evgeny Rogaev, Yuri Nikolsky, Ancha Baranova, Eran Elhaik, Tatiana V Tatarinova
The term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27345721/wrky-transcription-factor-genes-in-wild-rice-oryza-nivara
#10
Hengjian Xu, Kenneth A Watanabe, Liyuan Zhang, Qingxi J Shen
The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27345720/a-novel-skew-analysis-reveals-substitution-asymmetries-linked-to-genetic-code-gc-biases-and-poliii-a-subunit-isoforms
#11
Konstantinos Apostolou-Karampelis, Christoforos Nikolaou, Yannis Almirantis
Strand biases reflect deviations from a null expectation of DNA evolution that assumes strand-symmetric substitution rates. Here, we present strong evidence that nearest-neighbour preferences are a strand-biased feature of bacterial genomes, indicating neighbour-dependent substitution asymmetries. To detect such asymmetries we introduce an alignment free index (relative abundance skews). The profiles of relative abundance skews along coding sequences can trace the phylogenetic relations of bacteria, suggesting that the patterns of neighbour-dependent substitution strand-biases are not common among different lineages, but are rather species-specific...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27345719/complete-telomere-to-telomere-de-novo-assembly-of-the-plasmodium-falciparum-genome-through-long-read-11%C3%A2-kb-single-molecule-real-time-sequencing
#12
Shruthi Sridhar Vembar, Matthew Seetin, Christine Lambert, Maria Nattestad, Michael C Schatz, Primo Baybayan, Artur Scherf, Melissa Laird Smith
The application of next-generation sequencing to estimate genetic diversity of Plasmodium falciparum, the most lethal malaria parasite, has proved challenging due to the skewed AT-richness [∼80.6% (A + T)] of its genome and the lack of technology to assemble highly polymorphic subtelomeric regions that contain clonally variant, multigene virulence families (Ex: var and rifin). To address this, we performed amplification-free, single molecule, real-time sequencing of P. falciparum genomic DNA and generated reads of average length 12 kb, with 50% of the reads between 15...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27330141/whole-genomic-dna-sequencing-and-comparative-genomic-analysis-of-arthrospira-platensis-high-genome-plasticity-and-genetic-diversity
#13
Teng Xu, Song Qin, Yongwu Hu, Zhijian Song, Jianchao Ying, Peizhen Li, Wei Dong, Fangqing Zhao, Huanming Yang, Qiyu Bao
Arthrospira platensis is a multi-cellular and filamentous non-N2-fixing cyanobacterium that is capable of performing oxygenic photosynthesis. In this study, we determined the nearly complete genome sequence of A. platensis YZ. A. platensis YZ genome is a single, circular chromosome of 6.62 Mb in size. Phylogenetic and comparative genomic analyses revealed that A. platensis YZ was more closely related to A. platensis NIES-39 than Arthrospira sp. PCC 8005 and A. platensis C1. Broad gene gains were identified between A...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27298380/a-gene-based-map-of-the-nod-factor-independent-aeschynomene-evenia-sheds-new-light-on-the-evolution-of-nodulation-and-legume-genomes
#14
Clémence Chaintreuil, Ronan Rivallan, David J Bertioli, Christophe Klopp, Jérôme Gouzy, Brigitte Courtois, Philippe Leleux, Guillaume Martin, Jean-François Rami, Djamel Gully, Hugues Parrinello, Dany Séverac, Delphine Patrel, Joël Fardoux, William Ribière, Marc Boursot, Fabienne Cartieaux, Pierre Czernic, Pascal Ratet, Pierre Mournet, Eric Giraud, Jean-François Arrighi
Aeschynomene evenia has emerged as a new model legume for the deciphering of the molecular mechanisms of an alternative symbiotic process that is independent of the Nod factors. Whereas most of the research on nitrogen-fixing symbiosis, legume genetics and genomics has so far focused on Galegoid and Phaseolid legumes, A. evenia falls in the more basal and understudied Dalbergioid clade along with peanut (Arachis hypogaea). To provide insights into the symbiotic genes content and the structure of the A. evenia genome, we established a gene-based genetic map for this species...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27260513/8-oxo-7-8-dihydro-2-deoxyguanosine-and-other-lesions-along-the-coding-strand-of-the-exon-5-of-the-tumour-suppressor-gene-p53-in-a-breast-cancer-case-control-study
#15
Beniamino Brancato, Armelle Munnia, Filippo Cellai, Elisabetta Ceni, Tommaso Mello, Simonetta Bianchi, Sandra Catarzi, Gabriella G Risso, Andrea Galli, Marco E M Peluso
The next-generation sequencing studies of breast cancer have reported that the tumour suppressor P53 (TP53) gene is mutated in more than 40% of the tumours. We studied the levels of oxidative lesions, including 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), along the coding strand of the exon 5 in breast cancer patients as well as in a reactive oxygen species (ROS)-attacked breast cancer cell line using the ligation-mediated polymerase chain reaction technique. We detected a significant 'in vitro' generation of 8-oxodG between the codons 163 and 175, corresponding to a TP53 region with high mutation prevalence, after treatment with xanthine plus xanthine oxidase, a ROS-generating system...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27260512/selection-for-reduced-translation-costs-at-the-intronic-5-end-in-fungi
#16
Zohar Zafrir, Hadas Zur, Tamir Tuller
It is generally believed that introns are not translated; therefore, the potential intronic features that may be related to the translation step (occurring after splicing) have yet to be thoroughly studied. Here, focusing on four fungi, we performed for the first time a comprehensive study aimed at characterizing how translation efficiency is encoded in introns and affects their evolution. By analysing their intronome we provide evidence of selection for STOP codons close to the intronic 5' end, and show that the beginning of introns are selected for significantly high translation, presumably to reduce translation and metabolic costs in cases of non-spliced introns...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27106267/identifying-the-genome-wide-genetic-variation-between-precocious-trifoliate-orange-and-its-wild-type-and-developing-new-markers-for-genetics-research
#17
Jin-Zhi Zhang, Sheng-Rui Liu, Chun-Gen Hu
To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (Poncirus trifoliata L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27477585/artifactual-mutations-resulting-from-dna-lesions-limit-detection-levels-in-ultrasensitive-sequencing-applications
#18
Barbara Arbeithuber, Kateryna D Makova, Irene Tiemann-Boege
The need in cancer research or evolutionary biology to detect rare mutations or variants present at very low frequencies (<10(-5)) poses an increasing demand on lowering the detection limits of available methods. Here we demonstrated that amplifiable DNA lesions introduce important error sources in ultrasensitive technologies such as single molecule PCR (smPCR) applications (e.g. droplet-digital PCR), or next-generation sequencing (NGS) based methods. Using templates with known amplifiable lesions (8-oxoguanine, deaminated 5-methylcytosine, uracil, and DNA heteroduplexes), we assessed with smPCR and duplex sequencing that templates with these lesions were amplified very efficiently by proofreading polymerases (except uracil), leading to G->T, and to a lesser extent, to unreported G->C substitutions at 8-oxoguanine lesions, and C->T transitions in amplified uracil containing templates...
July 31, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27458999/draft-genome-sequence-of-an-inbred-line-of-chenopodium-quinoa-an-allotetraploid-crop-with-great-environmental-adaptability-and-outstanding-nutritional-properties
#19
Yasuo Yasui, Hideki Hirakawa, Tetsuo Oikawa, Masami Toyoshima, Chiaki Matsuzaki, Mariko Ueno, Nobuyuki Mizuno, Yukari Nagatoshi, Tomohiro Imamura, Manami Miyago, Kojiro Tanaka, Kazuyuki Mise, Tsutomu Tanaka, Hiroharu Mizukoshi, Masashi Mori, Yasunari Fujita
Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy...
July 25, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27426468/draft-genome-sequence-of-an-elite-dura-palm-and-whole-genome-patterns-of-dna-variation-in-oil-palm
#20
Jingjing Jin, May Lee, Bin Bai, Yanwei Sun, Jing Qu, Rahmadsyah, Yuzer Alfiko, Chin Huat Lim, Antonius Suwanto, Maria Sugiharti, Limsoon Wong, Jian Ye, Nam-Hai Chua, Gen Hua Yue
Oil palm is the world's leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18...
July 17, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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