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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/29718217/detection-of-genome-edited-cells-by-oligoribonucleotide-interference-pcr
#1
Toshitsugu Fujita, Miyuki Yuno, Fusako Kitaura, Hodaka Fujii
Genome editing by engineered sequence-specific nucleases, such as the clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for analysis of gene functions. Several techniques have been developed for detection of genome-edited cells, but simple, cost-effective, and positive detection methods remain limited. Recently, we developed oligoribonucleotide (ORN) interference-PCR (ORNi-PCR), in which hybridization of an ORN with a complementary DNA sequence inhibits amplification across the sequence...
April 27, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29659762/activation-of-%C3%AF-20-dependent-recombination-and-horizontal-gene-transfer-in-mycoplasma-genitalium
#2
Sergi Torres-Puig, Carlos Martínez-Torró, Ignasi Granero-Moya, Enrique Querol, Jaume Piñol, Oscar Q Pich
In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of σ20, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, σ20 activation is rare and the factors governing its intermittent activity are unknown. Two σ20-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for σ20 function...
April 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29617732/a-new-approach-for-comprehensively-describing-heterogametic-sex-chromosomes
#3
Shenglong Li, Masahiro Ajimura, Zhiwei Chen, Jianqiu Liu, Enxiang Chen, Huizhen Guo, Vidya Tadapatri, Chilakala Gangi Reddy, Jiwei Zhang, Hirohisa Kishino, Hiroaki Abe, Qingyou Xia, Kallare P Arunkumar, Kazuei Mita
Notwithstanding the rapid developments in sequencing techniques, Y and W sex chromosomes have still been mostly excluded from whole genome sequencing projects due to their high repetitive DNA content. Therefore, Y and W chromosomes are poorly described in most species despite their biological importance. Several methods were developed for identifying Y or W-linked sequences among unmapped scaffolds. However, it is not enough to discover functional regions from short unmapped scaffolds. Here, we provide a new and simple strategy based on k-mer comparison for comprehensive analysis of the W chromosome in Bombyx mori...
April 2, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29566130/unravelling-the-epigenomic-interactions-between-parental-inbreds-resulting-in-an-altered-hybrid-methylome-in-pigeonpea
#4
Alim Junaid, Himanshu Kumar, A R Rao, A N Patil, N K Singh, Kishor Gaikwad
DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation...
March 16, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29548032/sex-specific-markers-developed-by-next-generation-sequencing-confirmed-an-xx-xy-sex-determination-system-in-bighead-carp-hypophthalmichthys-nobilis-and-silver-carp-hypophthalmichthys-molitrix
#5
Haiyang Liu, Meixia Pang, Xiaomu Yu, Ying Zhou, Jingou Tong, Beide Fu
No abstract text is available yet for this article.
March 14, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29518182/homologue-specific-chromosome-sequencing-characterizes-translocation-junctions-and-permits-allelic-assignment
#6
Fumio Kasai, Jorge C Pereira, Arihiro Kohara, Malcolm A Ferguson-Smith
Chromosome translocations can be detected by cytogenetic analysis, but it is hard to characterize the breakpoints at the sequence level. Chromosome sorting by flow cytometry produces flow karyotypes that enable the isolation of abnormal chromosomes and the generation of chromosome-specific DNA. In this study, a derivative chromosome t(9; 14) and its homologous normal chromosomes 9 and 14 from the Ishikawa 3-H-12 cell line were sorted to collect homologue-specific samples. Chromosome sequencing identified the breakpoint junction in the der(9) at 9p24...
March 6, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29481587/functional-divergence-of-duplicate-genes-several-million-years-after-gene-duplication-in-arabidopsis
#7
Kousuke Hanada, Ayumi Tezuka, Masafumi Nozawa, Yutaka Suzuki, Sumio Sugano, Atsushi J Nagano, Motomi Ito, Shin-Ichi Morinaga
Lineage-specific duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selection pressures immediately after gene duplication is clear in the speciation process. Here, using Illumina DNA-sequencing reads from Arabidopsis halleri, which has multiple closely related species with high-quality genome assemblies (A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups in Brassicaceae...
February 21, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29481583/an-efficient-approach-for-the-development-of-genome-specific-markers-in-allohexaploid-wheat-triticum-aestivum-l-and-its-application-in-the-construction-of-high-density-linkage-maps-of-the-d-genome
#8
Goro Ishikawa, Mika Saito, Tsuyoshi Tanaka, Yuichi Katayose, Hiroyuki Kanamori, Kanako Kurita, Toshiki Nakamura
In common wheat, the development of genotyping platforms has been hampered by the large size of the genome, its highly repetitive elements and its allohexaploid nature. However, recent advances in sequencing technology provide opportunities to resolve these difficulties. Using next-generation sequencing and gene-targeting sequence capture, 12,551 nucleotide polymorphisms were detected in the common wheat varieties 'Hatsumochi' and 'Kitahonami' and were assigned to chromosome arms using International Wheat Genome Sequencing Consortium survey sequences...
February 21, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29444255/identification-of-the-dna-methyltransferases-establishing-the-methylome-of-the-cyanobacterium-synechocystis-sp-pcc-6803
#9
Martin Hagemann, Katrin Gärtner, Matthias Scharnagl, Paul Bolay, Steffen C Lott, Janina Fuss, Bruno Huettel, Richard Reinhardt, Stephan Klähn, Wolfgang R Hess
DNA methylation in bacteria is important for defense against foreign DNA, but is also involved in DNA repair, replication, chromosome partitioning, and regulatory processes. Thus, characterization of the underlying DNA methyltransferases in genetically tractable bacteria is of paramount importance. Here, we characterized the methylome and orphan methyltransferases in the model cyanobacterium Synechocystis sp. PCC 6803. Single molecule real-time (SMRT) sequencing revealed four DNA methylation recognition sequences in addition to the previously known motif m5CGATCG, which is recognized by M...
February 12, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29415277/complete-genome-sequence-and-analysis-of-the-industrial-saccharomyces-cerevisiae-strain-n85-used-in-chinese-rice-wine-production
#10
Weiping Zhang, Yudong Li, Yiwang Chen, Sha Xu, Guocheng Du, Huidong Shi, Jingwen Zhou, Jian Chen
Chinese rice wine is a popular traditional alcoholic beverage in China, while its brewing processes have rarely been explored. We herein report the first gapless, near-finished genome sequence of the yeast strain Saccharomyces cerevisiae N85 for Chinese rice wine production. Several assembly methods were used to integrate Pacific Bioscience (PacBio) and Illumina sequencing data to achieve high-quality genome sequencing of the strain. The genome encodes more than 6,000 predicted proteins, and 238 long non-coding RNAs, which are validated by RNA-sequencing data...
February 5, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29394339/the-genomes-of-two-eutrema-species-provide-insight-into-plant-adaptation-to-high-altitudes
#11
Xinyi Guo, Quanjun Hu, Guoqian Hao, Xiaojuan Wang, Dan Zhang, Tao Ma, Jianquan Liu
Eutrema is a genus in the Brassicaceae, which includes species of scientific and economic importance. Many Eutrema species are montane and/or alpine species that arose very recently, making them ideal candidates for comparative studies to understand both ecological speciation and high-altitude adaptation in plants. Here we provide de novo whole-genome assemblies for a pair of recently diverged perennials with contrasting altitude preferences, the high-altitude E. heterophyllum from the eastern Qinghai-Tibet Plateau and its lowland congener E...
January 30, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29365082/early-microbial-colonization-affects-dna-methylation-of-genes-related-to-intestinal-immunity-and-metabolism-in-preterm-pigs
#12
Xiaoyu Pan, Desheng Gong, Duc Ninh Nguyen, Xinxin Zhang, Qi Hu, Hanlin Lu, Merete Fredholm, Per T Sangild, Fei Gao
Epigenetic regulation may play an important role in mediating microbe-host interactions and adaptation of intestinal gene expression to bacterial colonization just after birth. This is particularly important after preterm birth because the immature intestine is hypersensitive to invading bacteria. We compared the intestinal DNA methylome and microbiome between conventional (CON) and antibiotics-treated (AB) preterm pigs, used as a model for preterm infants. Oral AB treatment reduced bacterial density (∼100-fold), diversity and fermentation, improved the resistance to necrotizing enterocolitis (NEC) and changed the genome-wide DNA methylation in the distal small intestine...
January 19, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29360973/transcriptome-profiling-reveals-infection-strategy-of-an-insect-maculavirus
#13
Susumu Katsuma, Munetaka Kawamoto, Keisuke Shoji, Takahiro Aizawa, Takashi Kiuchi, Natsuko Izumi, Moe Ogawa, Takaaki Mashiko, Hideki Kawasaki, Sumio Sugano, Yukihide Tomari, Yutaka Suzuki, Masashi Iwanaga
Bombyx mori macula-like virus (BmMLV) is a positive, single-stranded insect RNA virus that is closely related to plant maculaviruses. BmMLV is currently characterized as an unclassified maculavirus. BmMLV accumulates at extremely high levels in cell lines derived from the silkworm, Bombyx mori, but it does not lead to lethality and establishes persistent infections. It is unknown how this insect maculavirus replicates and establishes persistent infections in insect cells. Here, we showed that BmMLV p15, which is located on a subgenomic fragment and is not found in plant maculaviruses, is highly expressed in BmMLV-infected silkworm cells and that p15 protein is required to establish BmMLV infections in silkworm cells...
January 17, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29325017/cell-type-resolved-alternative-splicing-patterns-in-mouse-liver
#14
Peng Wu, Donghu Zhou, Weiran Lin, Yanyan Li, Handong Wei, Xiaohong Qian, Ying Jiang, Fuchu He
Alternative splicing (AS) is an important post-transcriptional regulatory mechanism to generate transcription diversity. However, the functional roles of AS in multiple cell types from one organ have not been reported. Here, we provide the most comprehensive profile for cell-type-resolved AS patterns in mouse liver. A total of 13,637 AS events are detected, representing 81.5% of all known AS events in the database. About 46.2% of multi-exon genes undergo AS from the four cell types of mouse liver: hepatocyte, liver sinusoidal endothelial cell, Kupffer cell and hepatic stellate cell, which regulates cell-specific functions and maintains cell characteristics...
January 8, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29315395/comparative-genomic-analyses-reveal-the-features-for-adaptation-to-nematodes-in-fungi
#15
Ruizhen Wang, Leiming Dong, Ran He, Qinghua Wang, Yuequ Chen, Liangjian Qu, Yong-An Zhang
Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche...
January 5, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29315393/sex-specific-markers-developed-by-next-generation-sequencing-confirmed-an-xx-xy-sex-determination-system-in-bighead-carp-hypophthalmichehys-nobilis-and-silver-carp-hypophthalmichthys-molitrix
#16
Haiyang Liu, Meixia Pang, Xiaomu Yu, Ying Zhou, Jingou Tong, Beide Fu
Sex-specific markers are powerful tools for identifying sex-determination system in various animals. Bighead carp (Hypophthalmichehys nobilis) and silver carp (Hypophthalmichthys molitrix) are two of the most important edible fish in Asia, which have a long juvenility period that can lasts for 4-5 years. In this study, we found one sex-specific marker by next-generation sequencing together with bioinformatics analysis in bighead carp. The male-specific markers were used to perform molecular sexing in the progenies of artificial gynogenetic diploids and found all progenies (n = 160) were females...
January 5, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29236947/earliness-traits-in-rapeseed-brassica-napus-snp-loci-and-candidate-genes-identified-by-genome-wide-association-analysis
#17
Qinghong Zhou, Depeng Han, Annaliese S Mason, Can Zhou, Wei Zheng, Yazhen Li, Caijun Wu, Donghui Fu, Yingjin Huang
Life cycle timing is critical for yield and productivity of Brassica napus (rapeseed) cultivars grown in different environments. To facilitate breeding for earliness traits in rapeseed, SNP loci and underlying candidate genes associated with the timing of initial flowering, maturity and final flowering, as well as flowering period (FP) were investigated in two environments in a diversity panel comprising 300 B. napus inbred lines. Genome-wide association studies (GWAS) using 201,817 SNP markers previously developed from SLAF-seq (specific locus amplified fragment sequencing) revealed a total of 131 SNPs strongly linked (P < 4...
December 11, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29211832/ultra-low-input-transcriptomics-reveal-the-spore-functional-content-and-phylogenetic-affiliations-of-poorly-studied-arbuscular-mycorrhizal-fungi
#18
Denis Beaudet, Eric C H Chen, Stephanie Mathieu, Gokalp Yildirir, Steve Ndikumana, Yolande Dalpé, Sylvie Séguin, Laurent Farinelli, Jason E Stajich, Nicolas Corradi
Arbuscular mycorrhizal fungi (AMF) are a group of soil microorganisms that establish symbioses with the vast majority of land plants. To date, generation of AMF coding information has been limited to model genera that grow well axenically; Rhizoglomus and Gigaspora. Meanwhile, data on the functional gene repertoire of most AMF families is non-existent. Here, we provide primary large-scale transcriptome data from eight poorly studied AMF species (Acaulospora morrowiae, Diversispora versiforme, Scutellospora calospora, Racocetra castanea, Paraglomus brasilianum, Ambispora leptoticha, Claroideoglomus claroideum and Funneliformis mosseae) using ultra-low input ribonucleic acid (RNA)-seq approaches...
December 2, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29211829/small-rna-repertoires-and-their-intraspecies-variation-in-aggregatibacter-actinomycetemcomitans
#19
Yuichi Oogai, Yasuhiro Gotoh, Yoshitoshi Ogura, Miki Kawada-Matsuo, Tetsuya Hayashi, Hitoshi Komatsuzawa
Aggregatibacter actinomycetemcomitans is a major periodontal pathogen that has several virulence factors such as leukotoxin and cytolethal distending toxin. Although the genes responsible for virulence have been identified, little is known about their regulatory mechanisms. Small RNA (sRNA) has been recognized as an important factor for gene regulation. To identify new regulatory mechanisms via sRNA in A. actinomycetemcomitans HK1651, we performed a systematic search for sRNAs by RNA-seq and identified 90 intergenic region sRNAs and 30 antisense sRNAs...
December 2, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29117310/sequencing-and-phasing-cancer-mutations-in-lung-cancers-using-a-long-read-portable-sequencer
#20
Ayako Suzuki, Mizuto Suzuki, Junko Mizushima-Sugano, Martin C Frith, Wojciech Makalowski, Takashi Kohno, Sumio Sugano, Katsuya Tsuchihara, Yutaka Suzuki
Here, we employed cDNA amplicon sequencing using a long-read portable sequencer, MinION, to characterize various types of mutations in cancer-related genes, namely, EGFR, KRAS, NRAS and NF1. For homozygous SNVs, the precision and recall rates were 87.5% and 91.3%, respectively. For previously reported hotspot mutations, the precision and recall rates reached 100%. The precise junctions of EML4-ALK, CCDC6-RET and five other gene fusions were also detected. Taking advantages of long-read sequencing, we conducted phasing of EGFR mutations and elucidated the mutational allelic backgrounds of anti-tumor drug-sensitive and resistant mutations, which could provide useful information for selecting therapeutic approaches...
December 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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