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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/30020434/design-and-evaluation-of-a-sequence-capture-system-for-genome-wide-snp-genotyping-in-highly-heterozygous-plant-genomes-a-case-study-with-a-keystone-neotropical-hardwood-tree-genome
#1
Orzenil Bonfim Silva-Junior, Dario Grattapaglia, Evandro Novaes, Rosane G Collevatti
Targeted sequence capture coupled to high-throughput sequencing has become a powerful method for the study of genome-wide sequence variation. Following our recent development of a genome assembly for the Pink Ipê tree (Handroanthus impetiginosus), a widely distributed Neotropical timber species, we now report the development of a set of 24,751 capture probes for single-nucleotide polymorphisms (SNPs) characterization and genotyping across 18,216 distinct loci, sampling more than 10 Mbp of the species genome...
July 17, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29982343/genome-wide-characterization-of-dna-methylation-small-rna-expression-and-histone-h3-lysine-nine-di-methylation-in-brassica-rapa-l
#2
Satoshi Takahashi, Kenji Osabe, Naoki Fukushima, Shohei Takuno, Naomi Miyaji, Motoki Shimizu, Takeshi Takasaki-Yasuda, Yutaka Suzuki, Elizabeth S Dennis, Motoaki Seki, Ryo Fujimoto
Epigenetic gene regulation is crucial to plant life and can involve dynamic interactions between various histone modifications, DNA methylation, and small RNAs. Detailed analysis of epigenome information is anticipated to reveal how the DNA sequence of the genome is translated into the plant's phenotype. The aim of this study was to map the DNA methylation state at the whole genome level and to clarify the relationship between DNA methylation and transcription, small RNA expression, and histone H3 lysine 9 di-methylation (H3K9me2) in Brassica rapa...
June 29, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29947776/the-genome-of-tapeworm-taenia-multiceps-sheds-light-on-understanding-parasitic-mechanism-and-control-of-coenurosis-disease
#3
Wenhui Li, Bo Liu, Yang Yang, Yuwei Ren, Shuai Wang, Conghui Liu, Nianzhang Zhang, Zigang Qu, Wanxu Yang, Yan Zhang, Hongbing Yan, Fan Jiang, Li Li, Shuqu Li, Wanzhong Jia, Hong Yin, Xuepeng Cai, Tao Liu, Donald P McManus, Wei Fan, Baoquan Fu
Coenurosis, caused by the larval coenurus of the tapeworm Taenia multiceps, is a fatal central nervous system disease in both sheep and humans. Though treatment and prevention options are available, the control of coenurosis still faces presents great challenges. Here, we present a high-quality genome sequence of T. multiceps in which 240 Mb (96%) of the genome has been successfully assembled using Pacbio single-molecule real-time (SMRT) and Hi-C data with a N50 length of 44.8 Mb. In total, 49.5 Mb (20.6%) repeat sequences and 13, 013 gene models were identified...
June 25, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29901694/the-gntr-family-transcriptional-regulator-pmm1637-regulates-the-highly-conserved-cyanobacterial-srna-yfr2-in-marine-picocyanobacteria
#4
S Joke Lambrecht, J Mascha L Wahlig, Claudia Steglich
Prochlorococcus is a marine picocyanobacterium with a streamlined genome that is adapted to different ecological niches in the oligotrophic oceans. There are currently >20 regulatory small RNAs (sRNAs) that have been identified in the model strain Prochlorococcus MED4. While most of these sRNAs are ecotype-specific, sRNA homologs of Yfr1 and of the Yfr2 family are widely found throughout the cyanobacterial phylum. Although they were identified 13 yrs ago, the functions of Yfr1 and Yfr2 have remained unknown...
June 12, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29897548/highly-dense-linkage-maps-from-31-full-sibling-families-of-turbot-scophthalmus-maximus-provide-insights-into-recombination-patterns-and-chromosome-rearrangements-throughout-a-newly-refined-genome-assembly
#5
F Maroso, M Hermida, A Millán, A Blanco, M Saura, A Fernández, G Dalla Rovere, L Bargelloni, S Cabaleiro, B Villanueva, C Bouza, P Martínez
Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families...
June 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29897438/optimization-of-single-strand-dna-incorporation-reaction-by-moloney-murine-leukaemia-virus-reverse-transcriptase
#6
Yoshiyuki Ohtsubo, Haruna Sasaki, Yuji Nagata, Masataka Tsuda
In this study, we investigated CIS reaction (clamping-mediated incorporation of single-stranded DNA with concomitant DNA syntheses) of Moloney murine leukaemia virus reverse transcriptase (MMLV-RT), and established a set of conditions with which single-stranded DNA is ligated to a G-tailed model substrate DNA at efficiencies close to 100%. Prior to the CIS reaction, a target blunt-end DNA was 3' G-tailed by MMLV-RT in the presence of a tailing enhancer, deoxycytidine. In the CIS reaction, the G-tail reacted with a single-stranded DNA carrying a stretch of Cs on its 3' end (termed as GAO for guide adaptor oligonucleotide), and MMLV-RT performed DNA polymerization, starting from the 3' overhang, using the GAO as a template...
June 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29893819/transposon-associated-epigenetic-silencing-during-pleurotus-ostreatus-life-cycle
#7
Alessandra Borgognone, Raúl Castanera, Marco Morselli, Leticia López-Varas, Liudmilla Rubbi, Antonio G Pisabarro, Matteo Pellegrini, Lucía Ramírez
Transposable elements constitute an important fraction of eukaryotic genomes. Given their mutagenic potential, host-genomes have evolved epigenetic defense mechanisms to limit their expansion. In fungi, epigenetic modifications have been widely studied in ascomycetes, although we lack a global picture of the epigenetic landscape in basidiomycetes. In this study, we analysed the genome-wide epigenetic and transcriptional patterns of the white-rot basidiomycete Pleurotus ostreatus throughout its life cycle. Our results performed by using high-throughput sequencing analyses revealed that strain-specific DNA methylation profiles are primarily involved in the repression of transposon activity and suggest that 21 nt small RNAs play a key role in transposon silencing...
June 8, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29873696/transcriptomic-and-functional-analyses-unveil-the-role-of-long-non-coding-rnas-in-anthocyanin-biosynthesis-during-sea-buckthorn-fruit-ripening
#8
Guoyun Zhang, Daoguo Chen, Tong Zhang, Aiguo Duan, Jianguo Zhang, Caiyun He
Fruit ripening is a developmental process regulated by a complex network of endogenous and exogenous cues. Sea buckthorn is an excellent material for fruit ripening studies due to its dramatic ripening process and high contents of nutritional and anti-oxidant compounds in berries. Here, the whole transcriptome of sea buckthorn fruit at three development stages were analysed using multiple high-throughput sequencings. We assembled and annotated 9,008 long non-coding RNAs (lncRNAs) in sea buckthorn fruits, and identified 118 differentially expressed lncRNAs (DE-lncRNAs) and 32 differentially expressed microRNAs in fruit developmental process...
June 4, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29850846/a-survey-of-transcriptome-complexity-in-sus-scrofa-using-single-molecule-long-read-sequencing
#9
Yao Li, Chengchi Fang, Yuhua Fu, An Hu, Cencen Li, Cheng Zou, Xinyun Li, Shuhong Zhao, Chengjun Zhang, Changchun Li
Alternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the extend of epigenetic mechanisms have not been adequately addressed due to its limitation of uncertainties about the complete structure of mRNA. Here we combined single-molecule real-time sequencing, Illumina RNA-seq and DNA methylation data to characterize the landscapes of DNA methylation on AS, fusion isoforms formation and lncRNA feature and further to unveil the transcriptome complexity of pig...
May 29, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29800113/draft-genome-of-a-high-value-tropical-timber-tree-teak-tectona-grandis-l-f-insights-into-ssr-diversity-phylogeny-and-conservation
#10
Ramasamy Yasodha, Ramesh Vasudeva, Swathi Balakrishnan, Ambothi Rathnasamy Sakthi, Nicodemus Abel, Nagarajan Binai, Balaji Rajashekar, Vijay Kumar Waman Bachpai, Chandrasekhara Pillai, Suma Arun Dev
Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes...
May 24, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29718217/detection-of-genome-edited-cells-by-oligoribonucleotide-interference-pcr
#11
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
#12
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
#13
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/29211832/ultra-low-input-transcriptomics-reveal-the-spore-functional-content-and-phylogenetic-affiliations-of-poorly-studied-arbuscular-mycorrhizal-fungi
#14
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...
April 1, 2018: 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
#15
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...
April 1, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29186399/construction-of-prdm9-allele-specific-recombination-maps-in-cattle-using-large-scale-pedigree-analysis-and-genome-wide-single-sperm-genomics
#16
Yang Zhou, Botong Shen, Jicai Jiang, Abinash Padhi, Ki-Eun Park, Adam Oswalt, Charles G Sattler, Bhanu P Telugu, Hong Chen, John B Cole, George E Liu, Li Ma
PRDM9 contributes to hybrid sterility and species evolution. However, its role is to be confirmed in cattle, a major domesticated livestock species. We previously found an association near PRDM9 with cattle recombination features, but the causative variants are still unknown. Using millions of genotyped cattle with pedigree information, we characterized five PRDM9 alleles and generated allele-specific recombination maps. By examining allele-specific recombination patterns, we observed the impact of PRDM9 on global distribution of recombination, especially in the two ends of chromosomes...
April 1, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29186379/development-of-a-high-density-linkage-map-and-chromosome-segment-substitution-lines-for-japanese-soybean-cultivar-enrei
#17
Satoshi Watanabe, Takehiko Shimizu, Kayo Machita, Yasutaka Tsubokura, Zhengjun Xia, Tetsuya Yamada, Makita Hajika, Masao Ishimoto, Yuichi Katayose, Kyuya Harada, Akito Kaga
Using progeny of a cross between Japanese soybean Enrei and Chinese soybean Peking, we developed a high-density linkage map and chromosomal segment substitution lines (CSSLs). The map consists of 2,177 markers with polymorphism information for 32 accessions and provides a detailed genetic framework for these markers. The marker order on the linkage map revealed close agreement with that on the chromosome-scale assembly, Wm82.a2.v1. The differences, especially on Chr. 5 and Chr. 11, in the present map provides information to identify regions in the genome assembly where additional information is required to resolve marker order and assign remaining scaffolds...
April 1, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29161365/genome-scale-analysis-of-escherichia-coli-with-a-comprehensive-prokaryotic-sequence-based-biophysical-model-of-translation-initiation-and-elongation
#18
Gilad Shaham, Tamir Tuller
Translation initiation in prokaryotes is affected by the mRNA folding and interaction of the ribosome binding site with the ribosomal RNA. The elongation rate is affected, among other factors, by the local biophysical properties of the coding regions, the decoding rates of different codons, and the interactions among ribosomes. Currently, there is no comprehensive biophysical model of translation that enables the prediction of mRNA translation dynamics based only on the transcript sequence and while considering all of these fundamental aspects of translation...
April 1, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149287/genomic-and-epigenomic-immunity-in-common-bean-the-unusual-features-of-nb-lrr-gene-family
#19
Manon M S Richard, Ariane Gratias, Vincent Thareau, Kyung Do Kim, Sandrine Balzergue, Johann Joets, Scott A Jackson, Valérie Geffroy
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu...
April 1, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149285/draft-genome-analysis-provides-insights-into-the-fiber-yield-crude-protein-biosynthesis-and-vegetative-growth-of-domesticated-ramie-boehmeria-nivea-l-gaud
#20
Chan Liu, Liangbin Zeng, Siyuan Zhu, Lingqing Wu, Yanzhou Wang, Shouwei Tang, Hongwu Wang, Xia Zheng, Jian Zhao, Xiaorong Chen, Qiuzhong Dai, Touming Liu
Plentiful bast fiber, a high crude protein content, and vigorous vegetative growth make ramie a popular fiber and forage crop. Here, we report the draft genome of ramie, along with a genomic comparison and evolutionary analysis. The draft genome contained a sequence of approximately 335.6 Mb with 42,463 predicted genes. A high-density genetic map with 4,338 single nucleotide polymorphisms (SNPs) was developed and used to anchor the genome sequence, thus, creating an integrated genetic and physical map containing a 58...
April 1, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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