journal
MENU ▼
Read by QxMD icon Read
search

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

journal
https://www.readbyqxmd.com/read/30215675/ariadna-machine-learning-method-for-ancient-dna-variant-discovery
#1
Joseph K Kawash, Sean D Smith, Spyros Karaiskos, Andrey Grigoriev
Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and despite showing extreme sensitivity to aDNA quality, these methods have been used in many published studies, sometimes with additions of arbitrary filters or modifications, designed to overcome aDNA degradation and contamination problems. The general lack of best practices for aDNA mutation calling may lead to inaccurate results...
September 11, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30188980/de-novo-transcriptome-sequencing-and-metabolite-profiling-analyses-reveal-the-complex-metabolic-genes-involved-in-the-terpenoid-biosynthesis-in-blue-anise-sage-salvia-guaranitica-l
#2
Mohammed Ali, Reem M Hussain, Naveed Ur Rehman, Guangbiao She, Penghui Li, Xiaochun Wan, Liang Guo, Jian Zhao
Many terpenoid compounds have been extracted from different tissues of Salvia guaranitica. However, the molecular genetic basis of terpene biosynthesis pathways is virtually unknown. In this study, approximately 4 Gb of raw data were generated from the transcriptome of S. guaranitica leaves using Illumina HiSeq 2000 sequencing. After filtering and removing the adapter sequences from the raw data, the number of reads reached 32 million, comprising 186 million of high-quality nucleotide bases. A total of 61,400 unigenes were assembled de novo and annotated for establishing a valid database for studying terpenoid biosynthesis...
September 4, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30085012/comparative-mitochondrial-genomics-reveals-a-possible-role-of-a-recent-duplication-of-nadh-dehydrogenase-subunit-5-in-gene-regulation
#3
Runsheng Li, Xiaoliang Ren, Yu Bi, Qiutao Ding, Vincy Wing Sze Ho, Zhongying Zhao
Mitochondrial genome (mtDNA) carries not only well-conserved protein coding, tRNA and rRNA genes, but also highly variable non-coding regions (NCRs). However, the NCRs show poor conservation across species, making their function and evolution elusive. Identification and functional characterization of NCRs across species would be critical for addressing these questions. To this end, we devised a computational pipeline and performed de novo assembly and annotation of mtDNA from 19 Caenorhabditis species using next-generation sequencing (NGS) data...
August 6, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30084885/transcriptome-referenced-association-study-of-clove-shape-traits-in-garlic
#4
Xiaojun Chen, Xia Liu, Siyuan Zhu, Shouwei Tang, Shiyong Mei, Jing Chen, Shan Li, Mengdi Liu, Yuejiao Gu, Qiuzhong Dai, Touming Liu
Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis...
August 6, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30060137/genome-wide-comparative-analysis-in-solanaceous-species-reveals-evolution-of-micrornas-targeting-defense-genes-in-capsicum-spp
#5
Eunyoung Seo, Taewook Kim, June Hyun Park, Seon-In Yeom, Seungill Kim, Min-Ki Seo, Chanseok Shin, Doil Choi
MicroRNAs (miRNAs) play roles in various biological processes in plants including growth, development, and disease resistance. Previous studies revealed that some plant miRNAs produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs), and they regulate a cascade of gene expression. We performed a genome-wide comparative analysis of miRNAs in Solanaceous species (pepper, tomato, and potato), from an evolutionary perspective. Microsynteny of miRNAs was analysed based on the genomic loci and their flanking genes and most of the well-conserved miRNA genes maintained microsynteny in Solanaceae...
July 27, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30052927/mobile-elements-contribute-to-the-uniqueness-of-human-genome-with-15-000-human-specific-insertions-and-14-mbp-sequence-increase
#6
Wanxiangfu Tang, Seyoung Mun, Aditya Joshi, Kyudong Han, Ping Liang
Mobile elements (MEs) collectively contribute to at least 50% of the human genome. Due to their past incremental accumulation and ongoing DNA transposition, MEs serve as a significant source for both inter- and intra-species genetic and phenotypic diversity during primate and human evolution. By making use of the most recent genome sequences for human and many other closely related primates and robust multi-way comparative genomic approach, we identified a total of 14,870 human-specific MEs (HS-MEs) with more than 8,000 being newly identified...
July 19, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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
#7
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
#8
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/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
#9
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...
August 1, 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
#10
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...
August 1, 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
#11
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...
August 1, 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
#12
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...
August 1, 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
#13
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...
August 1, 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
#14
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...
August 1, 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
#15
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...
August 1, 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
#16
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...
August 1, 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
#17
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...
August 1, 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
#18
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
#19
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/29897438/optimization-of-single-strand-dna-incorporation-reaction-by-moloney-murine-leukaemia-virus-reverse-transcriptase
#20
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
journal
journal
31665
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"