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/29325017/cell-type-resolved-alternative-splicing-patterns-in-mouse-liver
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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/29186399/construction-of-prdm9-allele-specific-recombination-maps-in-cattle-using-large-scale-pedigree-analysis-and-genome-wide-single-sperm-genomics
#7
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...
November 27, 2017: 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
#8
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...
November 24, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29161365/genome-scale-analysis-ofescherichia-coliwith-a-comprehensive-prokaryotic-sequence-based-biophysical-model-of-translation-initiation-and-elongation
#9
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...
November 17, 2017: 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
#10
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...
November 15, 2017: 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
#11
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...
November 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29149280/whole-genome-re-sequencing-of-two-italian-tomato-landraces-reveals-sequence-variations-in-genes-associated-with-stress-tolerance-fruit-quality-and-long-shelf-life-traits
#12
Valentina Tranchida-Lombardo, Riccardo Aiese Cigliano, Irantzu Anzar, Simone Landi, Samuela Palombieri, Chiara Colantuono, Hamed Bostan, Pasquale Termolino, Riccardo Aversano, Giorgia Batelli, Maria Cammareri, Domenico Carputo, Maria Luisa Chiusano, Clara Conicella, Federica Consiglio, Nunzio D'Agostino, Monica De Palma, Antonio Di Matteo, Silvana Grandillo, Walter Sanseverino, Marina Tucci, Stefania Grillo
Tomato is a high value crop and the primary model for fleshy fruit development and ripening. Breeding priorities include increased fruit quality, shelf life and tolerance to stresses. To contribute towards this goal, we re-sequenced the genomes of Corbarino (COR) and Lucariello (LUC) landraces, which both possess the traits of plant adaptation to water deficit, prolonged fruit shelf-life and good fruit quality. Through the newly developed pipeline Reconstructor, we generated the genome sequences of COR and LUC using datasets of 65...
November 14, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29096008/satellite-dnas-are-conserved-and-differentially-transcribed-among-gryllus-cricket-species
#13
Octavio Manuel Palacios-Gimenez, Vanessa Bellini Bardella, Bernardo Lemos, Diogo Cavalcanti Cabral-de-Mello
Satellite DNA (satDNA) is an abundant class of non-coding repetitive DNA that is preferentially found as tandemly repeated arrays in gene-poor heterochromatin but is also present in gene-rich euchromatin. Here, we used DNA- and RNA-seq from Gryllus assimilis to address the content and transcriptional patterns of satDNAs. We also mapped RNA-seq libraries for other Gryllus species against the satDNAs found in G. assimilis and G. bimaculatus genomes to investigate their evolutionary conservation and transcriptional profiles in Gryllus...
October 31, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29069301/investigating-transcription-factor-synergism-in-humans
#14
Fabio Cumbo, Davide Vergni, Daniele Santoni
Proteins are the core and the engine of every process in cells thus the study of mechanisms that drive the regulation of protein expression, is essential. Transcription factors play a central role in this extremely complex task and they synergically co-operate in order to provide a fine tuning of protein expressions. In the present study, we designed a mathematically well-founded procedure to investigate the mutual positioning of transcription factors binding sites related to a given couple of transcription factors in order to evaluate the possible association between them...
October 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29045613/genome-structure-of-rosa-multiflora-a-wild-ancestor-of-cultivated-roses
#15
Noriko Nakamura, Hideki Hirakawa, Shusei Sato, Shungo Otagaki, Shogo Matsumoto, Satoshi Tabata, Yoshikazu Tanaka
The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures...
October 16, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29036669/comparative-genome-and-transcriptome-analyses-reveal-adaptations-to-opportunistic-infections-in-woody-plant-degrading-pathogens-of-botryosphaeriaceae
#16
Ji Ye Yan, Wen Sheng Zhao, Zhen Chen, Qi Kai Xing, Wei Zhang, K W Thilini Chethana, Min Feng Xue, Jian Ping Xu, Alan J L Phillips, Yong Wang, Jian Hua Liu, Mei Liu, Ying Zhou, Ruvishika S Jayawardena, Ishara S Manawasinghe, Jin Bao Huang, Guang Hang Qiao, Chun Yuan Fu, Fei Fei Guo, Asha J Dissanayake, You Liang Peng, Kevin D Hyde, Xing Hong Li
Botryosphaeriaceae are an important fungal family that cause woody plant diseases worldwide. Recent studies have established a correlation between environmental factors and disease expression; however, less is known about factors that trigger these diseases. The current study reports on the 43.3 Mb de novo genome of Lasiodiplodia theobromae and five other genomes of Botryosphaeriaceae pathogens. Botryosphaeriaceous genomes showed an expansion of gene families associated with cell wall degradation, nutrient uptake, secondary metabolism and membrane transport, which contribute to adaptations for wood degradation...
October 3, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29036326/circular-rnas-are-abundant-and-dynamically-expressed-during-embryonic-muscle-development-in-chickens
#17
Hongjia Ouyang, Xiaolan Chen, Zhijun Wang, Jiao Yu, Xinzheng Jia, Zhenhui Li, Wei Luo, Bahareldin Ali Abdalla, Endashaw Jebessa, Qinghua Nie, Xiquan Zhang
The growth and development of skeletal muscle is regulated by proteins as well as non-coding RNAs. Circular RNAs (circRNAs) are universally expressed in various tissues and cell types, and regulate gene expression in eukaryotes. To identify the circRNAs during chicken embryonic skeletal muscle development, leg muscles of female Xinghua (XH) chicken at three developmental time points 11 embryo age (E11), 16 embryo age (E16) and 1 day post hatch (P1) were performed RNA sequencing. We identified 13,377 circRNAs with 3,036 abundantly expressed and most were derived from coding exons...
October 3, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28586432/locus-specific-chip-combined-with-ngs-analysis-reveals-genomic-regulatory-regions-that-physically-interact-with-the-pax5-promoter-in-a-chicken-b-cell-line
#18
Toshitsugu Fujita, Fusako Kitaura, Miyuki Yuno, Yutaka Suzuki, Sumio Sugano, Hodaka Fujii
Chromosomal interactions regulate genome functions, such as transcription, via dynamic chromosomal organization in the nucleus. In this study, we attempted to identify genomic regions that physically bind to the promoter region of the Pax5 gene, which encodes a master regulator for B cell lineage commitment, in a chicken B cell line, DT40, with the goal of obtaining mechanistic insight into transcriptional regulation through chromosomal interaction. We found that the Pax5 promoter bound to multiple genomic regions using locus-specific chromatin immunoprecipitation (locus-specific ChIP), a method for locus-specific isolation of target genomic regions, in combination with next-generation sequencing (NGS)...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28575165/genome-wide-profiling-of-sus-scrofa-circular-rnas-across-nine-organs-and-three-developmental-stages
#19
Guoming Liang, Yalan Yang, Guanglin Niu, Zhonglin Tang, Kui Li
The spatio-temporal expression patterns of Circular RNA (circRNA) across organs and developmental stages are critical for its function and evolution analysis. However, they remain largely unclear in mammals. Here, we comprehensively analysed circRNAs in nine organs and three skeletal muscles of Guizhou miniature pig (S. scrofa), a widely used biomedical model animal. We identified 5,934 circRNAs and analysed their molecular properties, sequence conservation, spatio-temporal expression pattern, potential function, and interaction with miRNAs...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28575160/dynamic-changes-in-methylome-and-transcriptome-patterns-in-response-to-methyltransferase-inhibitor-5-azacytidine-treatment-in-citrus
#20
Jidi Xu, Xia Wang, Hongbo Cao, Haidan Xu, Qiang Xu, Xiuxin Deng
DNA methylation is known to play an important role in various developmental processes in plants. However, there is a general lack of understanding about the possible functions of DNA methylation in fruit trees. Using callus as a model, methylome, transcriptome and metabolite changes were assessed after treatment with the DNA methyltransferase inhibitor 5-azacytidine (5azaC). Genome-wide methylome analysis revealed the demethylation of a diverse of genes, including many genes encoding transcription factors (TFs), genes involved in biological processes, and the up-regulation of a wide range of transposable elements (TEs)...
October 1, 2017: 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"