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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/29096008/satellite-dnas-are-conserved-and-differentially-transcribed-among-gryllus-cricket-species
#1
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
#2
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
#3
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
#4
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
#5
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/29036429/genome-re-annotation-of-the-wild-strawberry-fragaria-vesca-using-extensive-illumina-and-smrt-based-rna-seq-datasets
#6
Yongping Li, Wei Wei, Jia Feng, Huifeng Luo, Mengting Pi, Zhongchi Liu, Chunying Kang
The genome of the wild diploid strawberry species Fragaria vesca, an ideal model system of cultivated strawberry (Fragaria × ananassa, octoploid) and other Rosaceae family crops, was first published in 2011 and followed by a new assembly (Fvb). However, the annotation for Fvb mainly relied on ab initio predictions and included only predicted coding sequences, therefore an improved annotation is highly desirable. Here, a new annotation version named v2.0.a2 was created for the Fvb genome by a pipeline utilizing one PacBio library, 90 Illumina RNA-seq libraries, and 9 small RNA-seq libraries...
September 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28985305/genome-sequencing-and-comparative-genomics-reveal-the-potential-pathogenic-mechanism-of-cercospora-sojina-hara-on-soybean
#7
Xuming Luo, Jidong Cao, Junkai Huang, Zongyi Wang, Zhengyan Guo, Yihua Chen, Shumei Ma, Jun Liu
Frogeye leaf spot, caused by Cercospora sojina Hara, is a common disease of soybean in most soybean-growing countries of the world. In this study, we report a high-quality genome sequence of C. sojina by Single Molecule Real-Time sequencing method. The 40.8-Mb genome encodes 11,655 predicated genes, and 8,474 genes are revealed by RNA sequencing. Cercospora sojina genome contains large numbers of gene clusters that are involved in synthesis of secondary metabolites, including mycotoxins and pigments. However, much less carbohydrate-binding module protein encoding genes are identified in C...
September 18, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28985340/genome-wide-mapping-of-large-deletions-and-their-population-genetic-properties-in-dairy-cattle
#8
Md Mesbah-Uddin, Bernt Guldbrandtsen, Terhi Iso-Touru, Johanna Vilkki, Dirk-Jan De Koning, Didier Boichard, Mogens Sandø Lund, Goutam Sahana
Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp-773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining...
September 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28985339/a-re-sequencing-based-ultra-dense-genetic-map-reveals-a-gummy-stem-blight-resistance-associated-gene-in-cucumis-melo
#9
Zhongyuan Hu, Guancong Deng, Haipeng Mou, Yuhui Xu, Li Chen, Jinghua Yang, Mingfang Zhang
The melon (Cucumis melo) genome and genetic maps with hundreds to thousands of single nucleotide polymorphism markers were recently released. However, a high-resolution genetic map was lacking. Gummy stem blight (Gsb) is a destructive disease responsible for considerable economic losses during melon production. We herein describe the development of an ultra-dense genetic map consisting of 12,932 recombination bin markers covering 1,818 cM, with an average distance of 0.17 cM between adjacent tags. A comparison of the genetic maps for melon, watermelon, and cucumber revealed chromosome-level syntenic relationships and recombination events among the three Cucurbitaceae species...
September 7, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28985264/comparative-transcriptomics-of-cyprinid-minnows-and-carp-in-a-common-wild-setting-a-resource-for-ecological-genomics-in-freshwater-communities
#10
Trevor J Krabbenhoft, Thomas F Turner
Comparative transcriptomics can now be conducted on organisms in natural settings, which has greatly enhanced understanding of genome-environment interactions. Here, we demonstrate the utility and potential pitfalls of comparative transcriptomics of wild organisms, with an example from three cyprinid fish species (Teleostei:Cypriniformes). We present extensively filtered and annotated transcriptome assemblies that provide a valuable resource for studies of genome evolution (e.g. polyploidy), ecological and morphological diversification, speciation, and shared and unique responses to environmental variation in cyprinid fishes...
September 6, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28985356/multiple-hybrid-de-novo-genome-assembly-of-finger-millet-an-orphan-allotetraploid-crop
#11
Masaomi Hatakeyama, Sirisha Aluri, Mathi Thumilan Balachadran, Sajeevan Radha Sivarajan, Andrea Patrignani, Simon Grüter, Lucy Poveda, Rie Shimizu-Inatsugi, John Baeten, Kees-Jan Francoijs, Karaba N Nataraja, Yellodu A Nanja Reddy, Shamprasad Phadnis, Ramapura L Ravikumar, Ralph Schlapbach, Sheshshayee M Sreeman, Kentaro K Shimizu
Finger millet (Eleusine coracana (L.) Gaertn) is an important crop for food security because of its tolerance to drought, which is expected to be exacerbated by global climate changes. Nevertheless, it is often classified as an orphan/underutilized crop because of the paucity of scientific attention. Among several small millets, finger millet is considered as an excellent source of essential nutrient elements, such as iron and zinc; hence, it has potential as an alternate coarse cereal. However, high-quality genome sequence data of finger millet are currently not available...
September 5, 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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/28541388/the-genome-sequence-of-sweet-cherry-prunus-avium-for-use-in-genomics-assisted-breeding
#15
Kenta Shirasawa, Kanji Isuzugawa, Mitsunobu Ikenaga, Yutaro Saito, Toshiya Yamamoto, Hideki Hirakawa, Sachiko Isobe
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28460080/a-genomic-landscape-of-mitochondrial-dna-insertions-in-the-pig-nuclear-genome-provides-evolutionary-signatures-of-interspecies-admixture
#16
Giuseppina Schiavo, Orsolya Ivett Hoffmann, Anisa Ribani, Valerio Joe Utzeri, Marco Ciro Ghionda, Francesca Bertolini, Claudia Geraci, Samuele Bovo, Luca Fontanesi
Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28459978/short-and-long-term-evolutionary-dynamics-of-subtelomeric-pirna-clusters-in-drosophila
#17
Amna Asif-Laidin, Valérie Delmarre, Jeanne Laurentie, Wolfgang J Miller, Stéphane Ronsseray, Laure Teysset
Two Telomeric Associated Sequences, TAS-R and TAS-L, form the principal subtelomeric repeat families identified in Drosophila melanogaster. They are PIWI-interacting RNA (piRNA) clusters involved in repression of Transposable Elements. In this study, we revisited TAS structural and functional dynamics in D. melanogaster and in related species. In silico analysis revealed that TAS-R family members are composed of previously uncharacterized domains. This analysis also showed that TAS-L repeats are composed of arrays of a region we have named "TAS-L like" (TLL) identified specifically in one TAS-R family member, X-TAS...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28453813/identification-and-allelic-dissection-uncover-roles-of-lncrnas-in-secondary-growth-of-populus-tomentosa
#18
Daling Zhou, Qingzhang Du, Jinhui Chen, Qingshi Wang, Deqiang Zhang
Long non-coding RNAs (lncRNAs) function in various biological processes. However, their roles in secondary growth of plants remain poorly understood. Here, 15,691 lncRNAs were identified from vascular cambium, developing xylem, and mature xylem of Populus tomentosa with high and low biomass using RNA-seq, including 1,994 lncRNAs that were differentially expressed (DE) among the six libraries. 3,569 cis-regulated and 3,297 trans-regulated protein-coding genes were predicted as potential target genes (PTGs) of the DE lncRNAs to participate in biological regulation...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28449092/genome-wide-dna-methylomes-from-discrete-developmental-stages-reveal-the-predominance-of-non-cpg-methylation-in-tribolium-castaneum
#19
Xiaowen Song, Fei Huang, Juanjuan Liu, Chengjun Li, Shanshan Gao, Wei Wu, Mengfan Zhai, Xiaojuan Yu, Wenfeng Xiong, Jia Xie, Bin Li
Cytosine DNA methylation is a vital epigenetic regulator of eukaryotic development. Whether this epigenetic modification occurs in Tribolium castaneum has been controversial, its distribution pattern and functions have not been established. Here, using bisulphite sequencing (BS-Seq), we confirmed the existence of DNA methylation and described the methylation profiles of the four life stages of T. castaneum. In the T. castaneum genome, both symmetrical CpG and non-CpG methylcytosines were observed. Symmetrical CpG methylation, which was catalysed by DNMT1 and occupied a small part in T...
October 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29106502/isolation-of-highly-thermostable-%C3%AE-xylosidases-from-a-hot-spring-soil-microbial-community-using-a-metagenomic-approach
#20
Masaru Sato, Migiwa Suda, Jiro Okuma, Tomohiko Kato, Yoshitsugu Hirose, Asuka Nishimura, Yasuhiko Kondo, Daisuke Shibata
The DNA extracted from a high-temperature environment in which micro-organisms are living will be a good source for the isolation of thermostable enzymes. Using a metagenomic approach, we aimed to isolate thermostable β-xylosidases that will be exploited for biofuel production from lignocellulosic biomass. DNA samples obtained from the soil near a spout of a hot spring (70°C, pH7.2) were subjected to sequencing, which generated a total of 84.2 Gbp with 967,925 contigs of >500 bp in length. Similarity search for β-xylosidase in the contigs revealed the presence of 168 candidate sequences, each of which may have arisen from more than one gene...
August 7, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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