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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/28170034/comparative-analyses-of-the-major-royal-jelly-protein-gene-cluster-in-three-apis-species-with-long-amplicon-sequencing
#1
Sophie Helbing, H Michael G Lattorff, Robin F A Moritz, Anja Buttstedt
No abstract text is available yet for this article.
February 7, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28168289/ribo-seq-enlightens-codon-usage-bias
#2
Damien Paulet, Alexandre David, Eric Rivals
No abstract text is available yet for this article.
February 7, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28158431/prediction-of-bipartite-transcriptional-regulatory-elements-using-transcriptome-data-of-arabidopsis
#3
Yoshiharu Y Yamamoto, Hiroyuki Ichida, Ayaka Hieno, Daichi Obata, Mutsutomo Tokizawa, Mika Nomoto, Yasuomi Tada, Kazutaka Kusunoki, Hiroyuki Koyama, Natsuki Hayami
No abstract text is available yet for this article.
February 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28137825/somatic-transposition-and-meiotically-driven-elimination-of-an-active-helitron-family-in-pleurotus-ostreatus
#4
Alessandra Borgognone, Raúl Castanera, Elaia Muguerza, Antonio G Pisabarro, Lucía Ramírez
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny...
January 30, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28130384/the-draft-genome-of-ruellia-speciosa-beautiful-wild-petunia-acanthaceae
#5
Yongbin Zhuang, Erin A Tripp
The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR...
January 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28130383/large-scale-collection-of-full-length-cdna-and-transcriptome-analysis-in-hevea-brasiliensis
#6
Yuko Makita, Kiaw Kiaw Ng, G Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman, Minami Matsui
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer...
January 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28130382/integrated-high-density-consensus-genetic-map-of-pyrus-and-anchoring-of-the-bartlett-v1-0-pyrus-communis-genome
#7
Leiting Li, Cecilia H Deng, Mareike Knäbel, David Chagné, Satish Kumar, Jiangmei Sun, Shaoling Zhang, Jun Wu
Genetic maps are essential tools for pear genetics and genomics research. In this study, we first constructed an integrated simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)-based consensus genetic map for pear based on common SSR markers between nine published maps. A total of 5,085 markers, including 1,232 SSRs and 3,853 SNPs, were localized on a consensus map spanning 3,266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date...
January 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28119335/dna-double-strand-break-repair-in-penaeus-monodon-is-predominantly-dependent-on-homologous-recombination
#8
Shikha Srivastava, Sumedha Dahal, Sharanya J Naidu, Deepika Anand, Vidya Gopalakrishnan, Rajendran Kooloth Valappil, Sathees C Raghavan
DNA double-strand breaks (DSBs) are mostly repaired by nonhomologous end joining (NHEJ) and homologous recombination (HR) in higher eukaryotes. In contrast, HR-mediated DSB repair is the major double-strand break repair pathway in lower order organisms such as bacteria and yeast. Penaeus monodon, commonly known as black tiger shrimp, is one of the economically important crustaceans facing large-scale mortality due to exposure to infectious diseases. The animals can also get exposed to chemical mutagens under the culture conditions as well as in wild...
January 24, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28119334/genome-wide-analysis-of-cis-regulatory-element-structure-and-discovery-of-motif-driven-gene-co-expression-networks-in-grapevine
#9
Darren Chern Jan Wong, Rodrigo Lopez Gutierrez, Gregory Alan Gambetta, Simone Diego Castellarin
Coordinated transcriptional and metabolic reprogramming ensures a plant's continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters...
January 24, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28087610/long-non-coding-rna-exchange-during-the-oocyte-to-embryo-transition-in-mice
#10
Rosa Karlic, Sravya Ganesh, Vedran Franke, Eliska Svobodova, Jana Urbanova, Yutaka Suzuki, Fugaku Aoki, Kristian Vlahovicek, Petr Svoboda
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5' terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence...
January 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28065881/an-integrated-transcriptomics-guided-genome-wide-promoter-analysis-and-next-generation-proteomics-approach-to-mine-factor-s-regulating-cellular-differentiation
#11
Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, Subeer S Majumdar
Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28065880/complete-genome-sequence-and-expression-profile-of-the-commercial-lytic-enzyme-producer-lysobacter-enzymogenes-m497-1
#12
Hideto Takami, Atsushi Toyoda, Ikuo Uchiyama, Takehiko Itoh, Yoshihiro Takaki, Wataru Arai, Shinro Nishi, Mikihiko Kawai, Kazuo Shin-Ya, Haruo Ikeda
Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28028040/whole-genome-expression-analysis-of-mammalian-wide-interspersed-repeat-elements-in-human-cell-lines
#13
Davide Carnevali, Anastasia Conti, Matteo Pellegrini, Giorgio Dieci
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution...
December 27, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28028039/draft-genome-sequence-of-bitter-gourd-momordica-charantia-a-vegetable-and-medicinal-plant-in-tropical-and-subtropical-regions
#14
Naoya Urasaki, Hiroki Takagi, Satoshi Natsume, Aiko Uemura, Naoki Taniai, Norimichi Miyagi, Mai Fukushima, Shouta Suzuki, Kazuhiko Tarora, Moritoshi Tamaki, Moriaki Sakamoto, Ryohei Terauchi, Hideo Matsumura
Bitter gourd (Momordica charantia) is an important vegetable and medicinal plant in tropical and subtropical regions globally. In this study, the draft genome sequence of a monoecious bitter gourd inbred line, OHB3-1, was analyzed. Through Illumina sequencing and de novo assembly, scaffolds of 285.5 Mb in length were generated, corresponding to ∼84% of the estimated genome size of bitter gourd (339 Mb). In this draft genome sequence, 45,859 protein-coding gene loci were identified, and transposable elements accounted for 15...
December 27, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28028038/function-and-evolution-of-a-lotus-japonicus-ap2-erf-family-transcription-factor-that-is-required-for-development-of-infection-threads
#15
Koji Yano, Seishiro Aoki, Meng Liu, Yosuke Umehara, Norio Suganuma, Wataru Iwasaki, Shusei Sato, Takashi Soyano, Hiroshi Kouchi, Masayoshi Kawaguchi
Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1 LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2...
December 27, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28025319/molecular-cytogenetic-characterization-of-chromosome-site-specific-repetitive-sequences-in-the-arctic-lamprey-lethenteron-camtschaticum-petromyzontidae
#16
Junko Ishijima, Yoshinobu Uno, Mitsuo Nunome, Chizuko Nishida, Shigehiro Kuraku, Yoichi Matsuda
All extant lamprey karyotypes are characterized by almost all dot-shaped microchromosomes. To understand the molecular basis of chromosome structure in lampreys, we performed chromosome C-banding and silver staining and chromosome mapping of the 18S-28S and 5S ribosomal RNA (rRNA) genes and telomeric TTAGGG repeats in the Arctic lamprey (Lethenteron camtschaticum). In addition, we cloned chromosome site-specific repetitive DNA sequences and characterized them by nucleotide sequencing, chromosome in situ hybridization, and filter hybridization...
December 26, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28025318/alternative-splicing-in-tomato-pollen-in-response-to-heat-stress
#17
Mario Keller, Yangjie Hu, Anida Mesihovic, Sotirios Fragkostefanakis, Enrico Schleiff, Stefan Simm
Alternative splicing (AS) is a key control mechanism influencing signal response cascades in different developmental stages and under stress conditions. In this study, we examined heat stress (HS)-induced AS in the heat sensitive pollen tissue of two tomato cultivars. To obtain the entire spectrum of HS-related AS, samples taken directly after HS and after recovery were combined and analysed by RNA-seq. For nearly 9,200 genes per cultivar, we observed at least one AS event under HS. In comparison to control, for one cultivar we observed 76% more genes with intron retention (IR) or exon skipping (ES) under HS...
December 26, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28205672/alternative-splicing-in-tomato-pollen-in-response-to-heat-stress%C3%A2
#18
Mario Keller, Yangjie Hu, Anida Mesihovic, Sotirios Fragkostefanakis, Enrico Schleiff, Stefan Simm
No abstract text is available yet for this article.
December 24, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28011721/genome-analysis-of-hibiscus-syriacus-provides-insights-of-polyploidization-and-indeterminate-flowering-in-woody-plants
#19
Yong-Min Kim, Seungill Kim, Namjin Koo, Ah-Young Shin, Seon-In Yeom, Eunyoung Seo, Seong-Jin Park, Won-Hee Kang, Myung-Shin Kim, Jieun Park, Insu Jang, Pan-Gyu Kim, Iksu Byeon, Min-Seo Kim, JinHyuk Choi, Gunhwan Ko, JiHye Hwang, Tae-Jin Yang, Sang-Bong Choi, Je Min Lee, Ki-Byung Lim, Jungho Lee, Ik-Young Choi, Beom-Seok Park, Suk-Yoon Kwon, Doil Choi, Ryan W Kim
Hibiscus syriacus (L.) (rose of Sharon) is one of the most widespread garden shrubs in the world. We report a draft of the H. syriacus genome comprised of a 1.75 Gb assembly that covers 92% of the genome with only 1.7% (33 Mb) gap sequences. Predicted gene modeling detected 87,603 genes, mostly supported by deep RNA sequencing data. To define gene family distribution among relatives of H. syriacus, orthologous gene sets containing 164,660 genes in 21,472 clusters were identified by OrthoMCL analysis of five plant species, including H...
December 22, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28011720/exploiting-the-great-potential-of-sequence-capture-data-by-a-new-tool-super-cap
#20
Valentino Ruggieri, Irantzu Anzar, Andreu Paytuvi, Roberta Calafiore, Riccardo Aiese Cigliano, Walter Sanseverino, Amalia Barone
The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces...
December 22, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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