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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/30428014/3-branch-ligation-a-novel-method-to-ligate-non-complementary-dna-to-recessed-or-internal-3-oh-ends-in-dna-or-rna
#1
Lin Wang, Yang Xi, Wenwei Zhang, Weimao Wang, Hanjie Shen, Xiaojue Wang, Xia Zhao, Andrei Alexeev, Brock A Peters, Alayna Albert, Xu Xu, Han Ren, Ou Wang, Killeen Kirkconnell, Helena Perazich, Sonya Clark, Evan Hurowitz, Ao Chen, Xun Xu, Radoje Drmanac, Yuan Jiang
Nucleic acid ligases are crucial enzymes that repair breaks in DNA or RNA during synthesis, repair and recombination. Various genomic tools have been developed using the diverse activities of DNA/RNA ligases. Herein, we demonstrate a non-conventional ability of T4 DNA ligase to insert 5' phosphorylated blunt-end double-stranded DNA to DNA breaks at 3'-recessive ends, gaps, or nicks to form a Y-shaped 3'-branch structure. Therefore, this base pairing-independent ligation is termed 3'-branch ligation (3'BL). In an extensive study of optimal ligation conditions, the presence of 10% PEG-8000 in the ligation buffer significantly increased ligation efficiency to more than 80%...
November 13, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30395234/genome-assembly-and-gene-expression-in-the-american-black-bear-provides-new-insights-into-the-renal-response-to-hibernation
#2
Anuj Srivastava, Vishal Kumar Sarsani, Ian Fiddes, Susan M Sheehan, Rita L Seger, Mary E Barter, Selena Neptune-Bear, Charlotte Lindqvist, Ron Korstanje
The prevalence of chronic kidney disease (CKD) is rising worldwide and 10-15% of the global population currently suffers from CKD and its complications. Given the increasing prevalence of CKD there is an urgent need to find novel treatment options. The American black bear (Ursus americanus) copes with months of lowered kidney function and metabolism during hibernation without the devastating effects on metabolism and other consequences observed in humans. In a biomimetic approach to better understand kidney adaptations and physiology in hibernating black bears, we established a high-quality genome assembly...
November 5, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30380026/landscape-of-gene-transposition-duplication-within-the-brassicaceae-family
#3
Dong-Ha Oh, Maheshi Dassanayake
We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition-duplication (tr-d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents...
October 30, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30351380/multi-tissue-transcriptomes-of-caecilian-amphibians-highlight-incomplete-knowledge-of-vertebrate-gene-families
#4
María Torres-Sánchez, Christopher J Creevey, Etienne Kornobis, David J Gower, Mark Wilkinson, Diego San Mauro
RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order...
October 22, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30325414/overcoming-challenges-in-variant-calling-exploring-sequence-diversity-in-candidate-genes-for-plant-development-in-perennial-ryegrass-lolium-perenne
#5
Elisabeth Veeckman, Sabine Van Glabeke, Annelies Haegeman, Hilde Muylle, Frederik R D van Parijs, Stephen L Byrne, Torben Asp, Bruno Studer, Antje Rohde, Isabel Roldán-Ruiz, Klaas Vandepoele, Tom Ruttink
Revealing DNA sequence variation within the Lolium perenne genepool is important for genetic analysis and development of breeding applications. We reviewed current literature on plant development to select candidate genes in pathways that control agronomic traits, and identified 503 orthologues in L. perenne. Using targeted resequencing, we constructed a comprehensive catalogue of genomic variation for a L. perenne germplasm collection of 736 genotypes derived from current cultivars, breeding material and wild accessions...
October 15, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30295708/the-genome-of-the-oyster-saccostrea-offers-insight-into-the-environmental-resilience-of-bivalves
#6
Daniel Powell, Sankar Subramanian, Saowaros Suwansa-Ard, Min Zhao, Wayne O'Connor, David Raftos, Abigail Elizur
Oysters are keystone species in estuarine ecosystems and are of substantial economic value to fisheries and aquaculture worldwide. Contending with disease and environmental stress are considerable challenges to oyster culture. Here we report a draft genome of the Sydney Rock Oyster, Saccostrea glomerata, an iconic and commercially important species of edible oyster in Australia known for its enhanced resilience to harsh environmental conditions. This is the second reference genome to be reported from the family Ostreidae enabling a genus-level study of lophotrochozoan genome evolution...
October 8, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30272113/genome-wide-screening-and-analysis-of-imprinted-genes-in-rapeseed-brassica-napus-l-endosperm
#7
Jing Liu, Jun Li, Hong-Fang Liu, Shi-Hang Fan, Surinder Singh, Xue-Rong Zhou, Zhi-Yong Hu, Han-Zhong Wang, Wei Hua
Species-specific genomic imprinting is an epigenetic phenomenon leading to parent-of-origin-specific differential expression of maternally and paternally inherited alleles. To date, no studies of imprinting have been reported in rapeseed, a tetraploid species. Here, we analysed global patterns of allelic gene expression in developing rapeseed endosperms from reciprocal crosses between inbred lines YN171 and 93275. A total of 183 imprinted genes, consisting of 167 maternal expressed genes (MEGs) and 16 paternal expressed genes (PEGs), were identified from 14,394 genes found to harbour diagnostic SNPs between the parental lines...
September 28, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30256918/multiple-links-connect-central-carbon-metabolism-to-dna-replication-initiation-and-elongation-in-bacillus-subtilis
#8
Hamid Nouri, Anne-Françoise Monnier, Solveig Fossum-Raunehaug, Monika Maciag-Dorszynska, Armelle Cabin-Flaman, François Képès, Grzegorz Wegrzyn, Agnieszka Szalewska-Palasz, Vic Norris, Kirsten Skarstad, Laurent Janniere
DNA replication is coupled to growth by an unknown mechanism. Here, we investigated this coupling by analyzing growth and replication in 15 mutants of central carbon metabolism (CCM) cultivated in three rich media. In about one-fourth of the condition tested, defects in replication resulting from changes in initiation or elongation were detected. This uncovered 11 CCM genes important for replication and showed that some of these genes have an effect in one, two or three media. Additional results presented here and elsewhere (Jannière, L...
September 26, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/30215675/ariadna-machine-learning-method-for-ancient-dna-variant-discovery
#9
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
#10
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/30329019/the-yellowtail-seriola-quinqueradiata-genome-and-transcriptome-atlas-of-the-digestive-tract
#11
Motoshige Yasuike, Yuki Iwasaki, Issei Nishiki, Yoji Nakamura, Aiko Matsuura, Kazunori Yoshida, Tsutomu Noda, Tadashi Andoh, Atushi Fujiwara
Seriola quinqueradiata (yellowtail) is the most widely farmed and economically important fish in aquaculture in Japan. In this study, we used the genome of haploid yellowtail fish larvae for de novo assembly of whole-genome sequences, and built a high-quality draft genome for the yellowtail. The total length of the assembled sequences was 627.3 Mb, consisting of 1,394 scaffold sequences (>2 kb) with an N50 length of 1.43 Mb. A total of 27,693 protein-coding genes were predicted for the draft genome, and among these, 25,832 predicted genes (93...
October 1, 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
#12
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...
October 1, 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
#13
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...
October 1, 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
#14
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...
October 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
#15
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...
October 1, 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
#16
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...
October 1, 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
#17
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...
October 1, 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
#18
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...
October 1, 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
#19
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...
October 1, 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
#20
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
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