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

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https://read.qxmd.com/read/30768175/unraveling-the-complex-genome-of-saccharum-spontaneum-using-polyploid-gene-assembler
#1
Leandro Costa Nascimento, Karina Yanagui, Juliana Jose, Eduardo L O Camargo, Maria Carolina B Grassi, Camila P Cunha, José Antonio Bressiani, Guilherme M A Carvalho, Carlos Roberto Carvalho, Paula F Prado, Piotr Mieczkowski, Gonçalo A G Pereira, Marcelo F Carazzolle
The Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy to perform gene-space assembly from complex genomes using low coverage DNA sequencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content. Pipeline validation was conducted with wheat (Triticum aestivum), a hexaploid species, using barley (Hordeum vulgare) as reference, that resulted in the identification of more than 90% of genes and several new genes...
February 14, 2019: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30726896/search-for-potential-reading-frameshifts-in-cds-from-arabidopsis-thaliana-and-other-genomes
#2
Y M Suvorova, M A Korotkova, K G Skryabin, E V Korotkov
A new mathematical method for potential reading frameshift detection in protein-coding sequences (cds) was developed. The algorithm is adjusted to the triplet periodicity of each analysed sequence using dynamic programming and a genetic algorithm. This does not require any preliminary training. Using the developed method, cds from the Arabidopsis thaliana genome were analysed. In total, the algorithm found 9,930 sequences containing one or more potential reading frameshift(s). This is ∼21% of all analysed sequences of the genome...
February 4, 2019: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30715317/origin-of-wheat-b-genome-chromosomes-inferred-from-rna-sequencing-analysis-of-leaf-transcripts-from-section-sitopsis-species-of-aegilops
#3
Yuka Miki, Kentaro Yoshida, Nobuyuki Mizuno, Shuhei Nasuda, Kazuhiro Sato, Shigeo Takumi
Dramatic changes occasionally occur in intergenic regions leading to genomic alterations during speciation and will consequently obscure the ancestral species that have contributed to the formation of allopolyploid organisms. The S genome of five species of section Sitopsis of genus Aegilops is considered to be an origin of B-genome in cultivated tetraploid and hexaploid wheat species, although its actual donor is still unclear. Here, we attempted to elucidate phylogenetic relationship among Sitopsis species by performing RNA sequencing of the coding regions of each chromosome...
January 30, 2019: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30689773/de-novo-whole-genome-assembly-in-chrysanthemum-seticuspe-a-model-species-of-chrysanthemums-and-its-application-to-genetic-and-gene-discovery-analysis
#4
Hideki Hirakawa, Katsuhiko Sumitomo, Tamotsu Hisamatsu, Soichiro Nagano, Kenta Shirasawa, Yohei Higuchi, Makoto Kusaba, Masaji Koshioka, Yoshihiro Nakano, Masafumi Yagi, Hiroyasu Yamaguchi, Kenji Taniguchi, Michiharu Nakano, Sachiko N Isobe
Cultivated chrysanthemum (Chrysanthemum morifolium Ramat.) is one of the most economically important ornamental crops grown worldwide. It has a complex hexaploid genome (2n = 6x = 54) and large genome size. The diploid Chrysanthemum seticuspe is often used as a model of cultivated chrysanthemum, since the two species are closely related. To expand our knowledge of the cultivated chrysanthemum, we here performed de novo whole-genome assembly in C. seticuspe using the Illumina sequencing platform. XMRS10, a C...
January 27, 2019: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30624596/otux-v-region-specific-otu-database-for-improved-16s-rrna-otu-picking-and-efficient-cross-study-taxonomic-comparison-of-microbiomes
#5
Deepak Yadav, Anirban Dutta, Sharmila S Mande
Many microbiome studies employ reference-based operational taxonomic unit (OTU)-picking methods, which in general, rely on databases cataloguing reference OTUs identified through clustering full-length 16S rRNA genes. Given that the rate of accumulation of mutations are not uniform throughout the length of a 16S rRNA gene across different taxonomic clades, results of OTU identification or taxonomic classification obtained using 'short-read' sequence queries (as generated by next-generation sequencing platforms) can be inconsistent and of suboptimal accuracy...
January 8, 2019: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30615101/a-unique-life-strategy-of-an-endophytic-yeast-rhodotorula-mucilaginosa-jgta-s1-a-comparative-genomics-viewpoint
#6
Diya Sen, Karnelia Paul, Chinmay Saha, Gairik Mukherjee, Mayurakshi Nag, Samrat Ghosh, Abhisek Das, Anindita Seal, Sucheta Tripathy
Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides...
January 7, 2019: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30590473/molecular-characteristics-of-early-stage-female-germ-cells-revealed-by-rna-sequencing-of-low-input-cells-and-analysis-of-genome-wide-dna-methylation
#7
Binbin Ma, Tin-Lap Lee, Bian Hu, Jing Li, Xiaoyong Li, Xiaodong Zhao, Changliang Hou, Chen Zhang, Lin He, Xingxu Huang, Xuejin Chen, Jing Li, Ji Wu
High-throughput stage-specific transcriptomics provides an unbiased approach for understanding the process of cell development. Here, we report transcriptome analysis of primordial germ cell, female germline stem cell (FGSC), germinal vesicle and mature oocyte by performing RNA sequencing of freshly isolated cells in mice. As expected, these stages and gene-expression profiles are consistent with developmental timing. Analysis of genome-wide DNA methylation during female germline development was used for confirmation...
December 27, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30590457/identification-epistasis-loci-underlying-rice-flowering-time-by-controlling-population-stratification-and-polygenic-effect
#8
Asif Ahsan, Mamun Monir, Xianwen Meng, Matiur Rahaman, Hongjun Chen, Ming Chen
Flowering time is an important agronomic trait, attributed by multiple genes, gene-gene interactions and environmental factors. Population stratification and polygenic effects might confound genetic effects of the causal loci underlying this complex trait. We proposed a two-step approach for detecting epistasis interactions underlying rice flowering time by accounting population structure and polygenic effects. Simulation studies showed that the approach used in this study performs better than classical and PC-linear approaches in terms of powers and false discovery rates in the case of population stratification and polygenic effects...
December 24, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30535324/dna-methylation-dynamics-in-the-germline-of-the-marsupial-tammar-wallaby-macropus-eugenii
#9
Teruhito Ishihara, Danielle Hickford, Geoff Shaw, Andrew J Pask, Marilyn B Renfree
Parent specific-DNA methylation is the genomic imprint that induces mono-allelic gene expression dependent on parental origin. Resetting of DNA methylation in the germ line is mediated by a genome-wide re-methylation following demethylation known as epigenetic reprogramming. Most of our understanding of epigenetic reprogramming in germ cells is based on studies in mice, but little is known about this in marsupials. We examined genome-wide changes in DNA methylation levels by measuring 5-methylcytosine expression, and mRNA expression and protein localization of the key enzyme DNA methyltransferase 3 L (DNMT3L) during germ cell development of the marsupial tammar wallaby, Macropus eugenii...
December 7, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30520983/comparative-genome-analysis-of-aspergillus-flavus-clinically-isolated-in-japan
#10
Takahito Toyotome, Saho Hamada, Satoe Yamaguchi, Hiroki Takahashi, Daisuke Kondoh, Masahiko Takino, Yu Kanesaki, Katsuhiko Kamei
Aspergillus flavus is an important zoonotic pathogen and a well-known aflatoxin producer. Aspergillus flavus strains that are prevalent in Japanese environments are reported to be non-aflatoxigenic, although their aflatoxin productivity, especially among clinical isolates, has not been thoroughly investigated to date. In this study, we sequenced the genomes of ten strains of A. flavus isolated in Japan and compared their sequences with each other as well as with those of Aspergillus oryzae RIB40 and A. flavus NRRL3357...
December 5, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30462193/genome-sequence-of-the-non-conventional-wine-yeast-hanseniaspora-guilliermondii-utad222-unveils-relevant-traits-of-this-species-and-of-the-hanseniaspora-genus-in-the-context-of-wine-fermentation
#11
Isabel Seixas, Catarina Barbosa, Arlete Mendes-Faia, Ulrich Güldener, Rogério Tenreiro, Ana Mendes-Ferreira, Nuno P Mira
Hanseanispora species, including H. guilliermondii, are long known to be abundant in wine grape-musts and to play a critical role in vinification by modulating, among other aspects, the wine sensory profile. Despite this, the genetics and physiology of Hanseniaspora species remains poorly understood. The first genomic sequence of a H. guilliermondii strain (UTAD222) and the discussion of its potential significance are presented in this work. Metabolic reconstruction revealed that H. guilliermondii is not equipped with a functional gluconeogenesis or glyoxylate cycle, nor does it harbours key enzymes for glycerol or galactose catabolism or for biosynthesis of biotin and thiamine...
November 20, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.com/read/30462165/evaluation-and-application-of-rna-seq-by-minion
#12
Masahide Seki, Eri Katsumata, Ayako Suzuki, Sarun Sereewattanawoot, Yoshitaka Sakamoto, Junko Mizushima-Sugano, Sumio Sugano, Takashi Kohno, Martin C Frith, Katsuya Tsuchihara, Yutaka Suzuki
The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure for full-length cDNA sequencing using the Nanopore sequencer MinION. We applied MinION RNA-Seq for various applications, which would not always be easy using the usual RNA-Seq by Illumina. First, we examined and found that even though the sequencing accuracy was still limited to 92.3%, practically useful RNA-Seq analysis is possible...
November 20, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://read.qxmd.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
#13
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://read.qxmd.com/read/30395234/genome-assembly-and-gene-expression-in-the-american-black-bear-provides-new-insights-into-the-renal-response-to-hibernation
#14
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://read.qxmd.com/read/30380026/landscape-of-gene-transposition-duplication-within-the-brassicaceae-family
#15
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://read.qxmd.com/read/30351380/multi-tissue-transcriptomes-of-caecilian-amphibians-highlight-incomplete-knowledge-of-vertebrate-gene-families
#16
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://read.qxmd.com/read/30325414/overcoming-challenges-in-variant-calling-exploring-sequence-diversity-in-candidate-genes-for-plant-development-in-perennial-ryegrass-lolium-perenne
#17
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://read.qxmd.com/read/30295708/the-genome-of-the-oyster-saccostrea-offers-insight-into-the-environmental-resilience-of-bivalves
#18
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://read.qxmd.com/read/30329019/the-yellowtail-seriola-quinqueradiata-genome-and-transcriptome-atlas-of-the-digestive-tract
#19
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://read.qxmd.com/read/30052927/mobile-elements-contribute-to-the-uniqueness-of-human-genome-with-15-000-human-specific-insertions-and-14-mbp-sequence-increase
#20
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
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