scholarly journals Draft genome of Semisulcospira libertina, a species of freshwater snail

2021 ◽  
Vol 19 (3) ◽  
pp. e32
Author(s):  
Jeong-An Gim ◽  
Kyung-Wan Baek ◽  
Young-Sool Hah ◽  
Ho Jin Choo ◽  
Ji-Seok Kim ◽  
...  
Keyword(s):  
East Asia ◽  
De Novo Assembly ◽  
Food Source ◽  
De Novo ◽  
Draft Genome ◽  
Clinical Importance ◽  
Freshwater Snail ◽  
Whole Genome ◽  
Genome Data ◽  
First Time

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Although S. libertina has ecological, commercial, and clinical importance, its whole-genome has not been reported yet. Here, we revealed the genome of S. libertina through de novo assembly. We assembled the whole-genome of S. libertina and determined its transcriptome for the first time using Illumina NovaSeq 6000 platform. According to the k-mer analysis, the genome size of S. libertina was estimated to be 3.04 Gb. Using RepeatMasker, a total of 53.68% of repeats were identified in the genome assembly. Genome data of S. libertina reported in this study will be useful for identification and conservation of S. libertina in East Asia.

scholarly journals Employing whole genome mapping for optimal de novo assembly of bacterial genomes

2014 ◽  
Vol 7 (1) ◽  
pp. 484 ◽  
Author(s):  
Basil Xavier ◽  
Julia Sabirova ◽  
Moons Pieter ◽  
Jean-Pierre Hernalsteens ◽  
Henri de Greve ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Genome Mapping ◽  
Whole Genome ◽  
Bacterial Genomes ◽  
Whole Genome Mapping

scholarly journals Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis)

2020 ◽  
Author(s):  
Sabyasachi Mukherjee ◽  
Zexi Cai ◽  
Anupama Mukherjee ◽  
Imsusosang Longkumer ◽  
Moonmoon Mech ◽  
...  
Keyword(s):  
Genome Sequence ◽  
De Novo Assembly ◽  
De Novo ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genomic Architecture

scholarly journals Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms

2019 ◽  
Vol 7 (4) ◽  
Author(s):  
Frederique Pasquali ◽  
Federica Palma ◽  
Marcello Trevisani ◽  
Antonio Parisi ◽  
Alex Lucchi ◽  
...  
Keyword(s):  
Shiga Toxin ◽  
Iron Uptake ◽  
De Novo ◽  
Genetic Relationships ◽  
Draft Genome ◽  
Dairy Farms ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Type Assignment ◽  
Potential Biomarker

In the present study, the genetic relationships as well as the virulome and resistome of newly sequenced O26 and O157 Shiga-toxin producing E. coli (STEC) isolates, collected from dairy farms in Italy, were investigated in comparison to publicly available genomes collected worldwide. The whole genome of Italian isolates was sequenced on Illumina MiSeq Platform. Reads quality control, de novo draft genome assembly, species confirmation and the 7-loci Multi-Locus Sequence Type assignment were performed using INNUca pipeline. Reference-based SNPs calling was performed on O157 and O26 genomes, separately, mapping contigs to high-quality finished genomes. Virulence and antimicrobial resistance determinants were detected in silicousing the tool ABRicate. Phylogenetic reconstructions revealed that genomes clustered mainly based on their 7-loci MLST type. The virulome of tested genomes included 190 determinants. O157 genomes carried chu genes associated to heme mediated iron uptake, whereas O26 genomes harboured genes ybt associated to siderophore mediated iron uptake. Resistome analysis showed the presence of tet(34) on all but one O157 genomes and on only one O26 genomes. Only 4 genomes carried genes associated to multiresistance. In the present study, the genes chu and ybt were identified as potential biomarker for the differentiation of O157 and O26 serotypes.

scholarly journals Enhanced De Novo Assembly of High Throughput Pyrosequencing Data Using Whole Genome Mapping

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e61762 ◽  
Author(s):  
Fatma Onmus-Leone ◽  
Jun Hang ◽  
Robert J. Clifford ◽  
Yu Yang ◽  
Matthew C. Riley ◽  
...  
Keyword(s):  
High Throughput ◽  
De Novo Assembly ◽  
De Novo ◽  
Genome Mapping ◽  
Whole Genome ◽  
Whole Genome Mapping

Whole genome de-novo assembly and annotation protocol for Apostichopus japonicus genome v1 (protocols.io.gmabu2e)

protocols.io ◽  
2016 ◽  
Author(s):  
Jihoon Jo ◽  
Jooseong Oh ◽  
Hyun Gwan ◽  
Hyun Hee ◽  
Sung Gwon ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Apostichopus Japonicus ◽  
Whole Genome

scholarly journals A pilot study for channel catfish whole genome sequencing and de novo assembly

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Yanliang Jiang ◽  
Jianguo Lu ◽  
Eric Peatman ◽  
Huseyin Kucuktas ◽  
Shikai Liu ◽  
...  
Keyword(s):  
Pilot Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Channel Catfish ◽  
De Novo Assembly ◽  
De Novo ◽  
Whole Genome

scholarly journals Draft Genome Sequences of Two Salmonella enterica Strains Isolated from Sprouted Chia and Flax Seed Powders

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Jennifer Ronholm ◽  
Nicholas Petronella ◽  
Sandeep Tamber
Keyword(s):  
United States ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
The United States ◽  
Whole Genome ◽  
Flax Seed ◽  
Genome Sequences ◽  
Chia Seed ◽  
First Time

A 2014 foodborne salmonellosis outbreak in Canada and the United States implicated, for the first time, sprouted chia seed powder as the vehicle of transmission. Here, we report the draft whole genome sequences of two Salmonella enterica strains isolated from sprouted powders related to the aforementioned outbreak.

scholarly journals The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

2022 ◽  
Author(s):  
Shinichi Morita ◽  
Tomoko F. Shibata ◽  
Tomoaki Nishiyama ◽  
Yuuki Kobayashi ◽  
Katsushi Yamaguchi ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Genetic Regulation ◽  
Draft Genome ◽  
Evolutionary Developmental Biology ◽  
Rhinoceros Beetle ◽  
Insect Order ◽  
Trypoxylus Dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

scholarly journals When Less is More: "Slicing" Sequencing Data Improves Read Decoding Accuracy and De Novo Assembly Quality

2015 ◽  
Author(s):  
Stefano Lonardi ◽  
Hamid Mirebrahim ◽  
Steve Wanamaker ◽  
Matthew Alpert ◽  
Gianfranco Ciardo ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
De Novo Assembly ◽  
De Novo ◽  
Optimal Size ◽  
Sequencing Data ◽  
Less Is More ◽  
Bac Clones ◽  
Deep Sequencing Data ◽  
First Time

Since the invention of DNA sequencing in the seventies, computational biologists have had to deal with the problem de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, for the first time we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing. Specifically, we explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to BAC clones (in the context of the combinatorial pooling design proposed by our group), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on "divide and conquer": we "slice" a large dataset into smaller samples of optimal size, decode each slice independently, then merge the results. Experimental results on over 15,000 barley BACs and over 4,000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data.

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