scholarly journals CRISPR system acquisition and evolution of an obligate intracellular Chlamydia-related bacterium

2015 ◽  
Author(s):  
Claire Bertelli ◽  
Ousmane Cisse ◽  
Brigida Rusconi ◽  
Carole Kebbi-Beghdadi ◽  
Antony Croxatto ◽  
...  
Keyword(s):  
Genomic Island ◽  
De Novo ◽  
Crispr Locus ◽  
Crispr System ◽  
Sequencing Technologies ◽  
Related Organism ◽  
Second Generation Sequencing ◽  
System Acquisition ◽  
First Time ◽  
Main Chromosome

Recently, a new Chlamydia-related organism, Protochlamydia naegleriophila KNic, was discovered within a Naegleria amoeba. To decipher the mechanisms at play in the modeling of genomes from the Protochlamydia genus, we sequenced de novo the full genome of Pr. naegleriophila combining the advantages of two second-generation sequencing technologies. The assembled complete genome comprises a 2,885,111 bp chromosome and a 145,285 bp megaplasmid. For the first time within the Chlamydiales order, a CRISPR system, the immune system of bacteria, was discovered on the chromosome. It is composed of a small CRISPR locus comprising eight repeats and the associated cas and cse genes of the subtype I-E. A CRISPR locus was also found within Chlamydia sp. Diamant, another Pr. naegleriophila strain whose genome was recently released, suggesting that the CRISPR system was acquired by a common ancestor of these two members of Pr. naegleriophila, after the divergence from Pr. amoebophila. The plasmid encodes an F-type conjugative system similar to that found in the Pam100G genomic island of Pr. amoebophila suggesting an acquisition of this conjugative system before the divergence of both Protochlamydia species and the integration of a putative Pr. amoebophila plasmid into its main chromosome giving rise to the Pam100G genomic island. Overall, this new Pr. naegleriophila genome sequence enables to investigate further the dynamic processes shaping the genomes of Chlamydia-related bacteria.

scholarly journals Transcriptomic Analysis of Marine Gastropod Hemifusus tuba Provides Novel Insights into Conotoxin Genes

Marine Drugs ◽  
2019 ◽  
Vol 17 (8) ◽  
pp. 466 ◽  
Author(s):  
Ronghua Li ◽  
Michaël Bekaert ◽  
Luning Wu ◽  
Changkao Mu ◽  
Weiwei Song ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Average Length ◽  
Bioactive Molecules ◽  
Asian Countries ◽  
Marine Gastropod ◽  
Sequencing Technologies ◽  
First Time ◽  
Aquaculture Development ◽  
Simple Sequence

The marine gastropod Hemifusus tuba is served as a luxury food in Asian countries and used in traditional Chinese medicine to treat lumbago and deafness. The lack of genomic data on H. tuba is a barrier to aquaculture development and functional characteristics of potential bioactive molecules are poorly understood. In the present study, we used high-throughput sequencing technologies to generate the first transcriptomic database of H. tuba. A total of 41 unique conopeptides were retrieved from 44 unigenes, containing 6-cysteine frameworks belonging to four superfamilies. Duplication of mature regions and alternative splicing were also found in some of the conopeptides, and the de novo assembly identified a total of 76,306 transcripts with an average length of 824.6 nt, of which including 75,620 (99.1%) were annotated. In addition, simple sequence repeats (SSRs) detection identified 14,000 unigenes containing 20,735 SSRs, among which, 23 polymorphic SSRs were screened. Thirteen of these markers could be amplified in Hemifusus ternatanus and seven in Rapana venosa. This study provides reports of conopeptide genes in Buccinidae for the first time as well as genomic resources for further drug development, gene discovery and population resource studies of this species.

scholarly journals First Report of a Complete Genome Sequence of White spot syndrome virus from India

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
K. Vinaya Kumar ◽  
M. S. Shekhar ◽  
S. K. Otta ◽  
K. Karthic ◽  
J. Ashok Kumar ◽  
...  
Keyword(s):  
White Spot Syndrome Virus ◽  
De Novo ◽  
Economic Loss ◽  
White Spot ◽  
Nanopore Sequencing ◽  
Content Type ◽  
Sequencing Technologies ◽  
Aquaculture Industry ◽  
White Spot Syndrome ◽  
First Time

ABSTRACT White spot syndrome virus is a major pathogen of shrimp, causing economic loss to the aquaculture industry. For the first time, a complete de novo genome of an Indian isolate of this virus has been deciphered using Illumina and Nanopore sequencing technologies. The genome has 280,591 bp with 442 predicted coding genes.

scholarly journals Mapping Genomic Scaffolds to Chromosomes Using Laser Capture Microdissection in Application to Hawaiian Picture-Winged Drosophila

2017 ◽  
Vol 152 (4) ◽  
pp. 204-212 ◽  
Author(s):  
Lin Kang ◽  
Phillip George ◽  
Donald K. Price ◽  
Igor Sharakhov ◽  
Pawel Michalak
Keyword(s):  
Laser Capture Microdissection ◽  
De Novo ◽  
Chromosome Mapping ◽  
Drosophila Species ◽  
Sequencing Technologies ◽  
Physical Maps ◽  
New Information ◽  
Genome Assemblies ◽  
First Time ◽  
Laser Capture

Next-generation sequencing technologies have led to a decreased cost and an increased throughput in genome sequencing. Yet, many genome assemblies based on short sequencing reads have been assembled only to the scaffold level due to the lack of sufficient chromosome mapping information. Traditional ways of mapping scaffolds to chromosomes require a large amount of laboratory work and time to generate genetic and/or physical maps. To address this problem, we conducted a rapid technique which uses laser capture microdissection and enables mapping scaffolds of de novo genome assemblies directly to chromosomes in Hawaiian picture-winged Drosophila. We isolated and sequenced intact chromosome arms from larvae of D. differens. By mapping the reads of each chromosome to the recently assembled scaffolds from 3 Hawaiian picture-winged Drosophila species, at least 67% of the scaffolds were successfully assigned to chromosome arms. Even though the scaffolds are not ordered within a chromosome, the fast-generated chromosome information allows for chromosome-related analyses after genome assembling. We utilize this new information to test the faster-X evolution effect for the first time in these Hawaiian picture-winged Drosophila species.

scholarly journals Induction of Promoter DNA Methylation Upon High-Pressure Spraying of Double-Stranded RNA in Plants

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 789
Author(s):  
Athanasios Dalakouras ◽  
Ioannis Ganopoulos
Keyword(s):  
High Pressure ◽  
De Novo ◽  
Epigenetic Changes ◽  
Double Stranded Rna ◽  
Rna Molecules ◽  
Promoter Sequences ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
First Time ◽  
De Novo Methylation

Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic changes was never addressed. Here, we report for the first time that high-pressure spraying of dsRNAs can trigger de novo methylation of promoter sequences in plants.

scholarly journals Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongqing Zhang ◽  
Jiawen Yin ◽  
Shengkai Tang ◽  
Daming Li ◽  
Xiankun Gu ◽  
...  
Keyword(s):  
De Novo ◽  
Corbicula Fluminea ◽  
Gene Families ◽  
Ruditapes Philippinarum ◽  
Genomic Sequences ◽  
Future Research ◽  
Asian Clam ◽  
Sequencing Technologies ◽  
East And Southeast Asia ◽  
Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

scholarly journals Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 481 ◽  
Author(s):  
Chen ◽  
Lin ◽  
Xie ◽  
Zhong ◽  
Zhang ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Single Molecule ◽  
Functional Categories ◽  
Genetic Studies ◽  
Sequencing Technologies ◽  
Clusters Of Orthologous Groups ◽  
Long Read ◽  
Main Gene ◽  
First Time ◽  
Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

scholarly journals De Novo Partial 13q22-q34 Trisomy with Typical Neurological and Immunological Findings: A Case Report with New Genetic Insights

2020 ◽  
Vol 11 (1) ◽  
pp. 21
Author(s):  
Claudia Brogna ◽  
Valentina Milano ◽  
Barbara Brogna ◽  
Lara Cristiano ◽  
Giuseppe Rovere ◽  
...  
Keyword(s):  
Case Report ◽  
De Novo ◽  
Partial Trisomy ◽  
Cerebral Vasculitis ◽  
Radiological Findings ◽  
Cerebral Lesions ◽  
Brain Malformations ◽  
Vermian Hypoplasia ◽  
Callosal Dysgenesis ◽  
First Time

The partial trisomy 13q encompasses an extensive variability of phenotypic and radiological findings including leukoencephalopathy and brain malformations such as holoprosencephaly, callosal dysgenesis, hippocampal hypoplasia, olfactory hypoplasia, and vermian hypoplasia. We report for the first time a case of a 23-year-old patient affected by de novo partial 13q22.1q34 trisomy (41.7 Mb, 72,365,975-114,077,122x3) presenting with hemiparesis related to both ischemic and haemorrhagic cerebral lesions compatible with cerebral vasculitis due to a possible combination of genetic and immunological interaction.

scholarly journals Whole Exome Sequencing in Coloboma/Microphthalmia: Identification of Novel and Recurrent Variants in Seven Genes

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 65
Author(s):  
Patricia Haug ◽  
Samuel Koller ◽  
Jordi Maggi ◽  
Elena Lang ◽  
Silke Feil ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genetic Screening ◽  
De Novo ◽  
Efficient Tool ◽  
Sequencing Technologies ◽  
Whole Exome ◽  
Screening And Identification ◽  
High Throughput Dna Sequencing ◽  
New Mutations

Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.

scholarly journals MUM&Co: accurate detection of all SV types through whole-genome alignment

2020 ◽  
Vol 36 (10) ◽  
pp. 3242-3243 ◽  
Author(s):  
Samuel O’Donnell ◽  
Gilles Fischer
Keyword(s):  
De Novo ◽  
Supplementary Information ◽  
Genome Alignment ◽  
Whole Genome ◽  
Structural Variations ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Human Genomes ◽  
Whole Genome Alignment ◽  
Primary Output

Abstract Summary MUM&Co is a single bash script to detect structural variations (SVs) utilizing whole-genome alignment (WGA). Using MUMmer’s nucmer alignment, MUM&Co can detect insertions, deletions, tandem duplications, inversions and translocations greater than 50 bp. Its versatility depends upon the WGA and therefore benefits from contiguous de-novo assemblies generated by third generation sequencing technologies. Benchmarked against five WGA SV-calling tools, MUM&Co outperforms all tools on simulated SVs in yeast, plant and human genomes and performs similarly in two real human datasets. Additionally, MUM&Co is particularly unique in its ability to find inversions in both simulated and real datasets. Lastly, MUM&Co’s primary output is an intuitive tabulated file containing a list of SVs with only necessary genomic details. Availability and implementation https://github.com/SAMtoBAM/MUMandCo. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals RECORD: Reference-Assisted Genome Assembly for Closely Related Genomes

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Krisztian Buza ◽  
Bartek Wilczynski ◽  
Norbert Dojer
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Real Data ◽  
Reference Sequence ◽  
Individual Genome ◽  
Single Experiment ◽  
Sequencing Technologies ◽  
Sequencing Cost ◽  
The Individual ◽  
Assembly Software

Background. Next-generation sequencing technologies are now producing multiple times the genome size in total reads from a single experiment. This is enough information to reconstruct at least some of the differences between the individual genome studied in the experiment and the reference genome of the species. However, in most typical protocols, this information is disregarded and the reference genome is used.Results. We provide a new approach that allows researchers to reconstruct genomes very closely related to the reference genome (e.g., mutants of the same species) directly from the reads used in the experiment. Our approach applies de novo assembly software to experimental reads and so-called pseudoreads and uses the resulting contigs to generate a modified reference sequence. In this way, it can very quickly, and at no additional sequencing cost, generate new, modified reference sequence that is closer to the actual sequenced genome and has a full coverage. In this paper, we describe our approach and test its implementation called RECORD. We evaluate RECORD on both simulated and real data. We made our software publicly available on sourceforge.Conclusion. Our tests show that on closely related sequences RECORD outperforms more general assisted-assembly software.

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