Isolation and complete genome sequencing of Mimivirus bombay, a Giant Virus in sewage of Mumbai, India

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Abstract

We report the isolation and complete genome sequencing of a new Mimiviridae family member, infecting Acanthamoeba castellanii, from sewage in Mumbai, India. The isolated virus has a particle size of about 435 nm and a 1,182,200-bp genome. A phylogeny based on the DNA polymerase sequence placed the isolate as a new member of the Mimiviridae family lineage A and was named as Mimivirus bombay. Extensive presence of Mimiviridae family members in different environmental niches, with remarkably similar genome size and genetic makeup, point towards an evolutionary advantage that needs to be further investigated. The complete genome sequence of Mimivirus bombay was deposited at GenBank/EMBL/DDBJ under the accession number KU761889.

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GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

J Besemer (2001)

Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene start prediction can be improved by combining models of protein-coding and non-coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method, called GeneMarkS, utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions and the Gibbs sampling multiple alignment program. GeneMarkS predicted precisely 83.2% of the translation starts of GenBank annotated Bacillus subtilis genes and 94.4% of translation starts in an experimentally validated set of Escherichia coli genes. We have also observed that GeneMarkS detects prokaryotic genes, in terms of identifying open reading frames containing real genes, with an accuracy matching the level of the best currently used gene detection methods. Accurate translation start prediction, in addition to the refinement of protein sequence N-terminal data, provides the benefit of precise positioning of the sequence region situated upstream to a gene start. Therefore, sequence motifs related to transcription and translation regulatory sites can be revealed and analyzed with higher precision. These motifs were shown to possess a significant variability, the functional and evolutionary connections of which are discussed.

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A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.

David Coil, Guillaume Jospin, Aaron Darling (2015)

Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.

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The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel (2007)

Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element) are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at

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Author and article information

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Kiran Kondabagil

Journal

Journal ID (nlm-ta): Genom Data

Journal ID (iso-abbrev): Genom Data

Title: Genomics Data

Publisher: Elsevier

ISSN (Electronic): 2213-5960

Publication date PMC-release: 31 May 2016

Publication date Collection: September 2016

Publication date (Electronic): 31 May 2016

Volume: 9

Pages: 1-3

Affiliations

Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400076, India

Author notes

[* ]Corresponding author: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.Department of Biosciences and BioengineeringIndian Institute of Technology BombayPowaiMumbai400076India kirankondabagil@ 123456iitb.ac.in kirankondabagil@ 123456gmail.com

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Publisher ID: S2213-5960(16)30072-1

DOI: 10.1016/j.gdata.2016.05.013

PMC ID: 4906119

PubMed ID: 27330993

SO-VID: 700a4518-64b7-489f-9761-a70815dcdb0e

License:

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Isolation and complete genome sequencing of Mimivirus bombay, a Giant Virus in sewage of Mumbai, India

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Abstract

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Genome Engineering using CRISPR

Most cited references 8

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data.

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

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