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Genome characteristics of Kordia antarctica IMCC3317^T and comparative genome analysis of the genus Kordia.

ABSTRACT: The genus Kordia is one of many genera affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes, well known for its degradation of high molecular weight organic matters. The genus Kordia currently comprises eight species, type strains of which have been isolated from a diverse range of marine environments. As of this report, four genome sequences have been submitted for cultured strains of Kordia, but none are complete nor have they been analyzed comprehensively. In this study, we report the complete genome of Kordia antarctica IMCC3317^T, isolated from coastal seawater off the Antarctic Peninsula. The complete genome of IMCC3317^T consists of a single circular chromosome with 5.5 Mbp and a 33.2 mol% of G+C DNA content. The IMCC3317^T genome showed features typical of chemoheterotrophic marine bacteria and similar to other Kordia genomes, such as complete gene sets for the Embden-Meyerhof-Parnas glycolysis pathway, tricarboxylic acid cycle and oxidative phosphorylation. The genome also encoded many carbohydrate-active enzymes, some of which were clustered into approximately seven polysaccharide utilization loci, thereby demonstrating the potential for polysaccharide utilization. Finally, a nosZ gene encoding nitrous oxide reductase, an enzyme that catalyzes the reduction of N₂O to N₂ gas, was also unique to the IMCC3317^T genome.

SUBMITTER: Lim Y

PROVIDER: S-EPMC7477175 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Despite the significant progress that has been made in the genome sequencing of Beauveria species, mitochondrial genome (mitogenome) used to examine genetic diversity within fungal populations. Complete mitogenomes of Beauveria species can be easily sequenced and assembled using various sequencing techniques. However, since mitogenome annotations are mainly derived from similar species comparison and software prediction, and are not supported by RNA-seq transcripts data, it leads to problems with the accuracy of mitochondrial annotations and the inability to understand RNA processing. In this study, we assembled and annotated the mitogenome of eight Beauveria strains using Illumina DNA and RNA sequencing data. The circular mitogenome of eight Beauveria strains ranged from 26,850 bp (B. caledonica strain ATCC 64970) to 35,999 bp (B. brongniartii strain GYU-BMZ03), with the intronic insertions accounting for most of the size variation, thus contributing to a total mitochondrial genome (mitogenome) size of 7.01% and 28.95%, respectively. Intron number variations were not directly related to the evolutionary relationship distance. Besides ribosomal protein S3 (rps3), most introns are lost too quickly and lack the stability of protein-coding genes. The short RNA-seq reads from next-generation sequencing can improve the mitochondrial annotation accuracy and help study polycistronic transcripts and RNA processing. The transcription initiation sites may be located in the control region. Most introns do not serve as taxonomic markers and also lack open reading frames (ORFs). We assumed that the poly A tail was added to the polycistronic transcript before splicing and one polycistronic transcript (trnM (1)-trnL (1)-trnA-trnF-trnK-trnL (2)-trnQ-trnH-trnM (2)-nad2-nad3-atp9-cox2-trnR (1)-nad4L-nad5-cob-trnC-cox1-trnR (2)-nad1-nad4-atp8-atp6-rns-trnY-trnD-trnS-trnN-cox3-trnG-nad6-trnV-trnI-trnS-trnW-trnP-rnl(rps3)-trnT-trnE-trnM (3)) was first processed from the mitogenome and was subsequently processed into smaller mono-, di-, or tricistronic RNAs.

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Genome characteristics of Kordia antarctica IMCC3317^T and comparative genome analysis of the genus Kordia.

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Dataset Information

Genome characteristics of Kordia antarctica IMCC3317T and comparative genome analysis of the genus Kordia.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

Genome characteristics of Kordia antarctica IMCC3317^T and comparative genome analysis of the genus Kordia.