QUAST: quality assessment tool for genome assemblies

SummaryThe related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

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“…(2013)] with the default parameters and the minimum alignment length of 1000 bp. The genome of Oryza sativa ssp.…”

Section: Methodsmentioning

confidence: 99%

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brożyńska

Copetti

Furtado

et al. 2017

Plant Biotechnology Journal

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“…In particular, genomes recovered from single cells or metagenomic data require careful scrutiny due to the additional complications inherent in obtaining genomes using these approaches (Dick et al 2010;Albertsen et al 2013;Imelfort et al 2014). The quality of isolate genomes has traditionally been evaluated using assembly statistics such as N50 (Salzberg et al 2012;Gurevich et al 2013), but recent single cell and metagenomic studies have also used universal single-copy 'marker' genes for estimating genome completeness (Wrighton et al 2012;Haroon et al 2013;Rinke et al 2013;. Specifically, completeness is estimated as the fraction of expected marker genes present within a genome.…”

Section: Introductionmentioning

confidence: 99%

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Parks

Imelfort

Skennerton

et al. 2014

Preprint

433

561

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Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. While 25 this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of 'marker' genes conserved across all bacterial or archaeal 30 genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree along with information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate, single cell and metagenome derived genomes. CheckM is shown to provide accurate estimates of genome completeness and 35 contamination, and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene-and genome-centric analyses of microbial communities. CheckM is open 40 source software available at http://ecogenomics.github.io/CheckM.

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“…The nucleotide sequences of all strains were retrieved in FASTA format from the GenBank genome database. The quality of the assemblies for all genomes were assessed by using QUAST version 4.6.3 [9]. Whole genome alignment and Fragment all-against-all comparison analysis was done by using Gegenees software version 2.2.1 with BLAST+ version 2.7.1 installed in the pipeline [10].…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomic Analysis of Bacillus thuringiensis Reveals Molecular Adaptations to Copper Tolerance

Low

Chin

Joseph

et al. 2018

Preprint

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Bacillus thuringiensis is a type of Gram positive and rod shaped bacterium that is found in a wide range of habitats. Despite the intensive studies conducted on this bacterium, most of the information available are related to its pathogenic characteristics, with only a limited number of publications mentioning its ability to survive in extreme environments. Recently, a B. thuringiensis MCMY1 strain was successfully isolated from a copper contaminated site in Mamut Copper Mine, Sabah. This study aimed to conduct a comparative genomic analysis by using the genome sequence of MCMY1 strain published in GenBank (PRJNA374601) as a target genome for comparison with other available B. thuringiensis genomes at the GenBank. Whole genome alignment, Fragment all-againstall comparison analysis, phylogenetic reconstruction and specific copper genes comparison were applied to all forty-five B. thuringiensis genomes to reveal the molecular adaptation to copper tolerance. The comparative results indicated that B. thuringiensis MCMY1 strain is closely related to strain Bt407 and strain IS5056. This strain harbors almost all available copper genes annotated from the forty-five B. thuringiensis genomes, except for the gene for Magnesium and cobalt efflux protein (CorC) which plays an indirect role in reducing the oxidative stress that caused by copper and other metal ions. Furthermore, the findings also showed that the Copper resistance gene family, CopABCDZ and its repressor (CsoR) are conserved in almost all sequenced genomes but the presence of the genes for Cytoplasmic copper homeostasis protein (CutC) and CorC across the sample genomes are highly inconsonant. The variation of these genes across the B. thuringiensis genomes suggests that each strain may have adapted to their specific ecological niche. However, further investigations will be need to support this preliminary hypothesis.

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QUAST: quality assessment tool for genome assemblies

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 7,420 publications

References 15 publications

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Comparative Genomic Analysis of Bacillus thuringiensis Reveals Molecular Adaptations to Copper Tolerance

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