Approaches for in silico finishing of microbial genome sequences

Kremer, Frederico Schmitt; McBride, Alan J. A.; Pinto, Luciano da Silva

doi:10.1590/1678-4685-gmb-2016-0230

Cited by 17 publications

(14 citation statements)

References 111 publications

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“…Completeness and correctness of genic sequences in T . indica assemblies are of paramount importance for direct comparison of assembled sequences 28 . However, the improved draft version of assembly was generated by using an iterative merging strategy of Metassembler v1.5 29 by merging the inter-species draft monoteliosporic sequence-based assemblies from DAOM 236416 and RAKB_UP_1 isolates with the improved and reassembled hybrid assembly of TiK.…”

Section: Methodsmentioning

confidence: 99%

Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat

Mishra

Maurya

Gupta

et al. 2019

Sci Rep

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Tilletia indica (Ti) - a quarantined fungal pathogen of wheat and its pathogenesis is chiefly governed by pathogen effectors secreted inside the host plant. The de novo genome sequencing of several field isolates and stages available could be used for understanding the molecular pathogenesis. The presence of gaps and low coverage of assembled genomes poses a problem in accurate functional annotation of such functions. In the present study attempts were made to improve the Ti draft genome through reconciliation of globally available datasets of three highly virulent monoteliospore cultures of Ti field isolates. It has sequence depth of 107x and N50 scaffold size of 80,772 (more than 26 times as large as achieved in the draft assembly) with highest sequence contiguity, more accurate and nearly complete. Functional annotation revealed that Ti genome contains 9209 genes evolved with many expanded gene families and arranged mostly in a cluster. About 79% of Ti genes were orthologous to other basidiomycetes fungi, Around 7.93% proteins were having secretary signals and 6.66% were identified as highly virulent pathogenicity genes. Using improved Ti genome as a reference, the genomic variation was assessed with respect to repeats, SNPs/InDel, gene families and correct set of virulence associated genes during its life cycle. The comparative intra-species, inter-stage and inter-species genomic variation will have broader implications to understand the gene regulatory networks involved in growth, mating and virulence behaviour of Tilletia f. spp. and also for better appreciation of fungal biology and disease management.

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Section: Methodsmentioning

confidence: 99%

Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat

Mishra

Maurya

Gupta

et al. 2019

Sci Rep

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“…For bacterial genomes specifically, several pipelines for assembly finishing have been developed (Bosi et al, 2015). They usually take as input an assembly obtained with short-read data and align it to one or multiple close reference genomes, in order to find a contig ordering (Kremer et al, 2017). Recent work has examined the cause of assembly fragmentation for seven bacterial genomes sequenced using PacBio sequencing, and rejected the hypothesis that gaps were caused by strong secondary DNA structure (Utturkar et al, 2017).…”

Section: Related Workmentioning

confidence: 99%

Graph analysis of fragmented long-read bacterial genome assemblies

2019

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Motivation Long-read genome assembly tools are expected to reconstruct bacterial genomes nearly perfectly; however, they still produce fragmented assemblies in some cases. It would be beneficial to understand whether these cases are intrinsically impossible to resolve, or if assemblers are at fault, implying that genomes could be refined or even finished with little to no additional experimental cost. Results We propose a set of computational techniques to assist inspection of fragmented bacterial genome assemblies, through careful analysis of assembly graphs. By finding paths of overlapping raw reads between pairs of contigs, we recover potential short-range connections between contigs that were lost during the assembly process. We show that our procedure recovers 45% of missing contig adjacencies in fragmented Canu assemblies, on samples from the NCTC bacterial sequencing project. We also observe that a simple procedure based on enumerating weighted Hamiltonian cycles can suggest likely contig orderings. In our tests, the correct contig order is ranked first in half of the cases and within the top-three predictions in nearly all evaluated cases, providing a direction for finishing fragmented long-read assemblies. Availability and implementation https://gitlab.inria.fr/pmarijon/knot . Supplementary information Supplementary data are available at Bioinformatics online.

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“…Whole-genome optical mapping, the cutting edge technology offered for resolving the issues through estimating the gap length between the scaffolds and merges them into much longer sequences without introducing new bases (Ghurye and Pop, 2019;Kremer et al, 2017;Zhou et al, 2009;Aston et al, 1999;Samad et al, 1995). It also provides a valuable template for de novo genomic sequence assembly where large structural variations in the genome can accurately be detected and quantified (Long et al, 2018;Mak et al, 2016;Shukla et al, 2009;Teague et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Whole-genome optical mapping: Improving assembly of Macrophomina phaseolina MS6 through spanning of twelve blunt end chromosomes by obviating all errors and misassembles

Hossen¹,

Islam²,

Emdad³

et al. 2019

Afr. J. Biotechnol.

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Deciphering genetic information through next-generation sequencing (NGS) is considered as the basic platform to unveil in details of an organism. However, as it produces short reads that lead to difficulties in assembly, we generated long scaffold-based optical mapping (OM) data of previously sequenced devastating fungus, Macrophomina phaseolina MS6. In the process, KpnI identified as the most effective restriction endonuclease among tested 13, used to digest high molecular weight (HMW) DNA that generated 270,343 genomic DNA molecules size in more than 250 kb. The molecules were assembled and constructed 12 super-scaffolds (terminated with telomeric blunt-ends and denoted as chromosomes) that were aligned with NGS generated 17 (out of 88 reduced from 94) reference scaffolds. The state-of-the-art technology revealed concordances and different discordances viz., inversions, low-quality assembly, gaps, overlaps followed to correct the NGS misassembles. Based on the results, OM generated improved and validated assembly advance our understanding of the chromosome evolution of fungi. This furnished data might be considered as valuable resources to accelerate the precise planning for the protection of M. phaseolina MS6 infected sequenced crops through developing the cross-talk phenomenon between the host and pathogen.

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Approaches for in silico finishing of microbial genome sequences

Cited by 17 publications

References 111 publications

Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat

Comparative genomic analysis of monosporidial and monoteliosporic cultures for unraveling the complexity of molecular pathogenesis of Tilletia indica pathogen of wheat

Graph analysis of fragmented long-read bacterial genome assemblies

Whole-genome optical mapping: Improving assembly of Macrophomina phaseolina MS6 through spanning of twelve blunt end chromosomes by obviating all errors and misassembles

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