ploidyNGS: visually exploring ploidy with Next Generation Sequencing data

Santos, Renato Augusto Corrêa dos; Goldman, Gustavo H.; Riaño‐Pachón, Diego Mauricio

doi:10.1093/bioinformatics/btx204

Cited by 57 publications

(57 citation statements)

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“…2017 ) for identification of regions potentially involved in secondary metabolite production. To estimate the ploidy of the sequenced P. plurivora genome, we used ploidyNGS ( Corrêa dos Santos et al. 2017 ) that derives ploidy information from allele frequencies present in the Illumina short reads.…”

Section: Methodsmentioning

confidence: 99%

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Vetukuri

Tripathy

et al. 2018

Genome Biology and Evolution

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Species from the genus Phytophthora are well represented among organisms causing serious diseases on trees. Phytophthora plurivora has been implicated in long-term decline of woodland trees across Europe. Here we present a draft genome sequence of P. plurivora, originally isolated from diseased European beech (Fagus sylvatica) in Malmö, Sweden. When compared with other sequenced Phytophthora species, the P. plurivora genome assembly is relatively compact, spanning 41 Mb. This is organized in 1,919 contigs and 1,898 scaffolds, encompassing 11,741 predicted genes, and has a repeat content of approximately 15%. Comparison of allele frequencies revealed evidence for tetraploidy in the sequenced isolate. As in other sequenced Phytophthora species, P. plurivora possesses genes for pathogenicity-associated RXLR and Crinkle and Necrosis effectors, predominantly located in gene-sparse genomic regions. Comparison of the P. plurivora RXLR effectors with orthologs in other sequenced species in the same clade (Phytophthora multivora and Phytophthora capsici) revealed that the orthologs were likely to be under neutral or purifying selection.

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Section: Methodsmentioning

confidence: 99%

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Vetukuri

Tripathy

et al. 2018

Genome Biology and Evolution

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“…The utility of SNP data derived from WGS to identify and study mixtures has been demonstrated in different diploid and polyploid organisms [42-44]. Current approaches in bacterial organisms include a database of known STs and proportion estimates of the bacterial population [45], which requires prior knowledge of the specific bacterial population or long-read sequencing [46], the latter of which is costly and error-prone when used in isolation.…”

Section: Resultsmentioning

confidence: 99%

“…Current approaches in bacterial organisms include a database of known STs and proportion estimates of the bacterial population [45], which requires prior knowledge of the specific bacterial population or long-read sequencing [46], the latter of which is costly and error-prone when used in isolation. Bioinformatic solutions are available for ploidy inference of eukaryotic organisms [42-44, 47], which rely on the depth ratio of the two most abundant alleles sequenced for all heterozygous SNP positions across the genome (also referred to as ‘allele balance’). Such approaches assume SNP allele balances remain relative to each other; for example in a diploid sample, 50% of reads would support one allele while the other 50% support the other allele [42].…”

Section: Resultsmentioning

confidence: 99%

“…Bioinformatic solutions are available for ploidy inference of eukaryotic organisms [42-44, 47], which rely on the depth ratio of the two most abundant alleles sequenced for all heterozygous SNP positions across the genome (also referred to as ‘allele balance’). Such approaches assume SNP allele balances remain relative to each other; for example in a diploid sample, 50% of reads would support one allele while the other 50% support the other allele [42]. However, the allele balance assumption does not hold in bacterial mixtures, which may contain mixed ratios of any proportion.…”

Section: Resultsmentioning

confidence: 99%

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Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

Aziz

Currie

Mayo

et al. 2019

Preprint

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21Human-to-human transmission of the melioidosis bacterium, Burkholderia pseudomallei, is exceedingly 22 rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing 23 (WGS) to characterise one such unusual B. pseudomallei transmission event, which occurred between a 24 breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types 25 (STs) 259 and 261 were identified in the mother's sputum from both the primary culture sweep and in 26 purified colonies, confirming an unusual polyclonal infection in this patient. In contrast, primary culture 27 sweeps of the mother's breast milk and the child's cerebrospinal fluid and blood samples contained only 28 ST-259, indicating monoclonal transmission to the child. Analysis of purified ST-259 isolates showed no 29 genetic variation between mother and baby isolates, providing the strongest possible evidence of B. 30 pseudomallei transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, 31 including the mother's mixed ST-259/261 sputum sample was performed to investigate the effects of 32 mixtures on phylogenetic inference. Inclusion of this mixture caused a dramatic reduction in the number 33 of informative SNPs, resulting in branch collapse of ST-259 and ST-261 isolates, and several instances of 34 incorrect topology in a global B. pseudomallei phylogeny, resulting in phylogenetic incongruence. Although 35 phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results 36demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are not 37 correctly identified and omitted. Using current bioinformatic tools, we demonstrate a robust method for 38 bacterial mixture identification and strain parsing that avoids these pitfalls. 393 Impact Statement 40Burkholderia pseudomallei is the causative agent of melioidosis, a tropical disease of high mortality. B. 41 pseudomallei infections occur almost exclusively through contact with contaminated soil and water. Using 42 whole-genome sequencing (WGS), we investigated a rare case of suspected B. pseudomallei transmission 43 from mother to child. The mother's sputum, breast milk and the baby's blood and cerebrospinal fluid (CSF) 44 specimens were collected, and DNA was extracted from both pure colonies and primary culture sweeps to 45 capture potential strain mixtures. In-depth analysis of genetic variants identified two strains in the mother's 46 sputum belonging to multilocus sequence types ST-259 and ST-261, whereas the child was infected with 47 only ST-259. Comparative genomics revealed no genetic differences between mother and child ST-259 48 isolates, providing the strongest possible evidence of transmission to the child via breast milk. The sputum 49 strain mixture was subsequently used to develop a bioinformatic method for identification and 50 quantification of mixtures from WGS data. Using this method, we found ST-259 and ST-261 at an 87%:13% 51 rat...

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“…Public databases exist to capture C -value and ploidy levels in plants (e.g., http://data.kew.org/cvalues/ ). Recent tools have also been developed to infer the ploidy level using NGS data, such as ploidyNGS (Dos Santos et al, 2017 ), ConPADE (Margarido and Heckerman, 2015 ), and a pipeline using single nucleotide polymorphism (SNP) counts that was reported earlier by Yoshida et al ( 2013 ) for the estimation of ploidy level in the plant pathogen Phytophthora infestans . A general approach to estimate ploidy levels using NGS is by mapping the sequenced reads to the reference genome and then counting the number of mapped reads, representing the different alleles at each position.…”

Section: How To Estimate Ploidy Level In Plantsmentioning

confidence: 99%

Current Strategies of Polyploid Plant Genome Sequence Assembly

et al. 2018

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Polyploidy or duplication of an entire genome occurs in the majority of angiosperms. The understanding of polyploid genomes is important for the improvement of those crops, which humans rely on for sustenance and basic nutrition. As climate change continues to pose a potential threat to agricultural production, there will increasingly be a demand for plant cultivars that can resist biotic and abiotic stresses and also provide needed and improved nutrition. In the past decade, Next Generation Sequencing (NGS) has fundamentally changed the genomics landscape by providing tools for the exploration of polyploid genomes. Here, we review the challenges of the assembly of polyploid plant genomes, and also present recent advances in genomic resources and functional tools in molecular genetics and breeding. As genomes of diploid and less heterozygous progenitor species are increasingly available, we discuss the lack of complexity of these currently available reference genomes as they relate to polyploid crops. Finally, we review recent approaches of haplotyping by phasing and the impact of third generation technologies on polyploid plant genome assembly.

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ploidyNGS: visually exploring ploidy with Next Generation Sequencing data

Abstract: diriano@gmail.com.

Cited by 57 publications

References 7 publications

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Draft Genome Sequence for the Tree PathogenPhytophthora plurivora

Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality

Current Strategies of Polyploid Plant Genome Sequence Assembly

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