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ConPADE: genome assembly ploidy estimation from next-generation sequencing data.

Margarido GR, Heckerman D - PLoS Comput. Biol. (2015)

Bottom Line: As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace.Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions.We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.

View Article: PubMed Central - PubMed

Affiliation: Microsoft Research, Los Angeles, California, United States of America; Departamento de Genética, Escola Superior de Agricultura ''Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil.

ABSTRACT
As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled, including polyploid plant genomes. Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions. Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype. Here, we describe a first step in avoiding inappropriate collapse during assembly. In particular, we describe ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, we report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. We also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low. We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.

No MeSH data available.


Related in: MedlinePlus

Genotype distribution for switchgrass contigs with a ploidy estimate of four.Bars represent the frequency of each SNP genotype, for all identified variants in contigs estimated to have ploidy four.
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pcbi.1004229.g007: Genotype distribution for switchgrass contigs with a ploidy estimate of four.Bars represent the frequency of each SNP genotype, for all identified variants in contigs estimated to have ploidy four.

Mentions: It is also interesting to investigate the distribution of estimated genotypes, because doing so can provide insights about how the genome is structured. Because genotype AP13 is expected to be a tetraploid, we focus on contigs with an estimated ploidy of four (Fig 7). The apparent excess of SNPs with genotype 2/2 possibly reflects the (pseudo)tetraploid nature of this particular switchgrass individual, such that these SNPs likely arise from differences between the two sub-genomes. Additionally, this result provides empirical evidence that our uniform parameterization for genotypes does not excessively constrain a posteriori estimates of allele dosage, given moderate sequencing coverage levels.


ConPADE: genome assembly ploidy estimation from next-generation sequencing data.

Margarido GR, Heckerman D - PLoS Comput. Biol. (2015)

Genotype distribution for switchgrass contigs with a ploidy estimate of four.Bars represent the frequency of each SNP genotype, for all identified variants in contigs estimated to have ploidy four.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4400156&req=5

pcbi.1004229.g007: Genotype distribution for switchgrass contigs with a ploidy estimate of four.Bars represent the frequency of each SNP genotype, for all identified variants in contigs estimated to have ploidy four.
Mentions: It is also interesting to investigate the distribution of estimated genotypes, because doing so can provide insights about how the genome is structured. Because genotype AP13 is expected to be a tetraploid, we focus on contigs with an estimated ploidy of four (Fig 7). The apparent excess of SNPs with genotype 2/2 possibly reflects the (pseudo)tetraploid nature of this particular switchgrass individual, such that these SNPs likely arise from differences between the two sub-genomes. Additionally, this result provides empirical evidence that our uniform parameterization for genotypes does not excessively constrain a posteriori estimates of allele dosage, given moderate sequencing coverage levels.

Bottom Line: As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace.Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions.We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.

View Article: PubMed Central - PubMed

Affiliation: Microsoft Research, Los Angeles, California, United States of America; Departamento de Genética, Escola Superior de Agricultura ''Luiz de Queiroz", Universidade de São Paulo, Piracicaba, Brazil.

ABSTRACT
As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled, including polyploid plant genomes. Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions. Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype. Here, we describe a first step in avoiding inappropriate collapse during assembly. In particular, we describe ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, we report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. We also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low. We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.

No MeSH data available.


Related in: MedlinePlus