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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

Observed allele ratios of variants called by ConPADE for switchgrass contigs with various estimated ploidies.Each dot represents a significantly identified variant position. For each estimated ploidy, dashed lines represent expected genotypes.
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pcbi.1004229.g006: Observed allele ratios of variants called by ConPADE for switchgrass contigs with various estimated ploidies.Each dot represents a significantly identified variant position. For each estimated ploidy, dashed lines represent expected genotypes.

Mentions: Fig 6 displays observed allele ratios for called variants, from examples of contigs representative of each estimated ploidy. Allele ratios were in agreement with possible values given estimated ploidies, as visualized by distances of individual SNPs from the dashed lines. It is also interesting to note that allele ratios provide a rough guide to sequence diversity within a given segment. For instance, contig 238988 had an estimated ploidy of six and virtually all called variants displayed an allele ratio of 1:5 (Fig 6E). In other words, most identified SNPs presented only one copy of the less frequent allele. A closer look at the reads aligned against a region containing some of the variants in that contig provides a picture of how the alleles are organized in haplotypes (S7 Fig). Interestingly, in this case, most minor alleles are linked to each other in the same reads, forming a single haplotype. This haplotype is present in a roughly 1:5 ratio with regards to the underlying reference sequence.


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

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

Observed allele ratios of variants called by ConPADE for switchgrass contigs with various estimated ploidies.Each dot represents a significantly identified variant position. For each estimated ploidy, dashed lines represent expected genotypes.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi.1004229.g006: Observed allele ratios of variants called by ConPADE for switchgrass contigs with various estimated ploidies.Each dot represents a significantly identified variant position. For each estimated ploidy, dashed lines represent expected genotypes.
Mentions: Fig 6 displays observed allele ratios for called variants, from examples of contigs representative of each estimated ploidy. Allele ratios were in agreement with possible values given estimated ploidies, as visualized by distances of individual SNPs from the dashed lines. It is also interesting to note that allele ratios provide a rough guide to sequence diversity within a given segment. For instance, contig 238988 had an estimated ploidy of six and virtually all called variants displayed an allele ratio of 1:5 (Fig 6E). In other words, most identified SNPs presented only one copy of the less frequent allele. A closer look at the reads aligned against a region containing some of the variants in that contig provides a picture of how the alleles are organized in haplotypes (S7 Fig). Interestingly, in this case, most minor alleles are linked to each other in the same reads, forming a single haplotype. This haplotype is present in a roughly 1:5 ratio with regards to the underlying reference sequence.

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