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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

Ploidy estimate distribution for common wheat chromosome arm 5D contigs.Bars represent the frequency of each ploidy estimated by ConPADE, for a set of 16,684 wheat contigs from the de novo assembly of chromosome arm 5D.
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pcbi.1004229.g008: Ploidy estimate distribution for common wheat chromosome arm 5D contigs.Bars represent the frequency of each ploidy estimated by ConPADE, for a set of 16,684 wheat contigs from the de novo assembly of chromosome arm 5D.

Mentions: After stringent read alignment, we could evaluate the ploidy of a set of 16,684 contigs with varying levels of coverage. More than 80% of the contigs (13,385) were confirmed to have a ploidy of one, that is, were inferred to represent a single haploid segment. Contigs with a ploidy level of two represented almost 9% of the total (1,499), as did contigs with a ploidy of four (1,471). Only 329 contigs (1.97% of the total) had an estimated ploidy of three (Fig 8).


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

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

Ploidy estimate distribution for common wheat chromosome arm 5D contigs.Bars represent the frequency of each ploidy estimated by ConPADE, for a set of 16,684 wheat contigs from the de novo assembly of chromosome arm 5D.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi.1004229.g008: Ploidy estimate distribution for common wheat chromosome arm 5D contigs.Bars represent the frequency of each ploidy estimated by ConPADE, for a set of 16,684 wheat contigs from the de novo assembly of chromosome arm 5D.
Mentions: After stringent read alignment, we could evaluate the ploidy of a set of 16,684 contigs with varying levels of coverage. More than 80% of the contigs (13,385) were confirmed to have a ploidy of one, that is, were inferred to represent a single haploid segment. Contigs with a ploidy level of two represented almost 9% of the total (1,499), as did contigs with a ploidy of four (1,471). Only 329 contigs (1.97% of the total) had an estimated ploidy of three (Fig 8).

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