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Extensive error in the number of genes inferred from draft genome assemblies.

Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW - PLoS Comput. Biol. (2014)

Bottom Line: These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome.To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee.Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

View Article: PubMed Central - PubMed

Affiliation: School of Informatics and Computing, Indiana University, Bloomington, Indiana.

ABSTRACT
Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

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Differences in gene family size when comparing the initial chimpanzee assembly (Pan_troglodytes-1.0) to an updated version (Pan_troglodytes-2.1).Positive numbers indicate an excess number of genes in v1.0, while negative numbers indicate an excess. The small number of gene families with more than +/−3 differences from the reference are not shown.
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pcbi-1003998-g003: Differences in gene family size when comparing the initial chimpanzee assembly (Pan_troglodytes-1.0) to an updated version (Pan_troglodytes-2.1).Positive numbers indicate an excess number of genes in v1.0, while negative numbers indicate an excess. The small number of gene families with more than +/−3 differences from the reference are not shown.

Mentions: We find a similar result in chimpanzee as to that found in chicken, with a large proportion of the gene families having incorrect estimates for the number of genes (Fig. 3). Overall, 74% of families had the same number of genes in the two annotations, while 26% had either a greater or smaller number of genes. A major difference between the chicken analysis and the results found for chimpanzee is that the most common error in the draft chimpanzee genome was the addition of a single gene rather than the loss. The earlier assembly and annotation had predicted almost 1,800 more genes than the updated assembly and annotation.


Extensive error in the number of genes inferred from draft genome assemblies.

Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW - PLoS Comput. Biol. (2014)

Differences in gene family size when comparing the initial chimpanzee assembly (Pan_troglodytes-1.0) to an updated version (Pan_troglodytes-2.1).Positive numbers indicate an excess number of genes in v1.0, while negative numbers indicate an excess. The small number of gene families with more than +/−3 differences from the reference are not shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4256071&req=5

pcbi-1003998-g003: Differences in gene family size when comparing the initial chimpanzee assembly (Pan_troglodytes-1.0) to an updated version (Pan_troglodytes-2.1).Positive numbers indicate an excess number of genes in v1.0, while negative numbers indicate an excess. The small number of gene families with more than +/−3 differences from the reference are not shown.
Mentions: We find a similar result in chimpanzee as to that found in chicken, with a large proportion of the gene families having incorrect estimates for the number of genes (Fig. 3). Overall, 74% of families had the same number of genes in the two annotations, while 26% had either a greater or smaller number of genes. A major difference between the chicken analysis and the results found for chimpanzee is that the most common error in the draft chimpanzee genome was the addition of a single gene rather than the loss. The earlier assembly and annotation had predicted almost 1,800 more genes than the updated assembly and annotation.

Bottom Line: These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome.To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee.Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

View Article: PubMed Central - PubMed

Affiliation: School of Informatics and Computing, Indiana University, Bloomington, Indiana.

ABSTRACT
Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process.

Show MeSH
Related in: MedlinePlus