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Refined ab initio gene predictions of Heterorhabditis bacteriophora using RNA-seq.


ABSTRACT: Interest has recently grown in developing the entomopathogenic nematode Heterorhabditis bacteriophora as a model to genetically dissect the process of parasitic infection. Despite the availability of a full genome assembly, there is substantial variation in gene model accuracy. Here, a methodology is presented for leveraging RNA-seq evidence to generate improved annotations using ab initio gene prediction software. After alignment of reads and subsequent generation of a RNA-seq supported annotation, the new gene prediction models were verified on a selection of genes by comparison with sequenced 5' and 3' rapid amplification of cDNA ends products. By utilising a whole transcriptome for genome annotation, the current reference annotation was enriched, demonstrating the importance of coupling transcriptional data with genome assemblies.

SUBMITTER: Vadnal J 

PROVIDER: S-EPMC6004328 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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Refined ab initio gene predictions of Heterorhabditis bacteriophora using RNA-seq.

Vadnal Jonathan J   Granger Olivia G OG   Ratnappan Ramesh R   Eleftherianos Ioannis I   O'Halloran Damien M DM   Hawdon John M JM  

International journal for parasitology 20180309 8


Interest has recently grown in developing the entomopathogenic nematode Heterorhabditis bacteriophora as a model to genetically dissect the process of parasitic infection. Despite the availability of a full genome assembly, there is substantial variation in gene model accuracy. Here, a methodology is presented for leveraging RNA-seq evidence to generate improved annotations using ab initio gene prediction software. After alignment of reads and subsequent generation of a RNA-seq supported annotat  ...[more]

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