High throughput transcriptome sequencing of hybrids could be used to discovery potential im- printed transcription in animals. The approach is based on detecting differential gene expression by counting RNA- seq reads of alternative alleles identified by heterozygous single nucleotide polymorphisms in the hybrids. The parental origin of the two alleles can be easily identified if the parents ar e homozygous for alternative forms. The mule is a hybrid between a donkey father and a horse mother that can be analysed at the transcriptome level to identify the origin of the transcripts from the two donor species, taking advantages from the differences of their genomes. In this study we investigated the mule blood transcriptome by next generation semiconduc-tor-based sequencing. Four mules, two full-sibsand two half-sibs, generated by two different donkey fathers and three different horse mothers, were investigated. Genomic DNA of the parental donkeys and horses was sequenced using the Ion Proton sequencer, obtaining a coverage of ~5X (horses) and ~10X (donkeys). Whole blood sam-ples of the mules was used to obtainmRNAthat was sequenced using the same sequencing tech-nology. A total of ~34 Gbp of RNA- seq data was generated. All obtained sequencing reads were aligned with the horse reference genome (EquCab2). Duplicate reads were eliminated and common variants were filtered considering a minimum coverage of 4X for the donkey genome sequences and 50X for the mule transcriptome reads. More than one variable position in the same transcript was used to determine the origin of the reads. Only concordant results from all mule transcriptomes were filtered to ident ify pu-tative imprinted alleles. Results indicated that fifty genes were expressed only from one of the two original alleles. According to these first re-sults, the mule might constitute an interesting model to investigate the mechanisms and the ef-fects of the parent-of-origin gene expression
Transcriptome wide investigation of parent-of-origin expressed genes in mule (horse x donkey) by next-generation semiconductor-based sequencing
D'ALESSANDRO, ENRICO;Scimone C.;CHIOFALO, Vincenzo;
2014-01-01
Abstract
High throughput transcriptome sequencing of hybrids could be used to discovery potential im- printed transcription in animals. The approach is based on detecting differential gene expression by counting RNA- seq reads of alternative alleles identified by heterozygous single nucleotide polymorphisms in the hybrids. The parental origin of the two alleles can be easily identified if the parents ar e homozygous for alternative forms. The mule is a hybrid between a donkey father and a horse mother that can be analysed at the transcriptome level to identify the origin of the transcripts from the two donor species, taking advantages from the differences of their genomes. In this study we investigated the mule blood transcriptome by next generation semiconduc-tor-based sequencing. Four mules, two full-sibsand two half-sibs, generated by two different donkey fathers and three different horse mothers, were investigated. Genomic DNA of the parental donkeys and horses was sequenced using the Ion Proton sequencer, obtaining a coverage of ~5X (horses) and ~10X (donkeys). Whole blood sam-ples of the mules was used to obtainmRNAthat was sequenced using the same sequencing tech-nology. A total of ~34 Gbp of RNA- seq data was generated. All obtained sequencing reads were aligned with the horse reference genome (EquCab2). Duplicate reads were eliminated and common variants were filtered considering a minimum coverage of 4X for the donkey genome sequences and 50X for the mule transcriptome reads. More than one variable position in the same transcript was used to determine the origin of the reads. Only concordant results from all mule transcriptomes were filtered to ident ify pu-tative imprinted alleles. Results indicated that fifty genes were expressed only from one of the two original alleles. According to these first re-sults, the mule might constitute an interesting model to investigate the mechanisms and the ef-fects of the parent-of-origin gene expressionPubblicazioni consigliate
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