Is it normal to have low expression levels of house keeping genes in plant RNA-seq results

Question

[shuchen]

We had a RNA-seq experiment for a plant material (no genome reference available), 6 samples, 3Gb Illumina Hiseq PE reads for each sample. The transcriptome reference was constructed with Trinity and then the reads of each sample were aligned to this constructed reference with Bowtie2. The overall alignment rate is over 80%. But the reads count aligned to several housekeeping genes were extremely low, about 10-40 reads per gene. Is this result normal?

[VHahaut]

Can you compare those results to samples which are already known for your species or for a similar one? Some housekeeping genes are expressed at low levels so could be due to that. Otherwise 80% alignment is not bad in that case with no reference or bad reference at start.

[Titus]

Hi , Did you check if you don't have some enrichment step in your experiment ? That's the random think in RNA-seq even if you compare with other result sometime you have bias unknown, even if you have same species with the same condition growth plant and the same experimental sequencing...

Best

Tristan

[shuchen]

Thank you! I think this is a possible reason for that. I will check with the sequencing company if they did some enrichment.

[shuchen]

Thank you. I will check some similar experiments of similar species.