Forum:Is it still interesting to publish the profile of the transcriptome?
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7 days ago

Look friends,

I would like to raise a discussion about RNAseq.

You think it is still possible to publish works with the descriptions of the profile of the tissue transcriptome.

My doubt refers to the data I obtained from 3 species that make up a certain genus of insects, they are close species and the genus is formed by these 3 species. And would you like to publish the transcriptome profile and compare them?

Article RNA Transcriptome Suggestion RNAseq • 289 views
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nowadays any technically correct study can be published

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THANK YOU, colleagues. Very good suggestions.

I have Rnaseq of tissues from the head of the 3 species (6 samples per species = 18 total) at the same stage of development (nymphs of 5, males). We have already assembled (DENOVO), we checked the quality. also CDS, GOs. Now I intend to look for species from other nearby genres to make the analysis more robust.

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7 days ago

If your question is whether a paper comparing the transcriptomes of 3 closely related species is feasibly going to be published, then the answer is unequivocally "yes" given the very high number of RNA-seq-based papers published on a daily basis. As for whether it's interesting, that really depends on what you actually find and choose to focus on.

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I feel like the focus is key here. RNAseq-datasets tend to be huge piles of information. Its really comprehensive chaos of sequence- and expression information. A thorough research question is key, else it will become descriptive hell.

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7 days ago
geneticatt ▴ 120

You can accomplish some level of comparative genomic analysis with these datasets, but the route you take will be dependent on sequencing depth and the breadth of tissue types you've sampled from. It sounds to me like you isolated a single tissue type from each species and extracted DNA from that, which means that you can't draw conclusions about the whole set of coding sequences in the genome since any individual tissue is likely to express only a fraction of that set at any given time.

If the 'snapsshot' of gene expression that you captured during your RNA extraction was well controlled across the three species (i.e. they were same developmental stage and sex), then the comparison could be meaningful.

In any case, you can translate the assembled transcripts and compare inferred orthologs across the species. You can also try to resolve isoforms, which can lead to interesting implications.

How phylogenetically distant is the nearest reasonably complete and well-annotated reference genome? Having even a remotely close (say, same insect order) reference genome can be helpful.

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