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MCorentin / Solanum_sitiens_assembly

Instructions to reproduce the de novo assembly of Solanum sitiens (accession LA1974).
MIT License
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Request for clarification on RNA-Seq data and gene annotations #1

Open Cold7 opened 3 days ago

Cold7 commented 3 days ago

In our lab we are conducting research focused on drought resistance in tomato species. Recently we were reviewing your paper, which presents a valuable de novo genome assembly for Solanum sitiens. we found your study highly relevant to my work, as it provides crucial insights into drought and salt tolerance mechanisms. Thank you for your valuable contribution to this field.

However, I have encountered the following challenges regarding the associated RNA-Seq data:

The sequence read data (SRR) lacks detailed annotations on the experimental conditions. Specifically, it is unclear which of the six samples correspond to control or treatment groups. Additionally, I was unable to locate the associated gene annotations in the NCBI database. So, could you please provide us a clarification on the experimental conditions for the RNA-Seq samples (e.g., which samples are controls and which are treatments) and Information or access to the gene annotations associated with this study

Thank you very much for your time and assistance. I greatly appreciate your efforts in advancing this important area of study.

MCorentin commented 15 hours ago

Hi,

Thank you for your interest in the paper.

We did not have cases and controls here. We sequenced multiple tissues from the plant in order to make a de-novo transcriptome assembly, representing most of the expressed genes (and aid gene prediction with Augustus).

The gene annotation for the predicted genes is available as a gff in this repository (here: https://github.com/MCorentin/Solanum_sitiens_assembly/blob/master/Augustus/augustus_annotations.gff). We annotated the predicted genes against ITAG4.0 (annotation for Solanum lycopersicum, ids starting with Solyc04g) and TAIR10 (Arabidopsis thaliana annotation, ids starting with AT1G).

More files are available in this DropBox folder, if needed: https://www.dropbox.com/scl/fo/96pyatuj6e1zbz1fzknj4/ADjayIp9kmhOwI931pzy9kQ?rlkey=9b3rr5x3mv7oq6ktszi9shpey&e=1&dl=0

Let me know if anything is not clear.

Just in case, as it might be of interest to you, we have a similar paper on Solanum chilense, where we identified the probable dual role of some genes in drought resistance and fruit development: https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1342739/full