Hello,

I work on tomato and used ITAG2.3 for gene ontology analysis. I am quite happy with the results that MapMan provided. But still have some questions. And one of them is I found it is rather strange that genes involved in gibberellin biosynthesis such as 'gibberellin 20-oxidase' and 'gibberellin 2-oxidase' were classed in 'ethylene synthesis-degradation' (bin code 17.5.1). This may due to hormone crosstalk, but is not it more obviously that these two genes should be in 'gibberellin synthesis-degradation'? (You can also find the function of these two genes in a paper from Hedden et al., 2000, Trends in plant science). Do you have comments on it?

So my next question would be what are the most important criteria for classifying genes in relevant gene ontology terms? Is experimental data more important than sequences prediction?

Thank you very much for your reply in advance!

Hi yuxia Yang,

and thanks for your message. In principle, experimental information is regarded more important
than mere sequence similarity. In the case of the specific genes you pointed out the annotation
information will have to be updated to make sure that the proteins are properly classified.

That said, all genes that contain the text you mentioned ('gibberellin 20-oxidase' and 'gibberellin 2-oxidase')
in their description are classified as 17.6.1.13 hormone metabolism.gibberelin.synthesis-degradation.GA2 oxidase
or 17.6.1.11 hormone metabolism.gibberelin.synthesis-degradation.GA20 oxidase respectively
in the arabidopsis annotation... and since the ITAG annotation was generated in part based on
the arabidopsis annotation, it would be good to know exactly which ITAG genes are, according
to your report, misannotated. I'd be grateful if you could tell me the corresponding IDs so i can
investigate and correct this.

thanks in advance,
Marc

Hi Marc,

Thank you so much for your reply!

Herewith the gene IDs
Bincodes 17.5.1 ‘hormone metabolism.ethylene.synthesis-degradation’

solyc03g006880.2.1 Gibberellin 20-oxidase-1
solyc03g119910.2.1 Gibberellin 3-beta-hydroxylase
solyc06g035530.2.1 Gibberellin 20-oxidase-2
solyc07g056670.2.1 Gibberellin 2-oxidase 2

Bincodes 17.8.1 ‘hormone metabolism.salicylic acid.synthesis-degradation’

solyc08g069010.2.1 Pentatricopeptide repeat-containing protein (PRR)
solyc03g112190.2.1 Pentatricopeptide repeat-containing protein

So besides mentioned gene, I also found another two genes (PRR) classed in to SA synthesis-degradation. According to published experimental data(Laluk et al., 2011,Plant Physiology), PRR may function in negatively regulating ABA (abscisic acid) biosynthesis. Since ABA is antagonistic with SA, that might explain why putting PRR in SA synthesis-degradation. However, maybe these two gene can be better classified.

Thank you very much!

Regards,
Yuxia

Hi Yuxia

and thanks for the information!

cheers,
Marc