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plant housekeeping genes without paralogs

I am working on a tool for SNP calling in polyploid plants. To test my method I need a list of housekeeping genes common in almost all plants. for my case, these genes must be individual in whole genome, for example housekeeping gene A is not suitable for my check if it has one and/or more paralog locus(es) in a plant genome.

Briefly:

1) Which housekeeping genes are common in all plant genomes?

2) Where can I find an up-to-date list of plant housekeeping genes?

3) Where can I find some data or a list of housekeeping genes that haven't paralogs in genome(s)?

gene genome polyploidy
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updated by Ram Ram • written by utsafar utsafar

Might want to check BUSCO, which is short for "Benchmarking Universal Single-Copy Orthologs". So I'm guessing there is a way to download a dataset for plants and checking what it has.

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written by biofalconch biofalconch

1 answer

Check OrthoDB, a database of orthologs. You can query it online, or download a plant fasta to use locally. BUSCO uses OrthoDB to construct its catalog of orthologs

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written by h.mon h.mon

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