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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 single copy (ie each HK gene should have no paralogs).

Briefly I need a list of genes that are:

  1. House keeping
  2. Single copy
  3. Common in almost all genomes, or genomes of a taxa

Any help is appreciated.

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Just flying from the waist: filter approach: If there is a data source that has the expression data for cells in multiple tissues for any organism i would use that to find the housekeeping genes by sorting which genes are expressed in the greatest number of cells (think excel or XML). Next, I would check which of those genes are also found in/similar to the respective gene (homolog I thin its called) in the plants (using genome browser, e.g., ensembl and blast or just look it and click on the button to bring you to the plant genome). If your model organism does not have sequenced genome... get primers and see if you can sequence it for yourself to see if its there. Then check to see if its a single copy. Hardest part is finding an expressome database spanning multiple tissues in an organism to find housekeeping genes - then hoping they are conserved to the plant. Alternatively, you can consult literature to find housekeeping genes.

You probly just wanted a listing of the genes... sorry.

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The following is probably a good set, it's for Arabidopsis you need to check if it fits with your need.

CBP20 Gene Gene Locus: At5g44200

Actin-2 Gene Gene Locus: At3g18780

UBC Gene Gene Locus: At5g25760

SIGMA sells primers set for these: http://www.sigmaaldrich.com/life-science/molecular-biology/plant-biotechnology/plant-molecular-biology/control-primers-for-arabidopsis.html

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There is no single answer for a gene. The most correct thing to do is to use a set of genes across many locus and measure the correlation of copy number across them first, and only use the ones which co-segregate as single copy number as the measure of 'one copy'.

This is the same approach used for qPCR and is the basis of the widely used geNorm algorithm (11k citations). While in qRT-PCR the 'stability' of a gene expression is compared across mRNA which are at different stoichiometry, in your case you just further restrict that the genes should have stable stoichiometry.

If I was designing this, I would use the same set of genes which are 'housekeepers' defined in the two publications above and avoid sex chromosomes.

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