TABLE 1

Summary of probes on GeoChip 5.0M by functional gene categoriesc

Functional gene
category
No. of:% of probe
changes compared
to GeoChip 4
SubcategoriesGenes or
enzymes
Sequence-specific
probes
Group-specific
probes
Total
probes
Covered
CDS
C cycling31184,35419,26123,61550,040+114
N cycling7222,3973,6005,99711,654−19
S cycling5171,9692,3174,2866,823+38
P cycling479602,3003,2606,245+143
Metal homeostasis241055,08437,54342,62791,614+360
Organic contaminant
degradation
71572,2049,24111,44527,938−33
Electron transport3356121,3481,9603,351+72.3
Stress response18862,09823,63425,73279,356+19
Plant growth
promotion
7319572,2633,2205,720NAa
Microbial defense4873,28419,95423,23850,019+597
Virulence105871,2643,5964,86010,863+30
Virus specific41151,5211,3362,8575,182+167
Protozoan specific10848456151,4602,146NAa
Fungus specific9662,5592,0794,6386,987−7
GyrB115322,2342,7669,997+18
Total1161,44730,640131,321161,961365,651b+97
  • a NA (not applicable) because this is a new category for GeoChip 5.0.

  • b Total number of covered coding DNA sequences (CDS) does not equal the sum of those from individual categories due to the presence of CDS that were covered in two or more categories.

  • c Detailed information on individual subcategories of functional genes is presented in Table S1.