Large-Scale Housekeeping Genes Mining from Public Database: A Case in Gramineae Crop

Background: Housekeeping (HK) genes maintenance of basic cellular functions, therefore they played a very important role in biology and physiology. They ubiquitously, stably and high expressed in all tissue/cell and had shorter introns, untranslated regions and coding sequences. There was little research achievement of gramineae crop HK genes and few HK genes list at present.

Results: In this work, we collected 362 chips of 30 wheat experiments, 409 chips of 79 rice experiments, 250 chips of 37 maize experiments, 440 chips of 45 barley experiments from PLEXdb (Plant Expression Database) and Unigene database from NCBI (National Center for Biotechnology Information) of rice, wheat, maize, and barley. RMA (Robust multi-array average) treatment means format data of chips were used to screen stable expression by our method and classified ESTs were mapped and validated the candidate housekeeping genes. 5% of all probes were selected as the most stably expression genes. ESTs-rich contigs validated the candidate HK gene. Sequence structure, distribution on chromosome, and Gene Ontology (GO) annotation were analyzed to find the general character of the candidate HK genes. That the candidate HK genes (stably expression and ESTs-rich) has compacted gene structure: short exons and introns. Most HK genes are multi-copy because of duplicated, and have short distance to centromere.

Conclusion: We provide an example and effective method to screen HK genes by chips data produced from different laboratories. And the pipeline of this study could be applied to screen genome-wide HK gene for other plants and animals. Also HK genes of Gramineae crops characterized from this study will be useful for other genome-wide analyses in future research.