Genome-wide identification and expression analysis of the PTP family in Chinese cabbage (Brassica rapa subsp. pekinensis)

Abstract

Protein tyrosine phosphatases (PTPs) are signaling enzymes that play an important role in plant growth and development. Bioinformatics was used to analyze the PTP gene family of Brassica rapa subsp. pekinensis. Forty-six BrPTP family members were identified. These families were divided into eight subfamilies according to the protein domain. The relationship between gene structure and evolution was determined by comparing gene structure with the evolutionary tree. The 46 BrPTP genes were unevenly distributed across the chromosomes, and two pairs were identified to be tandem repeats. The BrPTP domain contained eight important motifs. Motifs of the same subfamily were basically identical, whereas that of each subfamily differed. These common motifs in these subfamilies are essential for PTP protein function. Analysis of BrPTP by quantitative reverse-transcription PCR revealed tissue-specific differences in expression. Most of the BrPTP genes were expressed in the five tissues examined, but not all. Expression patterns under stress showed that most genes were involved in the stress response. Further study of the PTP gene family may reveal more of its functions in Chinese cabbage.