Genome-wide identification and comparative analysis of the TUBBY-like protein gene family in maize

Abstract

The evolutionary history of TUBBY-like proteins (TLPs), which contain a highly conserved tubby domain, can be traced to the early stages of eukaryote evolution, on account of the identification of this gene family in organisms from single-celled to multicellular eukaryotes. While genome-wide structural and evolutionary analyses of the entire TLP gene family have recently been reported in Arabidopsis and rice, little is known about TLP genes in maize. To gain insight into how TLP genes have evolved in maize, we conducted comprehensive analysis of the molecular evolution of TLP genes in this crop. A total of 15 TLP genes (ZmTLP1–15) were identified in maize by genome-wide screening. This family was classified into four subfamilies based on phylogenetic relationships, protein domains, and motif organization. Gene duplication and chromosomal location analysis indicated that segmental duplication has played a major role in the expansion of the maize TLP family. The ZmTLP genes exhibited differential expression profiles under ABA, NaCl, 42, 4 °C, and PEG stress treatment. We performed microsynteny analysis across three gramineous species based on comparisons of the specific regions containing TLP genes, revealing numerous microsyntenic gene pairs among maize, rice, and sorghum, which suggests that the flanking regions of TLP genes may be derived from a common ancient Gramineae ancestor.