Molecular Evolution Of The HD-ZIP I Transcription Factor Families In Grasses

With the increase of global environmental degradation, environmental stresses, such as drought, salinity and low temperature, have adverse effects on plant growth and yield. Studies showed that HD-Zip I transcription factors are the relatively conservative factors which belong to the subtribe of homeodomain-leucine zipper (HD-Zip) proteins and have diverse functions in biological and environmental stress response, hormones and light signal response, regulating organ development. In this study we analyzed the HD-Zip I gene family from four grasses species for which substantial information about genomes or transcriptomes was available, namely Brachypodium distachyon, Sorghum bicolor, Oryza sativa and Zea mays. The origin and evolution, and gene duplication and loss of HD-Zip I gene families in grasses were studied based on investigation of intron/exon distribution patterns, protein domains and motifs, phylogenitic relationships, intraspecies and intersepecies gene colinearity (microsynteny) as well as environmental selection pressure. Main results are as follows:1. By searching published genome and transcriptome databases, according to the conserved domain, a total of 11,14,13 and 19 HD-Zip I genes were indentified in grasses Brachypodium distachyon, Sorghum bicolor, Oryza sativa and Zea mays, respectively.2. The phylogenetic analysis showed that the 57 HD-Zip I genes from the four grass species could be clearly delineated into 5 clades.3. By searching for intraspecies microsynteny between the genome segments of grasses, we found that 12 of 14 the chromosome regions hosting HD-Zip I genes in Oryza sativa fell into pairs, triples or quadruples and formed paralogous groups of segments, more than 85% HD-Zip I containing segments in Oryza sativa genomes have microsynteny, while only a few paralogous segments were identified in the genomes of Brachypodium distachyon, Sorghum bicolor and Zea mays.4. By comparing interspecies microsynteny between the genome segments, we determined that the great majority of HD-Zip I containing segments in Brachypodium distachyon, Sorghum bicolor, Oryza sativa and Zea mays show extensive conservation. These segments formed 17 groups of orthologous segments. Selection pressure analysis indicated that continuous purifying selection has played a key role in the maintenance of HD-Zip I genes in grasses, and the duplicated genes were subject to strong evolutionary constraints to retain the stability of their functions.By using the methods of comparative genomics, this study demonstrated that the evolution of Oryza sativa HD-Zip I gene family were coupling with proposed whole genome duplication events, HD-Zip I genome segments have extensive microsynteny between species. These results can serve as an important basis for resolving molecular evolution of the HD-Zip I gene family on the genome-wide level and identifying genes which have functions in stress response.