Abstract: Sugar transporter proteins are located in the cell membrane and are a group of important transmembrane proteins. Sugar transporter proteins transport carbohydrate from extracellular to intracellular for the use of cells. Sugar transporter proteins, as sugar sensors, play an important role in eukaryotic microalgae, breast-feeding animals and higher plants. In this study, comparative genomics analyses were applied to study sugar transporter proteins and to explore their distribution, classification, phylogeny, evolution and structure in eukaryotic microalgae. Twenty-eight eukaryotic microalgae genomes were examined for putative genes of sugar transporter proteins and 70 putative sugar transporter protein sequences were found, which were 9 types of HUP1， 39 types of HUP2 and 22 types of HUP3. Sugar transporter genes of eukaryotic microalgae were origin of bacterium. In this study, a general framework of the sequence-structure-function connections of the sugar transporter genes was revealed.

Key words: eukaryotic microalgae, sugar transporter proteins, comparative genomics