Evolutionary significance of amino acid permease transporters in 17 plants from Chlorophyta to Angiospermae

Abstract

Background: Nitrogen is an indispensable nutrient for plant growth. It is used and transported in the form of amino acids in living organisms. Transporting amino acids to various parts of plants requires relevant transport proteins, such as amino acid permeases (AAPs), which were our focus in this study.

Results: We found that 5 AAP genes were present in Chlorophyte species and more AAP genes were predicted in Bryophyta and Lycophytes. Two main groups were defined and group I comprised 5 clades. Our phylogenetic analysis indicated that the origin of clades 2, 3, and 4 is Gymnospermae and that these clades are closely related. The members of clade 1 included Chlorophyta to Gymnospermae. Group II, as a new branch consisting of non-seed plants, is first proposed in our research. Our results also indicated that the AAP family was already present in Chlorophyta and then expanded accompanying the development of vasculature. Concurrently, the AAP family experienced multiple duplication events that promoted the generation of new functions and differentiation of sub-functions.

Conclusions: Our findings suggest that the AAP gene originated in Chlorophyta, and some non-seed AAP genes clustered in one group. A second group, which contained plants of all evolutionary stages, indicated the evolution of AAPs. These new findings can be used to guide future research.

Keywords: AAP family; Duplication events; Evolution; Phylogenetic analysis; Sequencing plants.

Fig. 1

Phylogenetic tree of AAP proteins. The unroot tree contains 154 protiens from Chlorophyta to Angiosperms and 7 different colors indicate AAPs from different stages. The protein distribution can easily divide into 2 main parts which were showed by greenyellow and violet colors’ dash lines and the group II might be divided into 2 subgroups indicated by gray and lightgray lines, respectively

Fig. 2

The division of whole AAP proteins. The tree shows that the 2 main groups are divided; group I is represented by violet and group II by green. It can be inferred from the phylogenetic tree that the two groups are genetically. Eleven plants in 5 main different evolutionary stages were used to build the phylogenetic tree. The main domain, Aa_trans and transmembrane structure. The blue bar in each protein is the location and numbers of Aa_trans and the red boxes are transmembrane structures. There are no distinct differences between group members

Fig. 3

Phylogenetic tree of group I AAP members. Group I members are divided into 5 clades are indicated in different colors. The circles represent the bootstrap value. This value is an important for classifying the clades

Fig. 4

Hypothetical evolutionary models for AAPs from plants. The circles represent gene duplication events inferred from the phylogenetic analysis. The blue color indicates the number of tandem duplication and the green one means segmental duplication. The semicircle is divided into 6 parts, and each part is filled with color to represent a duplication event. Representative species of each major taxonomic group are shown at the branch tip. Branches are colored depending on their taxonomy classification

Fig. 5

The annotation of gene ontology in whole AAPs. Colors indicate the type of gene annotation. The x-axis indicates the logarithm of protein numbers and the y-axis, the number of AAP members in each GO term

Fig. 6

The presence of proteins in different groups and clades. The check mark within boxes indicate the group/clade have AAP members. This visually indicated the distribution of the group of proteins in each stage