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Genome-wide survey and expression analysis of the amino acid transporter gene family in poplar

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Abstract

Members of the amino acid transporters (AATs) gene family transported amino acid across cellular membranes and participated in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the AAT gene family in Populus has been reported. An investigation of the Populus genome revealed 100 putative AAT genes. These genes were classified into 11 subfamilies based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 100 genes were distributed on 19 chromosomes with 18-pair segmental duplication and 19-gene tandem duplication events, indicating that segmental and tandem duplications contribute almost equally to the expansion of the PtAAT gene family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the AAT family basically underwent purifying selection. The expression levels of the 17 amino acid/auxin permease (AAAP) subfamily genes under abiotic stresses and in different tissues were investigated by quantitative real-time PCR (qRT-PCR) to explore their stress-related and tissue-specific expression patterns. The qRT-PCR results to explore the precise role of individual PtAAT gene. This study presents a thorough overview of the Populus AAT gene family and provides a new perspective on the evolution of this gene family. The results indicate that AAT family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of AAT genes.

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Acknowledgments

This work was supported by fundings from National Natural Science Foundation (31370561), Specialized Research Fund for the Doctoral Program of Higher Education (20133418110005) Anhui Provincial Natural Science Foundation (1308085MC36), and Anhui Agricultural University Disciplinary Construction Foundation (XKTS2013001).

Conflict of interest

The authors declare that they have no competing interests.

Data archiving statement

All identified amino acid transporter gene sequences were deposited into the Phytozome database (http://www.phytozome.net/). The accession numbers are listed in Table 1.

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Authors and Affiliations

  1. Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, China

    Min Wu, Shengnan Wu, Zhu Chen, Hanwei Yan & Yan Xiang

  2. Key Laboratory of Biomass Improvement and Conversion of Anhui Province, He Fei, China

    Min Wu, Shengnan Wu, Qing Dong, Hanwei Yan & Yan Xiang

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  1. Min Wu
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  2. Shengnan Wu
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  3. Zhu Chen
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  4. Qing Dong
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Correspondence to Yan Xiang.

Additional information

Communicated by A. Brunner

This article is part of the Topical Collection on Gene Expression

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Table S1

Major MEME motif sequences in Populus AAT proteins. (DOC 31 kb)

Table S2

Number of AAT genes in the Populus, Arabidopsis, rice and maize genomes. (DOC 373 kb)

Table S3

The general information and sequence characterization of AAT genes in Arabidopsis, rice and maize. (DOCX 13 kb)

Table S4

Paralogous extensins identified in four modern plants. (DOCX 15 kb)

Table S5

Orthologous extensins identified in four modern plants. (DOCX 13 kb)

Table S6

Primers used in qRT-PCR analysis of PtAAP genes. (DOC 55 kb)

Figure S1

Prediction of the transmembrane regions of 100 PtAATs. The transmembrane regions of 100 PtAATs were predicted by using the TMHMM Server v2.0 (http://www.cbs.dtu.dk/services/TMHMM/). (TIFF 11622 kb)

Figure S2

Sliding window plots of representative duplicated AAT genes in Populus. As shown in the key, dark gray blocks and light gray blocks indicate the positions of the Aa-trans and AA-permease domain, respectively. The window size is 150 bp, and the step size is 9 bp. (TIFF 1465 kb)

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Wu, M., Wu, S., Chen, Z. et al. Genome-wide survey and expression analysis of the amino acid transporter gene family in poplar. Tree Genetics & Genomes 11, 83 (2015). https://doi.org/10.1007/s11295-015-0908-4

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