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. 2017 Dec 19:8:2150.
doi: 10.3389/fpls.2017.02150. eCollection 2017.

Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development

Piaojuan Chen  1 , Yi Li  1 , Lihua Zhao  1 , Zhimin Hou  1 , Maokai Yan  1 , Bingyan Hu  1 , Yanhui Liu  1 , Syed Muhammad Azam  1 , Ziyan Zhang  1 , Zia Ur Rahman  1 , Liping Liu  1 , Yuan Qin  1
Affiliations

Genome-Wide Identification and Expression Profiling of ATP-Binding Cassette (ABC) Transporter Gene Family in Pineapple (Ananas comosus (L.) Merr.) Reveal the Role of AcABCG38 in Pollen Development

Piaojuan Chen et al. Front Plant Sci. .

Abstract

Pineapple (Ananas comosus L.) cultivation commonly relies on asexual reproduction which is easily impeded by many factors in agriculture production. Sexual reproduction might be a novel approach to improve the pineapple planting. However, genes controlling pineapple sexual reproduction are still remain elusive. In different organisms a conserved superfamily proteins known as ATP binding cassette (ABC) participate in various biological processes. Whereas, till today the ABC gene family has not been identified in pineapple. Here 100 ABC genes were identified in the pineapple genome and grouped into eight subfamilies (5 ABCAs, 20 ABCBs, 16 ABCCs, 2 ABCDs, one ABCEs, 5 ABCFs, 42 ABCGs and 9 ABCIs). Gene expression profiling revealed the dynamic expression pattern of ABC gene family in various tissues and different developmental stages. AcABCA5, AcABCB6, AcABCC4, AcABCC7, AcABCC9, AcABCG26, AcABCG38 and AcABCG42 exhibited preferential expression in ovule and stamen. Over-expression of AcABCG38 in the Arabidopsis double mutant abcg1-2abcg16-2 partially restored its pollen abortion defects, indicating that AcABCG38 plays important roles in pollen development. Our study on ABC gene family in pineapple provides useful information for developing sexual pineapple plantation which could be utilized to improve pineapple agricultural production.

Keywords: ABC genes; expression profile; pineapple; pollen abortion; sexual reproduction.

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Figures

FIGURE 1
FIGURE 1
Phylogenetic relationship of ABC gene among Pineapple (Ac) and Arabidopsis (At). All the AcABC protein sequences were aligned by using MAFFT and phylogenetic tree was constructed using FastTree. Different colors represented individual subfamily. Every subfamily had another classified names: ATH (ABC1 homologous), AOH (ABC1 homologous), MDR (multidrug resistance protein), TAP (transporter associated with antigen processing), ATM (ABC transporter of the mitochondria), WBC (white-brown complex homolog), PDR (pleiotropic drug resistance). AcABCG38, AtABCG1 and AtABCG16 were indicated by asterisk.
FIGURE 2
FIGURE 2
Intron–exon structure of AcABC genes in pineapple genome. Yellow bars indicates exon (CDS), Blue bars indicated UTR while plain lines showing introns. black lines represented introns. On the left panel is the phylogenetic trees of ABC transporter proteins in pineapple which was constructed by Maximum likelihood method. The numbers on the right indicate the genomic length of the corresponding genes. bp, base pair.
FIGURE 3
FIGURE 3
The motif analysis of AcABCG proteins in pineapple. Motifs with specific colors can be find on respective AcABCG genes. The combined phylogenetic trees of AcABCG subfamily on the left panel. The motifs of corresponding proteins are shown on the right panel with specific colors on behalf of different motifs using the MEME motif search tool (http://meme-suite.org/tools/meme). The order of the motifs corresponds to their position within individual protein sequences.
FIGURE 4
FIGURE 4
Tissue-specific expression profiles of AcABC genes in pineapple. Heat-map of tissue-specific expression profiles of AcABC genes in pineapple. RNA-seq expression level can be understood using the given scale and roman numbers on right-side shows hierarchical clusters based on gene expression. The combined phylogenetic trees of pineapple ABC family on the left panel. Red color indicates high levels of transcript abundance, and green indicates low transcript abundance. The color scale is shown at the bottom. Samples are mentioned at the top of each lane: ovule S1–S7, sepal S1–S4, stamen S1–S5, petal S1–S3, root, leaf, flower, fruit S1–S7. “S” is abbreviation of word “stage.”
FIGURE 5
FIGURE 5
Validation of AcABC genes RNA-seq by qRT-PCR analysis of four genes’ expression at five different tissues. Line graphs are constructed from relative gene expression (Left side Y-Axis) in different tissues (qRT-PCR) data and FPKM values (RNA-seq) data (Right side Y-Axis) for these tissues.
FIGURE 6
FIGURE 6
Over-expressing of AcABCG38 can partly recover the fertility and pollen development defects of double mutant abcg1-2abcg16-2. (A) Alexander red staining of WT anther. (B) Alexander red staining of p35S:AcABCG38 anther. (C) Alexander red staining of double mutant of abcg1-2abcg16-2 anther. (D) Alexander red staining of the abcg1-2abcg16-2 p35S:AcABCG38 line 8# anther. (E) Main branch of the plants with genotype as indicated (left: col-0, mid: abcg1-2abcg16-2, right: abcg1-2abcg16-2 p35S:AcABCG3 line 2#). (F) Siliques of plants with genotype as indicated (left: col-0, mid: abcg1-2abcg16-2, right: transgenic plant 8# in abcg1-2abcg6-2 background). (G) Mature pollens of col-0. (H) Mature pollens of abcg1-2abcg16-2 plant. (I) Mature pollens of the abcg1-2abcg16-2 p35S:AcABCG38 8#. (J) Seed set phenotype of the 25 siliques from bottom to top in main branch of the abcg1-2abcg16-2 plants. Red dots represent the short siliques with reduced seed set; green dots represent the normal siliques with full seed set. (K) Seed set phenotype of the 25 siliques from bottom to top in main branch of the individual abcg1-2abcg16-2 p35S:AcABCG38 lines.
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