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BMC Biotechnol. 2016 May 31;16(1):47. doi: 10.1186/s12896-016-0277-6.

Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.

Author information

1
The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
2
Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
3
Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
4
Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
5
Florida Museum of Natural History, Gainesville, FL, 32611, USA.
6
Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
7
Department of Biology, Cologne Biocenter, University of Cologne, Cologne, 50674, Germany.
8
Department of Biology, University of British Columbia, Kelowna, BC, V1V 1V7, Canada.
9
Department of Biological Sciences, University of Georgia, Athens, GA, 30602, USA.
10
Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK.
11
Department of Biology, Duke University, Durham, NC, 27708, USA.
12
Department of Integrative Biology, University of California, University Herbarium, Berkeley, CA, 94720-2465, USA.
13
New York Botanical Garden, Bronx, New York, NY, 10458, USA.
14
Department of Botany, University of British Columbia, Vancouver, BC, Canada.
15
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
16
College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, People's Republic of China.
17
Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
18
BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
19
Department of Computer Science, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, University of Hong Kong, Pokfulam, Hong Kong.
20
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.
21
Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
22
Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
23
The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA. nealstewart@utk.edu.
24
Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA. nealstewart@utk.edu.

Abstract

BACKGROUND:

The ATP-binding cassette (ABC) transporter gene superfamily is ubiquitous among extant organisms and prominently represented in plants. ABC transporters act to transport compounds across cellular membranes and are involved in a diverse range of biological processes. Thus, the applicability to biotechnology is vast, including cancer resistance in humans, drug resistance among vertebrates, and herbicide and other xenobiotic resistance in plants. In addition, plants appear to harbor the highest diversity of ABC transporter genes compared with any other group of organisms. This study applied transcriptome analysis to survey the kingdom-wide ABC transporter diversity in plants and suggest biotechnology applications of this diversity.

RESULTS:

We utilized sequence similarity-based informatics techniques to infer the identity of ABC transporter gene candidates from 1295 phylogenetically-diverse plant transcriptomes. A total of 97,149 putative (approximately 25 % were full-length) ABC transporter gene members were identified; each RNA-Seq library (plant sample) had 88 ± 30 gene members. As expected, simpler organisms, such as algae, had fewer unique members than vascular land plants. Differences were also noted in the richness of certain ABC transporter subfamilies. Land plants had more unique ABCB, ABCC, and ABCG transporter gene members on average (p < 0.005), and green algae, red algae, and bryophytes had significantly more ABCF transporter gene members (p < 0.005). Ferns had significantly fewer ABCA transporter gene members than all other plant groups (p < 0.005).

CONCLUSIONS:

We present a transcriptomic overview of ABC transporter gene members across all major plant groups. An increase in the number of gene family members present in the ABCB, ABCC, and ABCD transporter subfamilies may indicate an expansion of the ABC transporter superfamily among green land plants, which include all crop species. The striking difference between the number of ABCA subfamily transporter gene members between ferns and other plant taxa is surprising and merits further investigation. Discussed is the potential exploitation of ABC transporters in plant biotechnology, with an emphasis on crops.

KEYWORDS:

ABC transporter; Computational biology; Taxonomic diversity; Transcriptomics

PMID:
27245738
PMCID:
PMC4886425
DOI:
10.1186/s12896-016-0277-6
[Indexed for MEDLINE]
Free PMC Article

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