title: Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.
abstract: 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.
  
  
  
  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).
  
  
  
  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.
authors.affiliation: The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.|Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Lane
authors.affiliation: The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.|Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Caroline S
authors.initials: CS
authors.lastname: Rempe
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Jack
authors.initials: J
authors.lastname: Davitt
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Margaret E
authors.initials: ME
authors.lastname: Staton
authors.affiliation: Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Yanhui
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Biology, University of Florida, Gainesville, FL, 32611, USA.|Florida Museum of Natural History, Gainesville, FL, 32611, USA.|Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
authors.forename: Douglas Edward
authors.initials: DE
authors.lastname: Soltis
authors.affiliation: Department of Biology, Cologne Biocenter, University of Cologne, Cologne, 50674, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Melkonian
authors.affiliation: Department of Biology, University of British Columbia, Kelowna, BC, V1V 1V7, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Deyholos
authors.affiliation: Department of Biological Sciences, University of Georgia, Athens, GA, 30602, USA.
authors.forename: James H
authors.initials: JH
authors.lastname: Leebens-Mack
authors.affiliation: Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK.|Department of Biology, Duke University, Durham, NC, 27708, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Chase
authors.affiliation: Department of Integrative Biology, University of California, University Herbarium, Berkeley, CA, 94720-2465, USA.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Rothfels
authors.affiliation: New York Botanical Garden, Bronx, New York, NY, 10458, USA.
authors.forename: Dennis
authors.initials: D
authors.lastname: Stevenson
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Sean W
authors.initials: SW
authors.lastname: Graham
authors.affiliation: 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.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.affiliation: College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, People's Republic of China.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: Bond Life Sciences Center, Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
authors.forename: J Chris
authors.initials: JC
authors.lastname: Pires
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
authors.forename: Patrick P
authors.initials: PP
authors.lastname: Edger
authors.affiliation: Department of Computer Science, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, University of Hong Kong, Pokfulam, Hong Kong.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.|Department of Computer Science, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory, University of Hong Kong, Pokfulam, Hong Kong.|School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China.
authors.forename: Yinlong
authors.initials: Y
authors.lastname: Xie
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Carpenter
authors.affiliation: BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.|Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.|Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.affiliation: The Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA. nealstewart@utk.edu.|Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA. nealstewart@utk.edu.
authors.forename: C Neal
authors.initials: CN
authors.lastname: Stewart
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000235:genetics*; D001709:Biotechnology / Q000639:trends; D002874:Chromosome Mapping / Q000379:methods; D057225:Data Mining / Q000379:methods; D030562:Databases, Protein; D017343:Genes, Plant / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D013045:Species Specificity
chemical_list: D018528:ATP-Binding Cassette Transporters; D010940:Plant Proteins
keywords: ABC transporter; Computational biology; Taxonomic diversity; Transcriptomics