Rees DC, Johnson E, Lewinson O. ABC transporters: the power to change. Nat Rev Mol Cell Biol. 2009;10(3):218–27.
Article
CAS
Google Scholar
Jones PM, George AM. The ABC transporter structure and mechanism: perspectives on recent research. Cell Mol Life Sci. 2004;61(6):682–99.
Article
CAS
Google Scholar
Kang J, Park J, Choi H, Burla B, Kretzschmar T, Lee Y, Martinoia E. Plant ABC transporters. Arabidopsis Book. 2011;9:e0153.
Article
Google Scholar
Schneider E, Hunke S. ATP-binding-cassette (ABC) transport systems: functional and structural aspects of the ATP-hydrolyzing subunits/domains. FEMS Microbiol Rev. 1998;22(1):1–20.
Article
CAS
Google Scholar
Hollenstein K, Frei DC, Locher KP. Structure of an ABC transporter in complex with its binding protein. Nature. 2007;446(7132):213–6.
Article
CAS
Google Scholar
Mishra AK, Choi J, Rabbee MF, Baek K-H. In silico genome-wide analysis of the ATP-binding cassette transporter gene family in soybean (Glycine max L.) and their expression profiling. Biomed Res Int. 2019;2019:14.
Google Scholar
Yan C, Duan W, Lyu S, Li Y, Hou X. Genome-wide identification, evolution, and expression analysis of the ATP-binding cassette transporter gene family in Brassica rapa. Front Plant Sci. 2017;8:349.
Gadsby DC, Vergani P, Csanády L. The ABC protein turned chloride channel whose failure causes cystic fibrosis. Nature. 2006;440(7083):477–83.
Article
CAS
Google Scholar
Pighin JA, Zheng H, Balakshin LJ, Goodman IP, Western TL, Jetter R, Kunst L, Samuels AL. Plant cuticular lipid export requires an ABC transporter. Science. 2004;306(5696):702–4.
Article
CAS
Google Scholar
Sipos G, Kuchler K. Fungal ATP-binding cassette (ABC) transporters in drug resistance & detoxification. Curr Drug Targets. 2006;7(4):471–81.
Article
CAS
Google Scholar
Sidler M, Hassa P, Hasan S, Ringli C, Dudler R. Involvement of an ABC transporter in a developmental pathway regulating hypocotyl cell elongation in the light. Plant Cell. 1998;10(10):1623–36.
Article
CAS
Google Scholar
Noh B, Murphy AS, Spalding EP. Multidrug resistance-like genes of Arabidopsis required for auxin transport and auxin-mediated development. Plant Cell. 2001;13(11):2441–54.
CAS
Google Scholar
Nagy R, Grob H, Weder B, Green P, Klein M, Frelet-Barrand A, Schjoerring JK, Brearley C, Martinoia E. The Arabidopsis ATP-binding cassette protein AtMRP5/AtABCC5 is a high affinity inositol hexakisphosphate transporter involved in guard cell signaling and phytate storage. J Biol Chem. 2009;284(48):33614–22.
Article
CAS
Google Scholar
Badone FC, Cassani E, Landoni M, Doria E, Panzeri D, Lago C, Mesiti F, Nielsen E, Pilu R. The low phytic acid1-241 (lpa1-241) maize mutation alters the accumulation of anthocyanin pigment in the kernel. Planta. 2010;231(5):1189–99.
Article
Google Scholar
Tagashira Y, Shimizu T, Miyamoto M, Nishida S, Yoshida KT. Overexpression of a gene involved in phytic acid biosynthesis substantially increases phytic acid and total phosphorus in rice seeds. Plants. 2015;4(2):196–208.
Article
CAS
Google Scholar
Park J, Song W-Y, Ko D, Eom Y, Hansen TH, Schiller M, Lee TG, Martinoia E, Lee Y. The phytochelatin transporters ATABCC1 and ATABCC2 mediate tolerance to cadmium and mercury. Plant J. 2012;69(2):278–88.
Article
CAS
Google Scholar
Kato T, Tabata S, Sato S. Analyses of expression and phenotypes of knockout lines for Arabidopsis ABCF subfamily members. Plant Biotech. 2009;26(4):409–14.
Article
CAS
Google Scholar
Bessire M, Borel S, Fabre G, Carraca L, Efremova N, Yephremov A, Cao Y, Jetter R, Jacquat AC, Metraux JP, et al. A member of the pleiotropic drug resistance family of ATP binding cassette transporters is required for the formation of a functional cuticle in Arabidopsis. Plant Cell. 2011;23(5):1958–70.
Article
CAS
Google Scholar
Chen G, Komatsuda T, Ma JF, Nawrath C, Pourkheirandish M, Tagiri A, Hu Y-G, Sameri M, Li X, Zhao X, et al. An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc Natl Acad Sci U S A. 2011;108(30):12354–9.
Article
CAS
Google Scholar
Fu S, Lu Y, Zhang X, Yang G, Chao D, Wang Z, Shi M, Chen J, Chao D-Y, Li R, et al. The ABC transporter ABCG36 is required for cadmium tolerance in rice. J Exp Bot. 2019;70(20):5909–18.
Article
CAS
Google Scholar
Kim D-Y, Bovet L, Maeshima M, Martinoia E, Lee Y. The ABC transporter ATPDR8 is a cadmium extrusion pump conferring heavy metal resistance. Plant J. 2007;50(2):207–18.
Article
CAS
Google Scholar
Bovet L, Eggmann T, Meylan-bettex M, Polier J, Kammer P, Marin E, Feller U, Martinoia E. Transcript levels of ATMRPS after cadmium treatment: induction of ATMRP3. Plant Cell Environ. 2003;26(3):371–81.
Article
CAS
Google Scholar
Emamverdian A, Ding Y, Mokhberdoran F, Xie Y. Heavy metal stress and some mechanisms of plant defense response. Sci World J. 2015;2015:756120.
Article
Google Scholar
Salla V, Hardaway CJ, Sneddon J. Preliminary investigation of Spartina alterniflora for phytoextraction of selected heavy metals in soils from Southwest Louisiana. Microchem J. 2011;97(2):207–12.
Article
CAS
Google Scholar
Yamaji N, Xia J, Mitani-Ueno N, Yokosho K, Feng Ma J. Preferential delivery of zinc to developing tissues in rice is mediated by P-type heavy metal ATPase OsHMA2. Plant Physiol. 2013;162(2):927–39.
Article
CAS
Google Scholar
Huang X-Y, Deng F, Yamaji N, Pinson SRM, Fujii-Kashino M, Danku J, Douglas A, Guerinot ML, Salt DE, Ma JF. A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain. Nat Commun. 2016;7(1):12138.
Article
CAS
Google Scholar
Mikkelsen MD, Pedas P, Schiller M, Vincze E, Mills RF, Borg S, Møller A, Schjoerring JK, Williams LE, Baekgaard L, et al. Barley HvHMA1 is a heavy metal pump involved in mobilizing organellar Zn and Cu and plays a role in metal loading into grains. PLoS One. 2012;7(11):–e49027.
Tan J, Wang J, Chai T, Zhang Y, Feng S, Li Y, Zhao H, Liu H, Chai X. Functional analyses of TaHMA2, a P1B-type ATPase in wheat. Plant Biotechnol J. 2013;11(4):420–31.
Article
CAS
Google Scholar
Morel M, Crouzet J, Gravot A, Auroy P, Leonhardt N, Vavasseur A, Richaud P. AtHMA3, a P1B-ATPase allowing cd/Zn/co/Pb vacuolar storage in Arabidopsis. Plant Physiol. 2009;149(2):894–904.
Article
CAS
Google Scholar
Wang Z, Hobson N, Galindo L, Zhu S, Shi D, McDill J, Yang L, Hawkins S, Neutelings G, Datla R, et al. The genome of flax (linum usitatissimum) assembled de novo from short shotgun sequence reads. Plant J. 2012;72(3):461–73.
Article
Google Scholar
You FM, Xiao J, Li P, Yao Z, Jia G, He L, Zhu T, Luo M-C, Wang X, Deyholos MK, et al. Chromosome-scale pseudomolecules refined by optical, physical and genetic maps in flax. Plant J. 2018;95(2):371–84.
Article
CAS
Google Scholar
Jasinski M, Ducos E, Martinoia E, Boutry M. The ATP-binding cassette transporters: structure, function, and gene family comparison between rice and Arabidopsis. Plant Physiol. 2003;131(3):1169–77.
Article
CAS
Google Scholar
Pang K, Li Y, Liu M, Meng Z, Yu Y. Inventory and general analysis of the ATP-binding cassette (ABC) gene superfamily in maize (Zea mays L.). Gene. 2013;526(2):411–28.
Article
CAS
Google Scholar
Cao Y, Zhao X, Liu Y, Wang Y, Wu W, Jiang Y, Liao C, Xu X, Gao S, Shen Y, et al. Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize. PeerJ. 2019;7:e7877.
Article
Google Scholar
Li N, Xiao H, Sun J, Wang S, Wang J, Chang P, Zhou X, Lei B, Lu K, Luo F, et al. Genome-wide analysis and expression profiling of the HMA gene family in Brassica napus under cd stress. Plant Soil. 2018;426(1):365–81.
Article
CAS
Google Scholar
Bhati KK, Sharma S, Aggarwal S, Kaur M, Shukla V, Kaur J, Mantri S, Pandey AK. Genome-wide identification and expression characterization of ABCC-MRP transporters in hexaploid wheat. Front Plant Sci. 2015;6:488.
Article
Google Scholar
Çakır B, Kılıçkaya O. Whole-genome survey of the putative ATP-binding cassette transporter family genes in Vitis Vinifera. PLoS One. 2013;8(11):e78860.
Article
Google Scholar
Lane TS, Rempe CS, Davitt J, Staton ME, Peng Y, Soltis DE, Melkonian M, Deyholos M, Leebens-Mack JH, Chase M, et al. Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnol. 2016;16(1):47.
Article
Google Scholar
Shivaraj SM, Deshmukh RK, Rai R, Bélanger R, Agrawal PK, Dash PK. Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax (Linum usitatissimum). Sci Rep. 2017;7(1):46137.
Article
CAS
Google Scholar
Corbin C, Drouet S, Markulin L, Auguin D, Lainé É, Davin LB, Cort JR, Lewis NG, Hano C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. Plant Mol Biol. 2018;97(1):73–101.
Article
CAS
Google Scholar
Eom SH, Hyun TK. Genome-wide identification and transcriptional expression analysis of chalcone synthase in flax (Linum usitatissimum L.). Gene Rep. 2016;5:51–6.
Article
Google Scholar
Ali E, Saand MA, Khan AR, Shah JM, Feng S, Ming C, Sun P. Genome-wide identification and expression analysis of detoxification efflux carriers (DTX) genes family under abiotic stresses in flax. Physiol Plant. 2020. https://doi.org/10.1111/ppl.13105.
Barvkar VT, Pardeshi VC, Kale SM, Kadoo NY, Gupta VS. Phylogenomic analysis of UDP glycosyltransferase 1 multigene family in Linum usitatissimum identified genes with varied expression patterns. BMC Genomics. 2012;13:175.
Article
CAS
Google Scholar
Fan W, Liu C, Cao B, Qin M, Long D, Xiang Z, Zhao A. Genome-wide identification and characterization of four gene families putatively involved in cadmium uptake, translocation and sequestration in mulberry. Front Plant Sci. 2018;9:879.
Article
Google Scholar
Verret F, Gravot A, Auroy P, Leonhardt N, David P, Nussaume L, Vavasseur A, Richaud P. Overexpression of AtHMA4 enhances root-to-shoot translocation of zinc and cadmium and plant metal tolerance. FEBS Lett. 2004;576(3):306–12.
Article
CAS
Google Scholar
Takahashi R, Ishimaru Y, Shimo H, Ogo Y, Senoura T, Nishizawa NK, Nakanishi H. The OsHMA2 transporter is involved in root-to-shoot translocation of Zn and cd in rice. Plant Cell Environ. 2012;35(11):1948–57.
Article
CAS
Google Scholar
Kuromori T, Miyaji T, Yabuuchi H, Shimizu H, Sugimoto E, Kamiya A, Moriyama Y, Shinozaki K. ABC transporter AtABCG25 is involved in abscisic acid transport and responses. Proc Natl Acad Sci U S A. 2010;107(5):2361–6.
Article
CAS
Google Scholar
Song W-Y, Yamaki T, Yamaji N, Ko D, Jung K-H, Fujii-Kashino M, An G, Martinoia E, Lee Y, Ma JF. A rice ABC transporter, OsABCC1, reduces arsenic accumulation in the grain. Proc Natl Acad Sci U S A. 2014;111(44):15699–704.
Article
CAS
Google Scholar
Kim D-Y, Jin J-Y, Alejandro S, Martinoia E, Lee Y. Overexpression of AtABCG36 improves drought and salt stress resistance in Arabidopsis. Physiol Plant. 2010;139(2):170–80.
Article
CAS
Google Scholar
Takeda S, Iwasaki A, Tatematsu K, Okada K. The half-size abc transporter folded petals 2/ABCG13 is involved in petal elongation through narrow spaces in Arabidopsis thaliana floral buds. Plants. 2014;3(3):348–58.
Article
Google Scholar
Acuña-Galindo MA, Mason RE, Subramanian NK, Hays DB. Meta-analysis of wheat QTL regions associated with adaptation to drought and heat stress. Crop Sci. 2015;55(2):477–92.
Article
Google Scholar
Gu X, Zou Y, Su Z, Huang W, Zhou Z, Arendsee Z, Zeng Y. An update of diverge software for functional divergence analysis of protein family. Mol Biol Evol. 2013;30(7):1713–9.
Article
CAS
Google Scholar
Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, et al. Ancestral polyploidy in seed plants and angiosperms. Nature. 2011;473(7345):97–100.
Article
CAS
Google Scholar
Clark JW, Donoghue PCJ. Whole-genome duplication and plant macroevolution. Trends Plant Sci. 2018;23(10):933–45.
Article
CAS
Google Scholar
Segraves KA. The effects of genome duplications in a community context. New Phytol. 2017;215(1):57–69.
Article
CAS
Google Scholar
Moghe GD, Shiu SH. The causes and molecular consequences of polyploidy in flowering plants. Ann N Y Acad Sci. 2014;1320:16–34.
Article
CAS
Google Scholar
Cannon SB, Mitra A, Baumgarten A, Young ND, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004;4:10.
Article
Google Scholar
Khan N, Fatima F, Haider MS, Shazadee H, Liu Z, Zheng T, Fang J. Genome-wide identification and expression profiling of the polygalacturonase (PG) and pectin methylesterase (PME) genes in grapevine (Vitis vinifera L.). Int J Mol Sci. 2019;20(13):3180.
Article
CAS
Google Scholar
Shazadee H, Khan N, Wang J, Wang C, Zeng J, Huang Z, Wang X. Identification and expression profiling of protein phosphatases (PP2C) gene family in Gossypium hirsutum L. Int J Mol Sci. 2019;20(6):1395.
Article
CAS
Google Scholar
Die JV, Gil J, Millan T. Genome-wide identification of the auxin response factor gene family in Cicer arietinum. BMC Genomics. 2018;19(1):301.
Article
Google Scholar
Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE. The evolutionary fate of mule-mediated duplications of host gene fragments in rice. Genome Res. 2005;15(9):1292–7.
Article
CAS
Google Scholar
Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. 2000;290(5494):1151–5.
Article
CAS
Google Scholar
Li J, Zhang Z, Vang S, Yu J, Wong GK, Wang J. Correlation between ka/ks and ks is related to substitution model and evolutionary lineage. J Mol Evol. 2009;68(4):414–23.
Article
CAS
Google Scholar
Mercereau-Puijalon O, Barale JC, Bischoff E. Three multigene families in plasmodium parasites: facts and questions. Int J Parasitol. 2002;32(11):1323–44.
Article
CAS
Google Scholar
Verrier PJ, Bird D, Burla B, Dassa E, Forestier C, Geisler M, Klein M, Kolukisaoglu Ü, Lee Y, Martinoia E, et al. Plant ABC proteins – a unified nomenclature and updated inventory. Trends Plant Sci. 2008;13(4):151–9.
Article
CAS
Google Scholar
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(Web Server issue):W29–37.
Article
CAS
Google Scholar
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC, Qureshi M, Richardson LJ, Salazar GA, Smart A, et al. The Pfam protein families database in 2019. Nucleic Acids Res. 2018;47(D1):D427–32.
Article
Google Scholar
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(Database issue):D1178–86.
Article
CAS
Google Scholar
Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017;45(D1):D200–3.
Article
CAS
Google Scholar
Letunic I, Bork P. 20 years of the smart protein domain annotation resource. Nucleic Acids Res. 2017;46(D1):D493–6.
Article
Google Scholar
Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–4.
Article
CAS
Google Scholar
Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee T-H, Jin H, Marler B, Guo H, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 2012;40(7):e49.
Article
CAS
Google Scholar
Koch MA, Haubold B, Mitchell-Olds T. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Bio Evol. 2000;17(10):1483–98.
Article
CAS
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME suite: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server issue):W202-208.
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, Xia R. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–202.
Article
CAS
Google Scholar
Horton P, Park K-J, Obayashi T, Fujita N, Harada H, Adams-Collier CJ, Nakai K. WoLF PSORT: protein localization predictor. Nucleic Acids Res. 2007;35(Web Server issue):W585–7.
Article
Google Scholar
Savojardo C, Martelli Pier L, Fariselli P, Profiti G, Casadio R. BUSCA: an integrative web server to predict subcellular localization of proteins. Nucleic Acids Res. 2018;46(W1):W459–66.
Article
CAS
Google Scholar
Yu Y, Ouyang Y, Yao W. shinyCircos: an R/shiny application for interactive creation of circos plot. Bioinformatics. 2017;34(7):1229–31.
Article
Google Scholar
Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2018;47(D1):D607–13.
Article
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504.
Article
CAS
Google Scholar
Venglat P, Xiang D, Qiu S, Stone SL, Tibiche C, Cram D, Alting-Mees M, Nowak J, Cloutier S, Deyholos M, et al. Gene expression analysis of flax seed development. BMC Plant Biol. 2011;11(1):74.
Article
CAS
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics. 2014;30(15):2114–20.
Article
CAS
Google Scholar
Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-Seq quantification. Nat Biotechnol. 2016;34(5):525–7.
Article
CAS
Google Scholar
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–40.
Article
CAS
Google Scholar
Metsalu T, Vilo J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 2015;43(W1):W566–70.
Article
CAS
Google Scholar