BACKGROUND: The ATP-binding cassette (ABC) transporter superfamily is comprised predominantly of proteins which directly utilize energy from ATP to move molecules across the plasma membrane. Although they have been the subject of frequent investigation across many taxa, arthropod ABCs have been less well studied. While the manual annotation of ABC transporters has been performed in many arthropods, there has so far been no systematic comparison of the superfamily within this order using the increasing number of sequenced genomes. Furthermore, functional work on these genes is limited. RESULTS: Here, we developed a standardized pipeline to annotate ABCs from predicted proteomes and used it to perform comparative genomics on ABC families across arthropod lineages. Using Kruskal-Wallis tests and the Computational Analysis of gene Family Evolution (CAFE), we were able to observe significant expansions of the ABC-B full transporters (P-glycoproteins) in Lepidoptera and the ABC-H transporters in Hemiptera. RNA-sequencing of epithelia tissues in the Lepidoptera Helicoverpa armigera showed that the 7 P-glycoprotein paralogues differ substantially in their tissue distribution, suggesting a spatial division of labor. It also seems that functional redundancy is a feature of these transporters as RNAi knockdown showed that most transporters are dispensable with the exception of the highly conserved gene Snu, which is probably due to its role in cuticular formation. CONCLUSIONS: We have performed an annotation of the ABC superfamily across > 150 arthropod species for which good quality protein annotations exist. Our findings highlight specific expansions of ABC transporter families which suggest evolutionary adaptation. Future work will be able to use this analysis as a resource to provide a better understanding of the ABC superfamily in arthropods.

CropScience Division Bayer AG R and D Pest Control D 40789 Monheim Germany

Department of Chemistry and Biochemistry Mendel University in Brno Zemedelska 1 613 00 Brno Czechia

Institute of Molecular Biology and Biotechnology Foundation for Research and Technology Hellas 100 N Plastira Street 700 13 Heraklion Crete Greece

Laboratory of Pesticide Science Department of Crop Science Agricultural University of Athens Athens Greece

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Theodoulou FL, Kerr ID. ABC transporter research: Going strong 40 years on. Biochem Soc Trans. 2015;43:1033–40. doi: 10.1042/BST20150139. PubMed DOI PMC

Dassa E. Natural history of ABC systems: Not only transporters. Essays Biochem. 2011;50:19–42. doi: 10.1042/BSE0500019. PubMed DOI

Higgins CF. ABC transporters: from microorganisms to man. Annu Rev Cell Biol. 1992;8:67–113. doi: 10.1146/annurev.cb.08.110192.000435. PubMed DOI

Saier MH, Reddy VS, Moreno-Hagelsieb G, Hendargo KJ, Zhang Y, Iddamsetty V, et al. The transporter classification database (TCDB): 2021 update. Nucleic Acids Res. 2021;49:D461–7. doi: 10.1093/nar/gkaa1004. PubMed DOI PMC

Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, et al. Gene content evolution in the arthropods. Genome Biol. 2020;21:15. doi: 10.1186/s13059-019-1925-7. PubMed DOI PMC

Dermauw W, Van Leeuwen T. The ABC gene family in arthropods: comparative genomics and role in insecticide transport and resistance. Insect Biochem Mol Biol. 2014;45:89–110. doi: 10.1016/j.ibmb.2013.11.001. PubMed DOI

Merzendorfer H. ABC Transporters and Their Role in Protecting Insects from Pesticides and Their Metabolites. Elsevier; 2014. 10.1016/B978-0-12-417010-0.00001-X.

Kalsi M, Palli SR. Cap n collar transcription factor regulates multiple genes coding for proteins involved in insecticide detoxification in the red flour beetle, Tribolium castaneum. Insect Biochem Mol Biol. 2017 doi: 10.1016/j.ibmb.2017.09.009. PubMed DOI

Adang MJ, Crickmore N, Jurat-Fuentes JL. Diversity of Bacillus thuringiensis Crystal Toxins and Mechanism of Action. 2014:39–87. 10.1016/B978-0-12-800197-4.00002-6.

Hodges LM, Markova SM, Chinn LW, Gow JM, Kroetz DL, Klein TE, et al. Very important pharmacogene summary: ABCB1 (MDR1, P-glycoprotein) Pharmacogenet Genomics. 2011;21:152–61. doi: 10.1097/FPC.0b013e3283385a1c. PubMed DOI PMC

Sreeramulu K, Liu R, Sharom FJ. Interaction of insecticides with mammalian P-glycoprotein and their effect on its transport function. Biochim Biophys Acta - Biomembr. 2007:1750-7. PubMed

Lanning CL, Fine RL, Corcoran JJ, Ayad HM, Rose RL, Abou-Donia MB. Tobacco budworm P-glycoprotein: biochemical characterization and its involvement in pesticide resistance. Biochim Biophys Acta - Gen Subj. 1996;1291:155–62. doi: 10.1016/0304-4165(96)00060-8. PubMed DOI

Luo L, Sun Y-J, Wu Y-J. Abamectin resistance in Drosophila is related to increased expression of P-glycoprotein via the dEGFR and dAkt pathways. Insect Biochem Mol Biol. 2013;43:627–34. doi: 10.1016/j.ibmb.2013.04.006. PubMed DOI

Figueira-Mansur J, Ferreira-Pereira A, Mansur JF, Franco TA, Alvarenga ESL, Sorgine MHF, et al. Silencing of P-glycoprotein increases mortality in temephos-treated Aedes aegypti larvae. Insect Mol Biol. 2013;22:648–58. doi: 10.1111/imb.12052. PubMed DOI

Denecke S, Fusetto R, Batterham P. Describing the role of Drosophila melanogaster ABC transporters in insecticide biology using CRISPR-Cas9 knockouts. Insect Biochem Mol Biol. 2017;91:1–9. doi: 10.1016/j.ibmb.2017.09.017. PubMed DOI

Sturm A, Cunningham P, Dean M. The ABC transporter gene family of Daphnia pulex. BMC Genomics. 2009:1-18. PubMed PMC

Tian L, Song T, He R, Zeng Y, Xie W, Wu Q, et al. Genome-wide analysis of ATP-binding cassette (ABC) transporters in the sweetpotato whitefly, Bemisia tabaci. BMC Genomics. 2017;18:330. doi: 10.1186/s12864-017-3706-6. PubMed DOI PMC

Liu X-Q, Jiang H-B, Xiong Y, Peng P, Li H-F, Yuan G-R, et al. Genome-wide identification of ATP-binding cassette transporters and expression profiles in the Asian citrus psyllid, Diaphorina citri, exposed to imidacloprid. Comp Biochem Physiol Part D Genomics Proteomics. 2019;30:305–11. doi: 10.1016/J.CBD.2019.04.003. PubMed DOI

Dermauw W, Wybouw N, Rombauts S, Menten B, Vontas J, Grbic M, et al. A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae. Proc Natl Acad Sci U S A. 2013;110:E113-22. doi: 10.1073/pnas.1213214110. PubMed DOI PMC

Zuber R, Norum M, Wang Y, Oehl K, Gehring N, Accardi D, et al. The ABC transporter Snu and the extracellular protein Snsl cooperate in the formation of the lipid-based inward and outward barrier in the skin of Drosophila. Eur J Cell Biol. 2017 doi: 10.1016/J.EJCB.2017.12.003. PubMed DOI

Guo Z, Kang S, Zhu X, Xia J, Wu Q, Wang S, et al. The novel ABC transporter ABCH1 is a potential target for RNAi-based insect pest control and resistance management. Sci Rep. 2015;5:13728. doi: 10.1038/srep13728. PubMed DOI PMC

Yu Z, Wang Y, Zhao X, Liu X, Ma E, Moussian B, et al. The ABC transporter ABCH-9 C is needed for cuticle barrier construction in Locusta migratoria. Insect Biochem Mol Biol. 2017;87:90–9. doi: 10.1016/j.ibmb.2017.06.005. PubMed DOI

i5K Consortium The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment. J Hered. 2013;104:595–600. doi: 10.1093/jhered/est050. PubMed DOI PMC

Qi W, Ma X, He W, Chen W, Zou M, Gurr GM, et al. Characterization and expression profiling of ATP-binding cassette transporter genes in the diamondback moth, Plutella xylostella (L.) BMC Genomics. 2016;17:760. doi: 10.1186/s12864-016-3096-1. PubMed DOI PMC

Figueira-Mansur J, Schrago CG, Salles TS, Alvarenga ESL, Vasconcellos BM, Melo ACA, et al. Phylogenetic analysis of the ATP-binding cassette proteins suggests a new ABC protein subfamily J in Aedes aegypti (Diptera: Culicidae) BMC Genomics. 2020;21:463. doi: 10.1186/s12864-020-06873-8. PubMed DOI PMC

Lane TS, Rempe CS, Davitt J, Staton ME, Peng Y, Soltis DE, et al. Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnol. 2016;16:47. doi: 10.1186/s12896-016-0277-6. PubMed DOI PMC

Denecke SM, Driva O, Luong HNB, Ioannidis P, Linka M, Nauen R, et al. The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods. Genome Biol Evol. 2020;12:1429–1439. doi: 10.1093/gbe/evaa153. PubMed DOI PMC

Rane RV, Ghodke AB, Hoffmann AA, Edwards OR, Walsh TK, Oakeshott JG. Detoxifying enzyme complements and host use phenotypes in 160 insect species. Curr Opin Insect Sci. 2019 doi: 10.1016/J.COIS.2018.12.008. PubMed DOI

Waterhouse RM, Seppey M, Simão FA, Zdobnov EM. Using BUSCO to Assess Insect Genomic Resources. Insect Genomics. Hatfield; 2019;59–74. 10.1007/978-1-4939-8775-7_6. PubMed

Eddy SR, Accelerated Profile HMM, Searches Accelerated Profile HMM, Searches. PLoS Comput Biol. 2011;7:e1002195. doi: 10.1371/journal.pcbi.1002195. PubMed DOI PMC

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. doi: 10.1186/1471-2105-10-421. PubMed DOI PMC

Dean M, Hamon Y, Chimini G. The human ATP-binding cassette (ABC) transporter superfamily. J Lipid Res. 2001;42:1007–17. http://www.ncbi.nlm.nih.gov/pubmed/11441126. Accessed 24 Mar 2016. PubMed

Broehan G, Kroeger T, Lorenzen M, Merzendorfer H. Functional analysis of the ATP-binding cassette (ABC) transporter gene family of Tribolium castaneum. BMC Genomics. 2013;14:6. doi: 10.1186/1471-2164-14-6. PubMed DOI PMC

Mendes FK, Vanderpool D, Fulton B, Hahn MW. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics. 2021;36:5516–8. doi: 10.1093/bioinformatics/btaa1022. PubMed DOI

Emms DM, Kelly S. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:1-14. PubMed PMC

Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol. 2013;30:772–80. doi: 10.1093/molbev/mst010. PubMed DOI PMC

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3. doi: 10.1093/bioinformatics/btp348. PubMed DOI PMC

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A, Wren J. RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019:4453–5. PubMed PMC

Misof B, Liu S, Meusemann K, Peters RS, Donath A, Mayer C, et al. Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014;346:763–7. doi: 10.1126/science.1257570. PubMed DOI

Yu G, Smith DK, Zhu H, Guan Y, Lam TT-Y. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36. doi: 10.1111/2041-210X.12628. DOI

Andrews S.  FastQC: a quality control tool for high throughput sequence data. 2010 Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc.

Chen S, Zhou Y, Chen Y, Gu J. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018:i884–90. PubMed PMC

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37:907–15. doi: 10.1038/s41587-019-0201-4. PubMed DOI PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9. doi: 10.1093/bioinformatics/btp352. PubMed DOI PMC

Riga M, Denecke S, Livadaras I, Geibel S, Nauen R, Vontas J. Development of efficient RNAi in Nezara viridula for use in insecticide target discovery. Arch Insect Biochem Physiol. 2020;103:e21650. doi: 10.1002/arch.21650. PubMed DOI

Pearce SL, Clarke DF, East PD, Elfekih S, Gordon KHJ, Jermiin LS, et al. Genomic innovations, transcriptional plasticity and gene loss underlying the evolution and divergence of two highly polyphagous and invasive Helicoverpa pest species. BMC Biol. 2017;15:63. doi: 10.1186/s12915-017-0402-6. PubMed DOI PMC

Denecke S, Ioannidis P, Buer B, Ilias A, Douris V, Topalis P, et al. A transcriptomic and proteomic atlas of expression in the Nezara viridula (Heteroptera: Pentatomidae) midgut suggests the compartmentalization of xenobiotic metabolism and nutrient digestion. BMC Genomics. 2020;21:129. doi: 10.1186/s12864-020-6459-6. PubMed DOI PMC

Rösner J, Merzendorfer H. Transcriptional plasticity of different ABC transporter genes from Tribolium castaneum contributes to diflubenzuron resistance. Insect Biochem Mol Biol. 2020;116:103282. doi: 10.1016/J.IBMB.2019.103282. PubMed DOI

Kowalski P, Baum M, Körten M, Donath A, Dobler S. ABCB transporters in a leaf beetle respond to sequestered plant toxins. Proc R Soc B Biol Sci. 2020;287:20201311. doi: 10.1098/rspb.2020.1311. PubMed DOI PMC

Mayer F, Mayer N, Chinn L, Pinsonneault RL, Kroetz D, Bainton RJ. Evolutionary conservation of vertebrate blood-brain barrier chemoprotective mechanisms in Drosophila. J Neurosci. 2009;29:3538–50. doi: 10.1523/JNEUROSCI.5564-08.2009. PubMed DOI PMC

Tian L, Yang J, Hou W, Xu B, Xie W, Wang S, et al. Molecular cloning and characterization of a P-glycoprotein from the diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae) Int J Mol Sci. 2013;14:22891–905. doi: 10.3390/ijms141122891. PubMed DOI PMC

Favell G, McNeil JN, Donly C. The ABCB Multidrug Resistance Proteins Do Not Contribute to Ivermectin Detoxification in the Colorado Potato Beetle, Leptinotarsa decemlineata (Say) Insects. 2020;11:135. doi: 10.3390/insects11020135. PubMed DOI PMC

Simmons J, D’Souza O, Rheault M, Donly C. Multidrug resistance protein gene expression in Trichoplusia ni caterpillars. Insect Mol Biol. 2013:62-71. PubMed

Jin M, Liao C, Chakrabarty S, Zheng W, Wu K, Xiao Y. Transcriptional response of ATP-binding cassette (ABC) transporters to insecticides in the cotton bollworm, Helicoverpa armigera. Pestic Biochem Physiol. 2018 doi: 10.1016/J.PESTBP.2018.12.007. PubMed DOI

Zuo Y, Huang J-L, Wang J, Feng Y, Han T-T, Wu Y-D, et al. Knockout of a P-glycoprotein gene increases susceptibility to abamectin and emamectin benzoate in Spodoptera exigua. Insect Mol Biol. 2017 doi: 10.1111/imb.12338. PubMed DOI

Aurade RM, Jayalakshmi SK, Sreeramulu K. P-glycoprotein ATPase from the resistant pest, Helicoverpa armigera: purification, characterization and effect of various insecticides on its transport function. Biochim Biophys Acta. 2010;1798:1135–43. doi: 10.1016/j.bbamem.2010.02.019. PubMed DOI

Jin M, Cheng Y, Guo X, Li M, Chakrabarty S, Liu K, et al. Down-regulation of lysosomal protein ABCB6 increases gossypol susceptibility in Helicoverpa armigera. Insect Biochem Mol Biol. 2020;103387. 10.1016/j.ibmb.2020.103387. PubMed

Ohbayashi T, Takeshita K, Kitagawa W, Nikoh N, Koga R, Meng X-Y, et al. Insect’s intestinal organ for symbiont sorting. Proc Natl Acad Sci U S A. 2015;112:E5179-88. doi: 10.1073/pnas.1511454112. PubMed DOI PMC