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

000      

00000naa a2200000 a 4500

001      

bmc21025331

003      

CZ-PrNML

005      

20211026133922.0

007      

ta

008      

211013s2021 xxk f 000 0|eng||

009      

AR

024    7_

$a 10.1186/s12864-021-07861-2 $2 doi

035    __

$a (PubMed)34281528

040    __

$a ABA008 $b cze $d ABA008 $e AACR2

041    0_

$a eng

044    __

$a xxk

100    1_

$a Denecke, Shane $u Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece. shane_denecke@imbb.forth.gr

245    10

$a Comparative and functional genomics of the ABC transporter superfamily across arthropods / $c S. Denecke, I. Rankić, O. Driva, M. Kalsi, NBH. Luong, B. Buer, R. Nauen, S. Geibel, J. Vontas

520    9_

$a 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.

650    _2

$a ABC transportéry $x genetika $7 D018528

650    _2

$a zvířata $7 D000818

650    12

$a členovci $x genetika $7 D001181

650    _2

$a genom $7 D016678

650    _2

$a genomika $7 D023281

650    _2

$a lidé $7 D006801

650    _2

$a anotace sekvence $7 D058977

655    _2

$a časopisecké články $7 D016428

700    1_

$a Rankić, Ivan $u Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, 613 00, Brno, Czechia

700    1_

$a Driva, Olympia $u Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece

700    1_

$a Kalsi, Megha $u Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece

700    1_

$a Luong, Ngoc Bao Hang $u Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece

700    1_

$a Buer, Benjamin $u CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany

700    1_

$a Nauen, Ralf $u CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany

700    1_

$a Geibel, Sven $u CropScience Division, Bayer AG, R&D Pest Control, D-40789, Monheim, Germany

700    1_

$a Vontas, John $u Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, 100 N. Plastira Street, 700 13, Heraklion Crete, Greece $u Laboratory of Pesticide Science, Department of Crop Science, Agricultural University of Athens, Athens, Greece

773    0_

$w MED00008181 $t BMC genomics $x 1471-2164 $g Roč. 22, č. 1 (2021), s. 553

856    41

$u https://pubmed.ncbi.nlm.nih.gov/34281528 $y Pubmed

910    __

$a ABA008 $b sig $c sign $y p $z 0

990    __

$a 20211013 $b ABA008

991    __

$a 20211026133928 $b ABA008

999    __

$a ok $b bmc $g 1714398 $s 1145838

BAS    __

$a 3

BAS    __

$a PreBMC

BMC    __

$a 2021 $b 22 $c 1 $d 553 $e 20210719 $i 1471-2164 $m BMC genomics $n BMC Genomics $x MED00008181

LZP    __

$a Pubmed-20211013