- Comparative and functional genomics of the ABC transporter superfamily across arthropods. - 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. - Conclusions: We have performed an annotation of the ABC superfamily across >. - Future work will be able to use this analysis as a resource to provide a better understanding of the ABC superfamily in arthropods.. - Less is known about the ABC superfamily in arthro- pods compared to other taxonomic groups such as mammals or bacteria [4]. - Xenobiotic transporting roles have been suggested for the ABC-A, ABC-B, ABC-C, and ABC-G families families [6, 8], while members of the ABC-C and ABC-A family often serve as targets for crystal toxins derived from Bacillus thuringiensis [9].. - One of the best studied ABC families is the ABC-B clade which consists of both full and half transporters that act on an array of substrates including neutral and cationic amphiphilic compounds [10]. - The ABC-H transporter family is also particularly in- teresting due to its distribution across species. - Structurally, ABC-H pro- teins are half-transporters and show the same inverted domain architecture as the ABC-G family. - The func- tional characterization of these proteins has been pio- neered in Drosophila where the ABC-H transporter Snustorr (Snu) was localized to the integument and shown to transport cuticular hydrocarbons [20]. - RNAi knockdown of Snu orthologues in other arthropods has led to lethality due to desiccation, suggesting a similar function [21, 22], but little information exists on other members of the ABC-H family.. - This has led to an avalanche of publications which manually annotate the ABC family of a species using a variety of different methodologies . - So far, there has been little effort to systematically com- pare the ABC transporter superfamily in arthropods.. - Such a comparative genomic analysis of the ABC super- family was previously accomplished in plants, [26] and a more recent study has considered the evolution of the Solute carrier (SLC) transporter superfamily in arthro- pods [27]. - Here, we extend the knowledge of the ABC trans- porter superfamily in arthropods through comparative and functional genomics. - First, we designed and imple- mented the ABC_scan algorithm to identify and classify ABC transporters from the predicted proteome of a spe- cies. - Proteins showing ambiguity between the ABC-B full and half transporter subfamilies were categorized based on their number of nucleotide binding domains;. - The ABC-I family was recently proposed in insects [25], but it was excluded in this study because it was not annotated in any of the model insect proteomes on which the analysis depends.. - The ABC_scan pipeline can be separated into inputs (orange), actions (grey), and outputs (blue). - In the first step the protein sets are searched with the ABC transporter (PF00005) HMM profile. - Family sizes for each ABC family in each species were estimated using the ABC_scan pipeline described above. - For the ABC-B full transporters, se- quences from Bombyx mori, Spodoptera frugiperda, Nezara viridula, Danaus plexipus, and Papilio polytes were used. - In the ABC-H family N. - The full source code for the ABC_scan pipeline is avail- able on GitHub (https://github.com/shanedenecke/ABC_. - Annotation of ABC transporters across arthropod species In order to understand and study the evolution of the ABC transporter superfamily across arthropods, we de- signed the ABC_scan pipeline to identify and classify ABCs in 193 non-model species (excluding the 4 model species used in the search algorithm) with sequenced ge- nomes derived from sources such as OrthoDB, NCBI, and others. - 80 % and were analyzed with the ABC_scan pipeline (Table S1). - The general quality of the ABC_scan identification algorithm was assessed by comparing the numbers of predicted transporters against numbers previously reported in the literature. - Discrepancies between the ABC_scan pipeline implemented in this study and literature derived pre- dicted transporters ranged from a 7 % overestimation to an 8 % underestimation with a mean deviation of 0.3 % (Figure S2. - Table S4), suggesting that the ABC_scan. - Small amounts of variation were observed among the ABC-BH, ABC-D, ABC-E, and ABC-F fam- ilies (Figure S3. - While there were statistical differences among the ABC-D family, the small magni- tude of the change made it difficult to explore in detail.. - The largest differences from the Kruskal-Wallis test comparisons were concentrated in the ABC-A, ABC-BF, ABC-C, ABC-G, and ABC-H families (Fig. - The ABC-G family was notable in that it appeared much smaller in all Arachnids (median of 3.5 genes) versus a median of 15 genes for all species combined. - The ABC-C family was significantly higher in Coleoptera with a median of 27 genes compared to 13 found among all arthropods. - The ABC-B family is known to play roles in physio- logical homeostasis and drug transport. - Further characterization of the ABC-BF expansion was performed by creating a phyl- ogeny of all ABC-BF transporters from 6 Lepidoptera species and N. - This suggests that the ABC-BF expansion in Lepidoptera likely occurred at the beginning of the Lepidoptera lineage.. - The ABC-H Family in Hemiptera. - However, the ABC-H proteins from D. - urticae grouped completely independently, suggesting independent expansions of the ABC-H family in each of these two species. - independent grouping of Sternorrhyncha and non- Sternorrhyncha ABC-H genes suggests that while the ABC-H family is larger in all Hemiptera, it may have undergone multiple expansions at different times in the evolution of this clade.. - 3 The ABC- B full transporters in Lepidoptera. - a The evolution within the ABC-B full transporter family was analyzed with CAFE. - Each tip of the tree represents a species mostly of Lepidoptera. - In contrast, the clustering of the N. - There has been substantial interest in the ABC super- family among arthropods both as mediators of pesticide resistance and as targets for pest control. - The ABC_scan pipeline. - 4 Expression of the ABC-B full transporters in. - a Heatmap showing differential expression of the ABC-B paralogues in different tissues of fifth larval stage H. - Deploying ABC_scan to search 158 non-model arthro- pods identified several interesting evolutionary trends in the ABC-C and ABC-BF families previously associated with xenobiotic transport. - The ABC-C family was not the subject of intense focus in this study but showed a. - a The evolution within the ABC-H transporter family was analyzed with CAFE. - Each tip of the tree represents a species mostly of Hemiptera. - A significant expansion of the ABC-BF in Lepidoptera was also detected and seems to have occurred soon after the divergence of this order (Fig. - Characterization of the expression patterns of the ABCB full transporter family in H. - In the H. - The essentiality of the ABC-H transporters was examined in N. - The predicted numbers of ABC transporters in the ABC_scan pipeline were benchmarked against previously published ABC transporter datasets. - https://doi.org/10.1042/BST20150139.. - https://doi.org/10.1042/BSE0500019.. - https://doi.org/10.1146/annurev.cb . - https://doi.org/10.1093/nar/gkaa1 004.. - https://doi.org/10.1186/s . - The ABC gene family in arthropods:. - https://doi.org/10.1016/j.ibmb . - https://doi.org/10.1016/. - https://doi.org/1 0.1016/j.ibmb . - https://doi.org/10.101 6/B . - https://doi.org/10.1097/FPC.. - https://doi.org . - https://doi.org/10.1111/imb.12052.. - https://doi.org/10.1016/j.. - The ABC transporter gene family of Daphnia pulex. - https://doi.. - https://doi.org/10.1073/pnas . - 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. - https://doi.org/10.1016/J.EJCB . - https://doi.org/10.1038/. - The ABC transporter ABCH-9 C is needed for cuticle barrier construction in Locusta migratoria.. - https://doi.org/10.1016/j.ibmb.2017.. - https://doi.org/10.1093/jhered/est050.. - https://doi.org/10.1016/J.COIS.2018.12.. - doi.org . - https://doi.org/10.1371/journa l.pcbi.1002195.. - Functional analysis of the ATP-binding cassette (ABC) transporter gene family of Tribolium castaneum.. - https://doi.org/10.1093/bioinformatics/btaa1022.. - https://doi.org/10.1093/molbev/mst010.. - https://doi.org/10.1093/bioinformatics/btp348.. - https://doi.org/10.1126/science.1257570.. - https://doi.org X.12628.. - https://doi.org/10.1038/s . - https://doi.org/10.1093/bioinformatics/btp352.. - https://doi.org/10.1002/arch.21650.. - https://doi.org/10.101 6/J.IBMB . - https://doi.org/10.1098/rspb.2020.1311.. - https://doi.org/10.1 523/JNEUROSCI . - doi.org/10.3390/ijms141122891.. - https://doi.org/10.3390/. - https://doi.org/10.1016/J.PESTBP . - https://doi.org/10.1016/j.bbamem
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