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Citation
Denecke, S.M., Driva, O., Luong, H.N.B., Ioannidis, P., Linka, M., Nauen, R., Geibel, S., Vontas, J. (2020). The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods.  Genome Biol. Evol. 12(8): 1429--1439.
FlyBase ID
FBrf0247791
Publication Type
Research paper
Abstract

The solute carrier (SLC) transporter superfamily comprises an ancient and ubiquitous group of proteins capable of translocating a range of nutrients, endogenous molecules, and xenobiotics. Although the group has been the subject of intense investigation in both bacteria and mammals, its systematic identification in arthropods has not yet been undertaken. Here, we present a genome-wide identification of all 66 human SLC families in 174 arthropod species. A pipeline (SLC_id) was constructed to identify and group SLCs using a combination of hidden Markov model and BLAST searches followed by filtering based on polypeptide length and the number of transmembrane domains. Comparative analysis of the number of transporters in each family across diverse arthropod lineages was accomplished using one-way analysis of variance (ANOVA) and the Computational Analysis of gene Family Evolution (CAFE). These results suggested that many SLC families have undergone expansions or contractions in particular evolutionary lineages. Notably, the sugar transporting SLC2 family was significantly larger in insects compared with arachnids. This difference may have been complemented by a rapid expansion of the SLC60 family in arachnids which also acts on dietary sugars. Furthermore, the SLC33 family underwent a recent and drastic expansion in aphids, although the biological relevance of this expansion was not possible to infer. Information on specific SLC transporter families across arthropod species can be accessed through an R shiny web application at http://chrysalida.imbb.forth.gr : 3838/Arthropod_SLC_Database/. The present study greatly facilitates further investigation of the diverse group of SLC transporters in arthropods.

PubMed ID
PubMed Central ID
PMC7487162 (PMC) (EuropePMC)
Related Publication(s)
Website

shiny: Web Application Framework for R.
Chang et al., 2020, shiny: Web Application Framework for R. [FBrf0247806]

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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Genome Biol. Evol.
    Title
    Genome biology and evolution
    ISBN/ISSN
    1759-6653
    Data From Reference