| URL: | http://chrysalida.imbb.forth.gr:3838/Arthropod_SLC_Database/ |
| Full name: | The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods |
| Description: | Arthropod SLC (solute carrier) presents a comprehensive identification of all 66 human SLC families in 174 arthropod species for which good quality protein sets exist. This was accomplished by designing and implementing an in silico pipeline for SLC annotation (SLC_id) which used HMM and BLAST searches followed by filtering based on length and TM domains. Variation among SLC family sizes was then used to determine evolutionary trends over time and ecological niche. This comprehensive data set will be a useful starting point for elucidating functional roles of the SLC superfamily in arthropods. |
| Year founded: | 2020 |
| Last update: | 2020-08-01 |
| Version: | |
| Accessibility: |
Accessible
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| Country/Region: | Greece |
| University/Institution: | Foundation for Research and Technology-Hellas |
| Address: | Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece |
| City: | |
| Province/State: | |
| Country/Region: | Greece |
| Contact name (PI/Team): | Shane M Denecke |
| Contact email (PI/Helpdesk): | shane_denecke@imbb.forth.gr |
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The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods. [PMID: 32681801]
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. |