TABLE 2.
Similarity of EV markers and biogenesis regulators between human and emerging models.
| Human EV marker/Regulator a | Hydra (Hydra vulgaris) | Planarians (Schmidtea mediterranea) | Axolotl (Ambystoma mexicanum) | Spiny Mouse (Acomys cahirinus) | ||||
|---|---|---|---|---|---|---|---|---|
| Identity (%) | E value | Identity (%) | E value | Identity (%) | E value | Identity (%) | E value | |
| TSG101 | 39 | 1.39 × 10−92 | 38 | 1.63 × 10−85 | 84 | 0 | 94 | 0 |
| Alix | 47 | 2.28 × 10−155 | 38 | 1.94 × 10−156 | 75 | 0 | 95 | 0 |
| Flotillin-1 | 61 | 4.44 × 10−155 | 61 | 8.98 × 10−154 | 82 | 0 | 97 | 0 |
| Syntenin-1 | 52 | 1.24 × 10−97 | 51 | 3.29 × 10−103 | 84 | 0 | 90 | 0 |
| Rab-7a | 85 | 1.62 × 10−127 | 76 | 3.35 × 10−117 | 99 | 3.55 × 10−155 | 100 | 9.32 × 10−154 |
| CD63 | 36 | 4.49 × 10−24 | 25 b | 3.27 × 10−15 | 79 | 1.16 × 10−139 | 76 | 1.94 × 10−108 |
See Supplementary Table S1 for the transcript/protein ID of the top ortholog in each species.
The top planarian CD63 homolog hit three human Tetraspanin-6 isoforms, followed by human CD63 in the reciprocal BLASTX query, suggesting high similarity, but a lack of one-to-one orthology in planarians.
Methods: Human TSG101 (NCBI NP_006283.1), Alix (NCBI NP_037506.2), Flotillin-1 (NCBI NP_005794.1), Syntenin-1 (NCBI NP_005616.2), Rab-7a (NCBI NP_004628.4), and CD63 (NCBI NP_001254627.1) proteins were used to query emerging model transcriptomes for orthologs using TBLASTN, or BLASTP (Axolotl). Presence of conserved protein domains in target sequences was verified using NCBI Conserved Domain Search, then Human RefSeq Protein was reciprocally queried with each top hit using BLASTX/BLASTP. All organisms’ top ortholog hit the corresponding human protein except for the top planarian CD63 hit. Amino acid identity and E values for these top orthologs are shown.
Databases: Hydra 2.0 Genome Project Portal (https://research.nhgri.nih.gov/hydra/)—Juliano Trinity (JT) assembly (Juliano et al., 2014); PlanMine (https://planmine.mpicbc.mpg.de)—Dresden dd_Smed_v6 assembly (Brandl et al., 2016); Axolotl Transcriptomics Database (https://portals.broadinstitute.org/axolotlomics/)—TransDecoder predicted protein sequences (Bryant et al., 2017) queried in Geneious Prime 2021.2.2; Spiny Mouse Sequence Server 2.0.0rc8 (spinymouse.erc.monash.edu/sequenceserver)—tr2aacds_v2 annotated protein assembly (Mamrot et al., 2017).