Abstract
The tripartite motif (TRIM) gene family encodes diverse distinct proteins that play important roles in many biological processes. However, the molecular evolution and phylogenetic relationships of TRIM genes in primates are still elusive. We performed a genomic approach to identify and characterize TRIM genes in human and other six primate genomes. In total, 537 putative functional TRIM genes were identified and TRIM members varied among primates. A neighbor joining (NJ) tree based on the protein sequences of 82 human TRIM genes indicates seven TRIM groups, which is consistent with the results based on the architectural motifs. Many TRIM gene duplication events were identified, indicating a recent expansion of TRIM family in primate lineages. Interestingly, the chimpanzee genome shows the greatest TRIM gene expansion among the primates; however, its congeneric species, bonobo, has the least number of TRIM genes and no duplication event. Moreover, we identified a ~ 200 kb deletion on chromosome 11 of bonobos that results in a loss of cluster3 TRIM genes. The loss of TRIM genes might have occurred within the last 2 mys. Analysis of positive selection recovered 9 previously reported and 21 newly identified positively selected TRIM genes. In particular, most positive selected sites are located in the B30.2 domains. Our results have provided new insight into the evolution of primate TRIM genes and will broaden our understanding on the functions of the TRIM family.
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Acknowledgements
The research was funded by the State Key Program of National Natural Science Foundation of China (Grants no. 31530068), and partial by National Natural Science Foundation of China (no. 31770415) and the Key Research Fund on Sciences and Technologies for Joint Academic Institute and Local Enterprises of Sichuan (2018JZ0008).
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Fig. S1
Phylogenetic relationships of 537 primate TRIM genes. The unrooted phylogenetic tree was constructed using MEGA 6.0 by Neighbor-Joining method and the bootstrap test was performed with 1,000 iterations. The three groups are indicated as different colors. (TIF 3514 kb)
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Qiu, S., Liu, H., Jian, Z. et al. Characterization of the primate TRIM gene family reveals the recent evolution in primates. Mol Genet Genomics 295, 1281–1294 (2020). https://doi.org/10.1007/s00438-020-01698-2
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DOI: https://doi.org/10.1007/s00438-020-01698-2