TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes

Kim, S.; Cheong, K.; Park, J.; Kim, M.-S.; Kim, J.-H.; Seo, M.-K.; Kwon, S.-H.; Kim, Y.-M.; Koo, N.; Kim, K.-S.; Oh, N.; Kim, K.-T.; Jeon, J.; Kim, H.; Lee, Y.-Y.; Sohn, K.-H.; McCann, H.; Ye, S.-K.; Park, K.-S.; Lee, Y.-H.; Choi, D.

doi:10.1101/372433

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bioRxiv · 10.1101/372433

TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes

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Abstract

Whole genome annotation errors that omit essential protein-coding genes hinder further research. We developed Target Gene Family Finder (TGFam-Finder), an optimal tool for structural annotation of protein-coding genes containing target domain(s) of interest in eukaryotic genomes. Large-scale re-annotation of 100 publicly available eukaryotic genomes led to the discovery of essential genes that were missed in previous annotations. An average of 117 (346%) and 148 (45%) additional FAR1 and NLR genes were newly identified in 50 plant genomes. Furthermore, 117 (47%) additional C2H2 zinc finger genes were detected in 50 animal genomes including human and mouse. Accuracy of the newly annotated genes was validated by RT-PCR and cDNA sequencing in human, mouse and rice. In the human genome, 26 newly annotated genes were identical with known functional genes. TGFam-Finder along with the new gene models provide an optimized platform for unbiased functional and comparative genomics and comprehensive evolutionary study in eukaryotes.

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Kim, S., Cheong, K., Park, J., Kim, M.-S., Kim, J.-H., Seo, M.-K., Kwon, S.-H., Kim, Y.-M., Koo, N., Kim, K.-S., Oh, N., Kim, K.-T., Jeon, J., Kim, H., Lee, Y.-Y., Sohn, K.-H., McCann, H., Ye, S.-K., Park, K.-S., Lee, Y.-H., Choi, D.. 2018-07-19. TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes. https://doi.org/10.1101/372433

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