Horizontal gene transfer is ubiquitous in eukaryote genomes

Horizontal gene transfer (HGT) is the transfer of genetic material between distantly related organisms. While most genes in prokaryotes can be horizontally transferred, HGT events in eukaryotes are considered as rare, existing in a small number of species. Here we reported the identification of HGT regions (HGTs) in 10 eukaryotes, including human, mouse, cow, lizard, frog, zebrafish, fruit fly, nematode, Arabidopsis and yeast. By comparing their genomes with thousands of eukaryotes, bacterial and virus genomes, we found between 10 and 237 non-redundant HGTs per eukaryote species. PCR and third-generation sequencing validation of HGTs excluded the probability of contamination. Genes impacted by HGTs are enriched in transmembrane transport. Some HGTs have transformed their host genomes with various numbers of copies and have impacted hundreds, even thousands of genes. Our findings reveal that HGT is ubiquitous in eukaryotic genomes, and HGT is an important driver of genome evolution for eukaryotes.

Supplementary Data
    

• Supplementary_Data_1.tar.gz (465G)

Supplementary Table
    

• Supplementary Table 1.xlsx (15K)
• Supplementary Table 2.xlsx (14K)
• Supplementary Table 3.xlsx (15K)
• Supplementary Table 4.xlsx (70K)
• Supplementary Table 5.xlsx (49K)
• Supplementary Table 6.xlsx (113K)
• Supplementary Table 7.xlsx (189K)
• Supplementary Table 8.xlsx (62K)
• Supplementary Table 9.xlsx (14K)
• Supplementary Table 10.xlsx (47K)
• Supplementary Table 11.xlsx (152K)
• Supplementary Table 12.xlsx (32K)
• Supplementary Table 13.xlsx (6.9M)
• Supplementary Table 14.xlsx (50K)
• Supplementary Table 15.xlsx (13K)
• Supplementary Table 16.xlsx (11K)
• Supplementary Table 17.xlsx (11K)
• Supplementary Table 18.xlsx (105K)
• Supplementary Table 19.xlsx (1.4M)
• Supplementary Table 20.xlsx (2.7M)

Analysis pipeline
    

• demo.tar.gz: The pipeline to identify HGTs, with source code, datasets and results (human as an example) (7.2G)
• Supplementary_Data_2.fa: The simulated data (genome H) with 175 HGTs (2.9G)

Citation
Please cite the following paper if you referred to this study.

Contact:
If you have any questions, feel free to contact us.
< likun_dawn@163.com >
< ccwei@sjtu.edu.cn >