LEMON : a method to construct the local strains at horizontal gene transfer sites in gut metagenomics
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Author(s)
Related Research Unit(s)
Detail(s)
| Original language | English |
|---|---|
| Article number | 702 |
| Number of pages | 12 |
| Journal / Publication | BMC Bioinformatics |
| Volume | 20 |
| Issue number | Suppl 23 |
| Online published | 27 Dec 2019 |
| Publication status | Published - 2019 |
Conference
| Title | 30th International Conference on Genome Informatics (GIW 2019) |
|---|---|
| Location | University of Sydney |
| Place | Australia |
| City | Sydney |
| Period | 9 - 12 December 2019 |
Link(s)
| DOI | DOI |
|---|---|
| Attachment(s) | Documents
Publisher's Copyright Statement
|
| Link to Scopus | https://www.scopus.com/record/display.uri?eid=2-s2.0-85077258058&origin=recordpage |
| Permanent Link | https://scholars.cityu.edu.hk/en/publications/publication(aa34fdc5-79d9-47f4-a4e8-e5018b1971ea).html |
Abstract
Background: Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of microorganisms, especially the gut microbiomes which the human body harbors. The transferred segments may lead to complicated local genome structural variations. Details of the local genome structure can elucidate the effects of the HGTs.
Results: In this work, we propose a graph-based method to reconstruct the local strains from the gut metagenomics data at the HGT sites. The method is implemented in a package named LEMON. The simulated results indicate that the method can identify transferred segments accurately on reference sequences of the microbiome. Simulation results illustrate that LEMON could recover local strains with complicated structure variation. Furthermore, the gene fusion points detected in real data near HGT breakpoints validate the accuracy of LEMON. Some strains reconstructed by LEMON have a replication time profile with lower standard error, which demonstrates HGT events recovered by LEMON is reliable.
Conclusions: Through LEMON we could reconstruct the sequence structure of bacteria, which harbors HGT events. This helps us to study gene flow among different microbial species.
Results: In this work, we propose a graph-based method to reconstruct the local strains from the gut metagenomics data at the HGT sites. The method is implemented in a package named LEMON. The simulated results indicate that the method can identify transferred segments accurately on reference sequences of the microbiome. Simulation results illustrate that LEMON could recover local strains with complicated structure variation. Furthermore, the gene fusion points detected in real data near HGT breakpoints validate the accuracy of LEMON. Some strains reconstructed by LEMON have a replication time profile with lower standard error, which demonstrates HGT events recovered by LEMON is reliable.
Conclusions: Through LEMON we could reconstruct the sequence structure of bacteria, which harbors HGT events. This helps us to study gene flow among different microbial species.
Research Area(s)
- HGT, Local strain, Gut metagenomics, Graph
Citation Format(s)
LEMON: a method to construct the local strains at horizontal gene transfer sites in gut metagenomics. / Li, Chen; Jiang, Yiqi; Li, Shuaicheng.
In: BMC Bioinformatics, Vol. 20, No. Suppl 23, 702, 2019.
In: BMC Bioinformatics, Vol. 20, No. Suppl 23, 702, 2019.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Download Statistics
No data available
