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Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes
Takashi Abe1, Yu Akazawa1, Atsushi Toyoda2,3
1Department of Information Engineering, Faculty of Engineering, Niigata University, Niigata, Japan.
Frontiers in Microbiology
|July 29, 2020
Summary
This study introduces a new alignment-free method using Batch-Learning Self-Organizing Maps (BLSOM) to detect horizontal gene transfer (HGT) in microbial genomes. The method reveals novel insights into microbial adaptation to cold environments by identifying HGT origins and functions.
Area of Science:
- Microbial genomics and evolutionary biology.
- Bioinformatics and computational biology.
Background:
- Horizontal gene transfer (HGT) is crucial for microbial environmental adaptation, but its frequency and origins are often underestimated due to limitations in detection methods.
- Existing phylogeny-based methods rely on sequence alignments, which can be challenging for novel or divergent genomes.
Purpose of the Study:
- To develop and apply an alignment-free method for detecting HGT candidates and their origins in entire microbial genomes.
- To investigate the role of HGT in the low-temperature adaptation of psychrotolerant Alphaproteobacteria from Antarctic environments.
Main Methods:
- Development of a Batch-Learning Self-Organizing Map (BLSOM) unsupervised neural network for clustering sequence fragments based on oligonucleotide similarity.
- Application of BLSOM to nearly all prokaryotic genomes to identify HGT candidates and assign their origins.
- Comparative analysis of HGT in Antarctic Sphingomonas strains versus continental strains, including gene function and amino acid frequency analysis.
Main Results:
- BLSOM successfully identified HGT candidates and their origins across diverse microbial genomes, including those with high novelty.
- Antarctic Sphingomonas strains showed a higher proportion of HGT candidates from Betaproteobacteria compared to continental strains, with distinct origins between the two Antarctic strains.
- Identified HGT candidates in Antarctic strains were enriched for genes related to cell wall/membrane biogenesis, and exhibited altered amino acid frequencies (increased Lys, Ser, Thr, Val; decreased Ala, Arg, Glu, Leu) compared to housekeeping genes.
Conclusions:
- The BLSOM method is a powerful tool for detecting HGT and its origins, offering new perspectives on microbial adaptation.
- The findings suggest convergent evolutionary strategies for low-temperature adaptation in Antarctic microbes, driven by HGT.
- Distinct amino acid composition in Antarctic strains points to specific adaptations potentially facilitated by horizontally acquired genes.
Keywords:
Antarctic environmentBatch-Learning Self-Organizing MapSphingomonas genomeamino acid frequencyconvergent evolutionhorizontal gene transferlow-temperature adaptationoligonucleotideMore Related Videos
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