Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, part...
Main Authors: | , , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
2020
|
Subjects: | |
Online Access: | https://doi.org/10.3389/fmicb.2020.01486.s012 https://figshare.com/articles/dataset/Table_2_Batch-Learning_Self-Organizing_Map_Identifies_Horizontal_Gene_Transfer_Candidates_and_Their_Origins_in_Entire_Genomes_XLSX/12608366 |
id |
ftfrontimediafig:oai:figshare.com:article/12608366 |
---|---|
record_format |
openpolar |
spelling |
ftfrontimediafig:oai:figshare.com:article/12608366 2023-05-15T14:04:47+02:00 Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX Takashi Abe Yu Akazawa Atsushi Toyoda Hironori Niki Tomoya Baba 2020-07-03T11:17:47Z https://doi.org/10.3389/fmicb.2020.01486.s012 https://figshare.com/articles/dataset/Table_2_Batch-Learning_Self-Organizing_Map_Identifies_Horizontal_Gene_Transfer_Candidates_and_Their_Origins_in_Entire_Genomes_XLSX/12608366 unknown doi:10.3389/fmicb.2020.01486.s012 https://figshare.com/articles/dataset/Table_2_Batch-Learning_Self-Organizing_Map_Identifies_Horizontal_Gene_Transfer_Candidates_and_Their_Origins_in_Entire_Genomes_XLSX/12608366 CC BY 4.0 CC-BY Microbiology Microbial Genetics Microbial Ecology Mycology horizontal gene transfer Antarctic environment Sphingomonas genome Batch-Learning Self-Organizing Map oligonucleotide low-temperature adaptation amino acid frequency convergent evolution Dataset 2020 ftfrontimediafig https://doi.org/10.3389/fmicb.2020.01486.s012 2020-07-08T22:55:30Z Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently ... Dataset Antarc* Antarctic Frontiers: Figshare Antarctic The Antarctic |
institution |
Open Polar |
collection |
Frontiers: Figshare |
op_collection_id |
ftfrontimediafig |
language |
unknown |
topic |
Microbiology Microbial Genetics Microbial Ecology Mycology horizontal gene transfer Antarctic environment Sphingomonas genome Batch-Learning Self-Organizing Map oligonucleotide low-temperature adaptation amino acid frequency convergent evolution |
spellingShingle |
Microbiology Microbial Genetics Microbial Ecology Mycology horizontal gene transfer Antarctic environment Sphingomonas genome Batch-Learning Self-Organizing Map oligonucleotide low-temperature adaptation amino acid frequency convergent evolution Takashi Abe Yu Akazawa Atsushi Toyoda Hironori Niki Tomoya Baba Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX |
topic_facet |
Microbiology Microbial Genetics Microbial Ecology Mycology horizontal gene transfer Antarctic environment Sphingomonas genome Batch-Learning Self-Organizing Map oligonucleotide low-temperature adaptation amino acid frequency convergent evolution |
description |
Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network “Batch-Learning Self-Organizing Map (BLSOM)” in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently ... |
format |
Dataset |
author |
Takashi Abe Yu Akazawa Atsushi Toyoda Hironori Niki Tomoya Baba |
author_facet |
Takashi Abe Yu Akazawa Atsushi Toyoda Hironori Niki Tomoya Baba |
author_sort |
Takashi Abe |
title |
Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX |
title_short |
Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX |
title_full |
Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX |
title_fullStr |
Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX |
title_full_unstemmed |
Table_2_Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes.XLSX |
title_sort |
table_2_batch-learning self-organizing map identifies horizontal gene transfer candidates and their origins in entire genomes.xlsx |
publishDate |
2020 |
url |
https://doi.org/10.3389/fmicb.2020.01486.s012 https://figshare.com/articles/dataset/Table_2_Batch-Learning_Self-Organizing_Map_Identifies_Horizontal_Gene_Transfer_Candidates_and_Their_Origins_in_Entire_Genomes_XLSX/12608366 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
doi:10.3389/fmicb.2020.01486.s012 https://figshare.com/articles/dataset/Table_2_Batch-Learning_Self-Organizing_Map_Identifies_Horizontal_Gene_Transfer_Candidates_and_Their_Origins_in_Entire_Genomes_XLSX/12608366 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2020.01486.s012 |
_version_ |
1766276073157296128 |