Build a Bioinformatics Analysis Platform and Apply it to Routine Analysis of Microbial Genomics and Comparative Genomics

Abstract Genomics and comparative genomics have been increasingly used as routine methods for general microbiological researches. However, it is usually necessary to call several tools or even write some scripts to complete some simple analysis, which is complicated for most biological researchers. To simplify the operation process, especially for the convenience of microbiologists in the analysis, here we have developed PGCGAP, a comprehensive, malleable and easily-installed prokaryotic genomics and comparative genomics analysis pipeline, which implements genome assembly, gene prediction and annotation, average nucleotide identity (ANI) calculation, phylogenetic analysis, COG annotation, pan-genome analysis, inference of orthologous gene groups, variants calling and annotation and screening for antimicrobial and virulence genes. Although we have tried our best to simplify the installation and usage of PGCGAP, it may be difficult for non-bioinformatician users to master it. So, a protocol was created to help microbiologists without any experience in bioinformatics to establish their own bioinformatics platform and perform routine analysis. This protocol shows how to choose equipment, to install a Linux subsystem on a laptop with windows 10 system, to install PGCGAP and perform all analysis with an example dataset. The protocol requires a basic understanding of Linux, so an additional web page was written to help uninitiated users learn Linux and whole-genome sequencing (http://bcam.hzau.edu.cn/linuxwgs.php).

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Build a Bioinformatics Analysis Platform and Apply it to Routine Analysis of Microbial Genomics and Comparative Genomics

10.21203/rs.2.21224/v3 ◽

2020 ◽

Author(s):

Hualin Liu ◽

Bingyue Xin ◽

Jinshui Zheng ◽

Hao Zhong ◽

Yun Yu ◽

...

Keyword(s):

Comparative Genomics ◽

Bioinformatics Analysis ◽

Gene Prediction ◽

Orthologous Gene ◽

Routine Analysis ◽

Simple Analysis ◽

Analysis Pipeline ◽

Operation Process ◽

Comparative Genomics Analysis ◽

Analysis Platform

Abstract Genomics and comparative genomics have been increasingly used as routine methods for general microbiological researches. However, it is usually necessary to call several tools or even write some scripts to complete some simple analysis, which is complicated for most biological researchers. To simplify the operation process, especially for the convenience of microbiologists in the analysis, here we have developed PGCGAP, a comprehensive, malleable and easily-installed prokaryotic genomics and comparative genomics analysis pipeline, which implements genome assembly, gene prediction and annotation, average nucleotide identity (ANI) calculation, phylogenetic analysis, COG annotation, pan-genome analysis, inference of orthologous gene groups, variants calling and annotation and screening for antimicrobial and virulence genes. Although we have tried our best to simplify the installation and usage of PGCGAP, it may be difficult for non-bioinformatician users to master it. So, a protocol was created to help microbiologists without any experience in bioinformatics to establish their own bioinformatics platform and perform routine analysis. This protocol shows how to choose equipment, to install a Linux subsystem on a laptop with windows 10 system, to install PGCGAP and perform all analysis with an example dataset. The protocol requires a basic understanding of Linux, so an additional web page was written to help uninitiated users learn Linux and whole-genome sequencing (https://github.com/liaochenlanruo/pgcgap/wiki/Learning-bioinformatics).

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Build a Bioinformatics Analysis Platform and Apply it to Routine Analysis of Microbial Genomics and Comparative Genomics

10.21203/rs.2.21224/v4 ◽

2020 ◽

Author(s):

Hualin Liu ◽

Bingyue Xin ◽

Jinshui Zheng ◽

Hao Zhong ◽

Yun Yu ◽

...

Keyword(s):

Comparative Genomics ◽

Bioinformatics Analysis ◽

Gene Prediction ◽

Orthologous Gene ◽

Routine Analysis ◽

Simple Analysis ◽

Analysis Pipeline ◽

Operation Process ◽

Comparative Genomics Analysis ◽

Analysis Platform

Abstract Genomics and comparative genomics have been increasingly used as routine methods for general microbiological researches. However, it is usually necessary to call several tools or even write some scripts to complete some simple analysis, which is complicated for most biological researchers. To simplify the operation process, especially for the convenience of microbiologists in the analysis, here we have developed PGCGAP, a comprehensive, malleable and easily-installed prokaryotic genomics and comparative genomics analysis pipeline, which implements genome assembly, gene prediction and annotation, average nucleotide identity (ANI) calculation, phylogenetic analysis, COG annotation, pan-genome analysis, inference of orthologous gene groups, variants calling and annotation and screening for antimicrobial and virulence genes. Although we have tried our best to simplify the installation and usage of PGCGAP, it may be difficult for non-bioinformatician users to master it. So, a protocol was created to help microbiologists without any experience in bioinformatics to establish their own bioinformatics platform and perform routine analysis. This protocol shows how to choose equipment, to install a Linux subsystem on a laptop with windows 10 system, to install PGCGAP and perform all analysis with an example dataset. The protocol requires a basic understanding of Linux, so an additional web page was written to help uninitiated users learn Linux and whole-genome sequencing (http://bcam.hzau.edu.cn/linuxwgs.php).

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Build a Bioinformatic Analysis Platform and Apply it to Routine Analysis of Microbial Genomics and Comparative Genomics

10.21203/rs.2.21224/v5 ◽

2021 ◽

Author(s):

Hualin Liu ◽

Bingyue Xin ◽

Jinshui Zheng ◽

Hao Zhong ◽

Yun Yu ◽

...

Keyword(s):

Comparative Genomics ◽

Gene Prediction ◽

Distance Estimation ◽

Variant Calling ◽

Genomic Analysis ◽

Orthologous Gene ◽

Bioinformatic Analysis ◽

Comparative Genomic ◽

Operation Process ◽

Analysis Platform

Abstract More and more frequently, genomics and comparative genomics have been used as routine methods for general microbiological research. However, using several tools or even writing some scripts are required for completing a simple analysis, which is complicated for most biological researchers. To simplify the operation process, particularly for the convenience of microbiologists, here we have developed PGCGAP, a comprehensive, malleable, and easily installed prokaryotic genomic and comparative genomic analysis pipeline. PGCGAP implements genome assembly, gene prediction and annotation, genome and metagenome distance estimation, phylogenetic analysis, COG annotation, pan-genome analysis, inference of orthologous gene groups, variant calling and annotation, and screening for antimicrobial and virulence genes. Although we have tried our best to simplify the installation and usage of PGCGAP, it may be difficult for non-bioinformaticians to master it. Therefore, a protocol was created to help microbiologists without any experience in bioinformatics to establish their bioinformatics platform and perform routine analyses. This protocol shows how to choose the equipment to install a Linux subsystem on a laptop with a Windows 10 system, to install the PGCGAP and perform all analyses with an example dataset. The protocol requires a basic understanding of Linux, so an additional web page was written to help uninitiated users learn Linux and whole-genome sequencing (https://github.com/liaochenlanruo/pgcgap/wiki/Learning-bioinformatics or http://bcam.hzau.edu.cn/linuxwgs.php).

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Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

Journal of Fungi ◽

10.3390/jof7050337 ◽

2021 ◽

Vol 7 (5) ◽

pp. 337

Author(s):

Daniel Peterson ◽

Tang Li ◽

Ana M. Calvo ◽

Yanbin Yin

Keyword(s):

Comparative Genomics ◽

Orthologous Gene ◽

Gene Clusters ◽

Phytopathogenic Fungi ◽

Secreted Proteins ◽

Economic Losses ◽

Comparative Genomic ◽

Signal Peptides ◽

Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

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EuMicrobedbLite: A lightweight genomic resource and analytic platform for draft oomycete genomes

10.1101/084483 ◽

2016 ◽

Author(s):

Arijit Panda ◽

Diya Sen ◽

Arup Ghosh ◽

Akash Gupta ◽

Mathu Malar C ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Annotation ◽

Gene Prediction ◽

Trna Genes ◽

Light Weight ◽

Orthologous Genes ◽

Emboss Package ◽

Key Features ◽

Genomic Resource ◽

Analysis Platform

We have developed EuMicrobedbLite A light weight comprehensive genome resource and sequence analysis platform for oomycete organisms. EuMicrobedbLite is a successor of the VBI Microbial Database (VMD) that was built using the Genome Unified Schema (GUS). In this version, the GUS schema has been greatly simplified with removal of many obsolete modules and redesign of others to incorporate contemporary data. Several dependencies such as perl object layers used for data loading in VMD have been replaced with independent light weight scripts. EumicrobedbLite now runs on a powerful annotation engine developed at our lab called Genome Annotator Lite. Currently this database has 26 publicly available genomes and 10 EST datasets of oomycete organisms. The browser page has dynamic tracks presenting comparative genomics analyses, coding and non-coding data, tRNA genes, repeats and EST alignments. In addition, we have defined 44,777 core conserved proteins from twelve oomycete organisms that form 2974 clusters. Synteny viewing is enabled by incorporation of the Genome Synteny Viewer (GSV) tool. The user interface has undergone major changes for ease of browsing. Queryable comparative genomics information, conserved orthologous genes and pathways are among the new key features updated in this database. The browser has been upgraded to enable user upload of GFF files for quick view of genome annotation comparisons. The toolkit page integrates the EMBOSS package and has a gene prediction tool. Annotations for the organisms are updated once every six months to ensure quality. The database resource is available at www.eumicrobedb.org.

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