BuscoPhylo: A webserver for Busco-Based Phylogenomic Analysis for Non-specialists

doi:10.21203/rs.3.rs-1997596/v1

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BuscoPhylo: A webserver for Busco-Based Phylogenomic Analysis for Non-specialists

https://doi.org/10.21203/rs.3.rs-1997596/v1

This work is licensed under a CC BY 4.0 License

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Here we present BuscoPhylo tool that enables to both students and established scientists to easily perform Busco-Based Phylogenomic Analysis starting from a set of genomes sequences.

BuscoPhylo is an efficient and user-friendly web server freely accessible at https://buscophylo.inra.org.ma/. The source code, along with documentation, is freely available under an MIT license at https://github.com/alaesahbou/BuscoPhylo.

Phylogenomics

Webserver

Genome

Evolution

In the last two decades, the development of next generation sequencing technologies of DNA has revolutionized the way of deciphering the genome patrimony of the living organisms. As results, the cost of DNA sequencing has decrease drastically leading to an unprecedented flood of genomic data that is being generated through divers sequencing platforms around the world. This makes the development of high-throughput approaches handling storage, management and analysis of this huge volume of data, ever more important to overcomes the bottleneck in biological discovery.

Phylogenetic analyses lie at the core of the genomics analysis methods leading to the reconstruction of the evolutionary history of organisms [1]. Thus, taking advantage of the huge amounts of sequence data available for both model and non-model organisms, the traditional molecular phylogenetics approaches have been transformed into phylogenomic where genome-scale data were integrated [2]. As a consequence, this approach led to insightful gains in terms of phylogenetically informative characters compared to few loci used in the traditional phylogenetic studies that could be hampered by frequent horizontal gene transfers events or the low phylogenetic signal of traditional markers (housekeeping genes, SSU, etc.)[3, 4]. The phylogenomic approaches provide concrete description of molecular evolution and highly resolved relationships between groups and taxa on the tree of life [1, 5–7]. Technically, phylogenomic studies often include complex pipelines involving many steps and several tools and scripts, such as downloading, renaming, reformatting the sequences, identification of homologous sequences, alignments, graphical rendering, which makes them challenging for scientist lacking of programming experiences and willing to harness novel methods and data to reveal the evolutionary relationship within their targeted group. Many user-friendly programs and web sites were developed to provide phylogenetic analysis from sequences sets but none of them is addressing the phylogenomic approach [8–11].

In this context, BuscoPhylo, has been implemented to provide a fully automated and complete pipeline intending to quickly perform BUSCO-based phylogenomic analysis starting from assembled genome sequences as single input. The BuscoPhylo is a free, on-line and user-friendly webserver enabling the user to export phylogenomic tree ready for publication.

BuscoPhylo is developed in PHP, Python and Bash scripts as backend. HTML5, CSS3 and JavaScript are used as front-end programming language. The storage of the inputs uses MySQL.

BuscoPhylo receives FASTA files (one genome per file) as an input (Fig. 1) with a minimum of 4 genomes sequences, once a project is created. The pipeline proceeds to run BUSCO software v5.4.1 [12] for each genome sequence using the appropriate lineage and mode. The next step consists in retrieving the shared protein Single Copy Busco genes (SCBg) between queried genome sequences and creating a multi-FASTA file for each BUSCO gene family. Then, individual alignments of protiens sequences are performed using muscle v3.8.31 [13]. Subsequently, the alignments are trimmed using trimAl 1.2rev59 [14] then concatenated into one super-matrix alignment using seqkit v0.13.2 [15]. Afterwards, this step consists in inferring the tree using IQ-TREE version 1.6.12 [16] with the model selection from ModelFinder [17] using the following defaults parameters: “-bb 1000 -alrt 1000 -nt AUTO -ntmax”. The generated tree file is visualized using ETE Toolkit [18]. Finally, the results of each steps are provided in addition to phylogenetic tree inferred that could be retrieved in png, svg and pdf formats.

Interface

BuscoPhylo was developed with Graphical User Interface (GUI) that could be executed using any modern internet browser without installation of any tool or software.

BuscoPhylo enables the user to sign up for a personal account facilitating the management of the project submissions. The project manager implemented helps the user to check the project’s history and progress, reexport data and to avoid redundancy in projects running. To tackle issues of storage capacities, each project is stored for a period of 7 days.

Outputs and intermediates data

BuscoPhylo aims to provide the user with phylogenomic tree inferred from the shared BSCg in png, svg and pdf formats. Also, it provides the output Newick tree file that could be visualized using any external tool enabling advanced customization of graphical presentation of the phylogenomic tree. Furthermore, BuscoPhylo provides the ability to retrieve all intermediate files generated throughout the core pipeline including BUSCO output, shared BSCg and their individual alignment, the super-matrix alignment and the log files generated during the process of tree inferring.

Webserver and Stand-alone version

We deployed BuscoPhylo at https://buscophylo.inra.org.ma/ which enabled its use online without installation. Users are encouraged to install and run BuscoPhylo on personal computers very easily with required software installed. Advanced users can deploy BuscoPhylo on local or public servers to provide the online use to other users. Advanced users can also contribute to the development of BuscoPhylo, as its source code is available in GitHub (https://github.com/alaesahbou/BuscoPhylo).

The phylogenomic approaches have evolved with the growing of genomic datasets tackling problems of incongruencies and reconstructing well supported molecular revolutionary history of the studied organisms. The era of big data in genomics implies the development of straightforward GUI transformed pipelines and workflow to fix bioinformatics bottleneck that hindrances data analysis and interpretation. To our knowledge, BuscoPhylo is the first web tools developed for both non-specialists and specialists, which provides a complete automated phylogenomic pipeline starting from FASTA files to ready for publication phylogenomic tree. This tool will fill the gap between two major pillar of genomics analysis methods that are genome assembly and phylogenomic analysis providing the researchers much more time to focus on interpretation and downstream analysis.

We are engaged to maintain BuscoPhylo for at least 2 years. In the future, we also intend on adding a raw read as starting point for the prokaryotic organism, at first stage, including an assembly step, so users can go directly from post-sequencing steps to phylogenomics analysis.

Authors’ contributions

SK and AS designed the study and implemented the software. RM and DI performed the data analysis. SK, AS, DI and RM drafted and reviewed the manuscript. All authors edited and approved the manuscript.

Competing interests

The authors have declared no competing interests

Acknowledgements

We would like to thank MR Otman Sebbata for his help in setting up the webserver

Data availability

All data and codes used to implement this tool are available through the webserver and Github repository respectively https://buscophylo.inra.org.ma/ ; https://github.com/alaesahbou/BuscoPhylo.

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No competing interests reported.

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Editorial decision: Major revision
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You are reading this latest preprint version

BuscoPhylo: A webserver for Busco-Based Phylogenomic Analysis for Non-specialists

Status:

Version 1

Abstract

Figures

Introduction

Methods

Results

Interface

Outputs and intermediates data

Webserver and Stand-alone version

Conclusion

Declarations

References

Additional Declarations

Status:

Version 1