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Orthology Prediction and Phylogenetic Analysis Methods in Plants

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Plant Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2512))

Abstract

In this chapter, we outline a pipeline for ortholog prediction and phylogenetic analysis in plants. This computational pipeline uses algorithms from different software to enable bioinformatic-beginner biologists to predict orthologs that can be shared with many distinct plant nonmodel and model species and identify gene loss events. Prediction of orthologs allows (1) investigation of the evolutionary relationships of plant genomes, (2) discovery of their origin, function, and (3) the impact of their adaptability to the environment.

We developed a pipeline to fit, not only eukaryote but also prokaryote organisms, with small or large genomes. All results acquired from the orthologs predication will enable phylogenetic tree construction, using gene and species (phylogenomic) phylogeny approaches.

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Acknowledgments

This work was supported by the Czech Academy of Sciences, ERC-CZ, grant number [ERC200961901]. The work also supported by the Science and Technology Development Fund (STDF) and the Partnership for Research and Innovation in the Mediterranean Area (PRIMA), GENDIBAR project. Computational resources were provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, funded under the programme “Projects of Large Research, Development, and Innovations Infrastructures.” The authors thank Dr. Chayma Ben Saoud for improving the graphs, and Dr. Iva Mozgová for proofreading the manuscript.

Author information

Authors and Affiliations

  1. Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic

    Abdoallah Sharaf

  2. Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt

    Abdoallah Sharaf & Sawsan Elateek

Authors
  1. Abdoallah Sharaf
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  2. Sawsan Elateek
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Corresponding author

Correspondence to Abdoallah Sharaf .

Editor information

Editors and Affiliations

  1. Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Jalisco, Mexico

    Alejandro Pereira-Santana

  2. Unidad de Biotecnología, Centro de Investigación CientÚfica de Yucatán, Mérida, Yucatán, Mexico

    Samuel David Gamboa-Tuz

  3. Unidad de Biotecnología., Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico

    Luis Carlos Rodríguez-Zapata

1 Electronic Supplementary Material

File S1

A Jackhammer output example file contains homology search results (TXT 801 bytes)

File S2

An emapper output example file with the query protein sequence rbcL annotation, including the target COG/KOG category (TXT 2 kb)

File S3

An emapper output example file with the Selaginella moellendorffii rbcL hits sequences annotation, including the COG/KOG category (TXT 3 kb)

File S4

An emapper output example file with the Zea mays rbcL hits sequences annotation. The only hit “tr|A0A1D6EVW0|A0A1D6EVW0_MAIZE” with different annotation and COG category is highlighted in yellow (XLSX 6 kb)

File S5

A hmmscan output example file contains domain screening search results (TXT 1 kb)

File S6

A list of required software and packages which are available in conda (TXT 1 kb)

File S7

A Bayesian Inference phylogeny using the example data (TXT 985 bytes)

File S8

A map file for the ASTRAL-III tool based on the example phylogenetic trees (TXT 725 bytes)

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Sharaf, A., Elateek, S. (2022). Orthology Prediction and Phylogenetic Analysis Methods in Plants. In: Pereira-Santana, A., Gamboa-Tuz, S.D., Rodríguez-Zapata, L.C. (eds) Plant Comparative Genomics. Methods in Molecular Biology, vol 2512. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2429-6_1

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  • DOI: https://doi.org/10.1007/978-1-0716-2429-6_1

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2428-9

  • Online ISBN: 978-1-0716-2429-6

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