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Pangenome Analysis of Plant Transcripts and Coding Sequences

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Plant Comparative Genomics

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

Abstract

The pangenome of a species is the sum of the genomes of its individuals. As coding sequences often represent only a small fraction of each genome, analyzing the pangene set can be a cost-effective strategy for plants with large genomes or highly heterozygous species. Here, we describe a step-by-step protocol to analyze plant pangene sets with the software GET_HOMOLOGUES-EST . After a short introduction, where the main concepts are illustrated, the remaining sections cover the installation and typical operations required to analyze and annotate pantranscriptomes and gene sets of plants. The recipes include instructions on how to call core and accessory genes, how to compute a presence–absence pangenome matrix, and how to identify and analyze private genes, present only in some genotypes. Downstream phylogenetic analyses are also discussed.

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Acknowledgments

A first draft of this protocol was funded by Centro de Bioinformática y Biología Computacional de Colombia—BIOS for a workshop organized by Marco Cristancho at Manizales, Colombia, in March 2017. We also received funding from Fundación ARAID and the Spanish Ministry of Economy and Competitivity (CSIC13-4E-249, AGL2013-48756-R, AGL2016-80967-R, CGL2016-79790-P). PV acknowledges support from CONACyT Mexico (A1-S-11242) and PAPIIT-UNAM (IN206318 and IN209321). We thank Brett Chapman for proofreading the manuscript.

Author information

Authors and Affiliations

  1. Estación Experimental de Aula Dei-CSIC, Zaragoza, Spain

    Bruno Contreras-Moreira, Álvaro Rodríguez del Río, Carlos P. Cantalapiedra & Rubén Sancho

  2. Escuela Politécnica Superior, Universidad de Zaragoza, Huesca, Spain

    Rubén Sancho

  3. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico

    Pablo Vinuesa

Authors
  1. Bruno Contreras-Moreira
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  2. Álvaro Rodríguez del Río
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  3. Carlos P. Cantalapiedra
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  4. Rubén Sancho
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  5. Pablo Vinuesa
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Corresponding author

Correspondence to Bruno Contreras-Moreira .

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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

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Contreras-Moreira, B., del Río, Á.R., Cantalapiedra, C.P., Sancho, R., Vinuesa, P. (2022). Pangenome Analysis of Plant Transcripts and Coding Sequences. 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_9

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  • DOI: https://doi.org/10.1007/978-1-0716-2429-6_9

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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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