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Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants

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Plant Comparative Genomics

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

Abstract

In comparative genomics, the study of synteny can be a powerful method for exploring genome rearrangements, inferring genomic ancestry, defining orthology relationships, determining gene and genome duplications, and inferring gene positional conservation patterns across taxa. In this chapter, we present a step-by-step protocol for microsynteny network (SynNet) analysis, as an alternative to traditional methods of synteny comparison, where nodes in the network represent protein-coding genes and edges represent the pairwise syntenic relationships. The SynNet pipeline consists of six main steps: (1) pairwise genome comparisons between all the genomes being analyzed, (2) detection of inter- and intrasynteny blocks, (3) generation of an entire synteny database (i.e., edgelist), (4) network clustering, (5) phylogenomic profiling of the gene family of interest, and (6) evolutionary inference. The SynNet approach facilitates the rapid analysis and visualization of synteny relationships (from specific genes, specific gene families up to all genes) across a large number of genomes.

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Author information

Authors and Affiliations

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

    Samuel David Gamboa-Tuz

  2. 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

  3. State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, China

    Tao Zhao

  4. Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands

    M. Eric Schranz

Authors
  1. Samuel David Gamboa-Tuz
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  2. Alejandro Pereira-Santana
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  3. Tao Zhao
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  4. M. Eric Schranz
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Corresponding author

Correspondence to M. Eric Schranz .

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

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© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Gamboa-Tuz, S.D., Pereira-Santana, A., Zhao, T., Schranz, M.E. (2022). Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes 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_12

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  • DOI: https://doi.org/10.1007/978-1-0716-2429-6_12

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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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