Legume pangenome construction using an iterative mapping and assembly approach

Haifei Hu, Yuxuan Yuan, Philipp E. Bayer, Cassandria T. Fernandez, Armin Scheben, Agnieszka A. Golicz, David Edwards

Research output: Chapter in Book/Conference paperChapter

Abstract

A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.

Original languageEnglish
Title of host publicationLegume Genomics
Subtitle of host publicationMethods and Protocols
EditorsMukesh Jain, Rohini Garg
Place of PublicationNew York
PublisherHumana Press
Pages35-47
Number of pages13
Volume2107
ISBN (Electronic)978-1-0716-0235-5
ISBN (Print)978-1-0716-0234-8
DOIs
Publication statusPublished - 1 Jan 2020

Publication series

NameMethods in Molecular Biology
Volume2107
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Fabaceae
Genome
Technology
Phenotype
Genes

Cite this

Hu, H., Yuan, Y., Bayer, P. E., Fernandez, C. T., Scheben, A., Golicz, A. A., & Edwards, D. (2020). Legume pangenome construction using an iterative mapping and assembly approach. In M. Jain, & R. Garg (Eds.), Legume Genomics: Methods and Protocols (Vol. 2107, pp. 35-47). (Methods in Molecular Biology; Vol. 2107). New York: Humana Press. https://doi.org/10.1007/978-1-0716-0235-5_3
Hu, Haifei ; Yuan, Yuxuan ; Bayer, Philipp E. ; Fernandez, Cassandria T. ; Scheben, Armin ; Golicz, Agnieszka A. ; Edwards, David. / Legume pangenome construction using an iterative mapping and assembly approach. Legume Genomics: Methods and Protocols. editor / Mukesh Jain ; Rohini Garg. Vol. 2107 New York : Humana Press, 2020. pp. 35-47 (Methods in Molecular Biology).
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Hu, H, Yuan, Y, Bayer, PE, Fernandez, CT, Scheben, A, Golicz, AA & Edwards, D 2020, Legume pangenome construction using an iterative mapping and assembly approach. in M Jain & R Garg (eds), Legume Genomics: Methods and Protocols. vol. 2107, Methods in Molecular Biology, vol. 2107, Humana Press, New York, pp. 35-47. https://doi.org/10.1007/978-1-0716-0235-5_3

Legume pangenome construction using an iterative mapping and assembly approach. / Hu, Haifei; Yuan, Yuxuan; Bayer, Philipp E.; Fernandez, Cassandria T.; Scheben, Armin; Golicz, Agnieszka A.; Edwards, David.

Legume Genomics: Methods and Protocols. ed. / Mukesh Jain; Rohini Garg. Vol. 2107 New York : Humana Press, 2020. p. 35-47 (Methods in Molecular Biology; Vol. 2107).

Research output: Chapter in Book/Conference paperChapter

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AU - Golicz, Agnieszka A.

AU - Edwards, David

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AB - A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.

KW - Assembly

KW - De novo

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KW - Mapping

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Hu H, Yuan Y, Bayer PE, Fernandez CT, Scheben A, Golicz AA et al. Legume pangenome construction using an iterative mapping and assembly approach. In Jain M, Garg R, editors, Legume Genomics: Methods and Protocols. Vol. 2107. New York: Humana Press. 2020. p. 35-47. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-0716-0235-5_3