Skip to Main content Skip to Navigation
Book sections

Eukaryotic Pangenomes

Guy-Franck Richard 1, *
* Corresponding author
Abstract : The first eukaryotes emerged from their prokaryotic ancestors more than 1.5 billion years ago and rapidly spread over the planet, first in the ocean, later on as land animals, plants, and fungi. Taking advantage of an expanding genome complexity and flexibility, they invaded almost all known ecological niches, adapting their body plan, physiology, and metabolism to new environments. This increase in genome complexity came along with an increase in gene repertoire, mainly from molecular reassortment of existing protein domains, but sometimes from the capture of a piece of viral genome or of a transposon sequence. With increasing sequencing and computing powers, it has become possible to undertake deciphering eukaryotic genome contents to an unprecedented scale, collecting all genes belonging to a given species, aiming at compiling all essential and dispensable genes making eukaryotic life possible. In this chapter, eukaryotic core- and pangenomes concepts will be described, as well as notions of closed or open genomes. Among all eukaryotes presently sequenced, ascomycetous yeasts are arguably the most well-described clade and the pangenome of Saccharomyces cerevisiae, Candida glabrata, Candida albicans as well as Schizosaccharomyces species will be reviewed. For scientific and economical reasons, many plant genomes have been sequenced too and the gene content of soybean, cabbage, poplar, thale cress, rice, maize, and barley will be outlined. Planktonic life forms, such as Emiliana huxleyi, a chromalveolate or Micromonas pusilla, a green alga, will be detailed and their pangenomes pictured. Mechanisms generating genetic diversity, such as interspecific hybridization, whole-genome duplications, segmental duplications, horizontal gene transfer, and single-gene duplication will be depicted and exemplified. Finally, computing approaches used to calculate core- and pangenome contents will be briefly described, as well as possible future directions in eukaryotic comparative genomics.
Document type :
Book sections
Complete list of metadatas

Cited literature [121 references]  Display  Hide  Download

https://hal-pasteur.archives-ouvertes.fr/pasteur-02864633
Contributor : Guy-Franck Richard <>
Submitted on : Thursday, June 11, 2020 - 11:05:01 AM
Last modification on : Monday, June 15, 2020 - 3:10:40 PM

File

2020-Eukaryotic pangenomes.pdf
Files produced by the author(s)

Licence


Distributed under a Creative Commons Attribution 4.0 International License

Identifiers

Collections

Citation

Guy-Franck Richard. Eukaryotic Pangenomes. Hervé Tettelin; Duccio Medini. The pan-genome: diversity, dynamics and evolution of genomes., Springer, pp.253-291, 2020, 978-3-030-38280-3. ⟨10.1007/978-3-030-38281-0_12⟩. ⟨pasteur-02864633⟩

Share

Metrics

Record views

21

Files downloads

45