Plant Pangenome: Impacts on Phenotypes and Evolution

Abstract

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Pan‐genome: A promising resource for noncoding RNA discovery in plants

“…(2019) compared uniformly annotated genome sequences of two more maize genotypes (W22 and PH207) with B73 and Mo17 reference genomes and found that TEs are located within or near 78% of all genes in all four maize genotypes [the authors also identified that 78% of the variable TEs are missing in at least one of the maize genotypes (Anderson et al., 2019)]. Similar genomic diversity has also been observed in other plant species (Golicz, Batley, & Edwards, 2016; Hurgobin & Edwards, 2017; Morgante et al., 2007; Tao, Zhao, Mace, Henry, & Jordan, 2018; Tranchant‐Dubreuil, Rouard, & Sabot, 2019). Additionally, recent studies showed that TEs are the prime source of ncRNAs (Hou et al., 2019).…”

“…The advantage of a sequence-based pan-genome is that it captures genic as well as nongenic sequences. On the other hand, a genebased pan-genome contains a complete set of genes or orthologous genes families within members of a species (Hubner et al, 2019;Sun et al, 2016;Tranchant-Dubreuil et al, 2019;Wang et al, 2018). The pan-genome is further categorized as the core genome or variable genome (Golicz et al, 2020;Khan et al, 2019).…”

“…The pan‐genome is further categorized as the core genome or variable genome (Golicz et al., 2020; Khan et al., 2019). The core genome refers to a common set of sequences or genes present in all individuals of a species and is described as a minimal genome required for an individual to survive and perform basic functions (Gordon et al., 2017; Segerman, 2012; Tranchant‐Dubreuil et al., 2019; Wang et al., 2018). The variable genome (also known as an accessory, dispensable, or shell genome) is a collection of sequences or genes present in only some members of a species (Gordon et al., 2017; Li et al., 2014; Segerman, 2012; Vernikos, Medini, Riley, & Tettelin, 2015) (Supplemental Figure S2a).…”

“…The variable genome (also known as an accessory, dispensable, or shell genome) is a collection of sequences or genes present in only some members of a species (Gordon et al., 2017; Li et al., 2014; Segerman, 2012; Vernikos, Medini, Riley, & Tettelin, 2015) (Supplemental Figure S2a). Genes present in the variable genome of an individual are usually involved in biotic and abiotic stress responses (Tranchant‐Dubreuil et al., 2019). The core and variable genomes are further subdivided into core or soft‐core and variable or member‐specific genomes, respectively (Gordon et al., 2017; Medini, Donati, Tettelin, Masignani, & Rappuoli, 2005; Tranchant‐Dubreuil et al., 2019).…”

“…Genes present in the variable genome of an individual are usually involved in biotic and abiotic stress responses (Tranchant‐Dubreuil et al., 2019). The core and variable genomes are further subdivided into core or soft‐core and variable or member‐specific genomes, respectively (Gordon et al., 2017; Medini, Donati, Tettelin, Masignani, & Rappuoli, 2005; Tranchant‐Dubreuil et al., 2019).…”