Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum

Abstract

Clonally reproducing plants have the potential to bear a significantly greater mutational load than sexually reproducing species. To investigate this possibility, we examined the breadth of genome-wide structural variation in a panel of monoploid/ doubled monoploid clones generated from native populations of diploid potato (Solanum tuberosum), a highly heterozygous asexually propagated plant. As rare instances of purely homozygous clones, they provided an ideal set for determining the degree of structural variation tolerated by this species and deriving its minimal gene complement. Extensive copy number variation (CNV) was uncovered, impacting 219.8 Mb (30.2%) of the potato genome with nearly 30% of genes subject to at least partial duplication or deletion, revealing the highly heterogeneous nature of the potato genome. Dispensable genes (>7000) were associated with limited transcription and/or a recent evolutionary history, with lower deletion frequency observed in genes conserved across angiosperms. Association of CNV with plant adaptation was highlighted by enrichment in gene clusters encoding functions for environmental stress response, with gene duplication playing a part in species-specific expansions of stress-related gene families. This study revealed unique impacts of CNV in a species with asexual reproductive habits and how CNV may drive adaption through evolution of key stress pathways.

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

“…Hence, the variability of sequence conservation extends to the subspecies or individual organism level (Cao et al, 2011;Hirsch et al, 2014;Marroni et al, 2014). The dispensable genome contains genes with high biological relevance, illustrated by possible roles in adaptation to abiotic and biotic stresses (Hardigan et al, 2016), species diversification and development of novel gene functions (Wang et al, 2006), and agronomic and metabolic traits (Yao et al, 2015). This clearly limits the definition of the expected gene space and, consequently, the precision and accuracy of completeness estimates of both the genome and the gene space.…”

The wheat pangenome: assembly and analysis

“…The GO terms enriched are highly concordant with what has been found in the all other major plant pangenome studies done so far , Liu et al, 2016, Jin et al, 2016, Hardigan et al, 2016, Golikz, 2016, Li et al, 2014b, Gordon et al, 2014.…”

“…In Solanum tuberosum, 55.7Mb of additional sequence were found after resequencing 12 potato landraces from 30X to 69X and de novo assembly of the unmapped reads (Hardigan et al, 2016). This additional sequence had not been captured in the original reference genome assembly and can be considered part of the potato pangenome (PGSC, 2011).…”

“…The authors found evidence that 21.9% of the genes annotated in the reference genome (DM) are dispensable and that only 30,401 genes were shared by all sequenced accessions of potato. This is still a conservative approximation of the real size of the dispensable genome of potato, because the monoploid panel used in this study has been freed from deleterious or dysfunctional haplotypes that could still be present in diploid or polyploid varieties, but would not survive anther culture and in vitro propagation (Hardigan et al, 2016). Similarly, the additional sequence assembled in this wheat study is likely an underestimation of the total sequence available in the wheat gene pool.…”

“…Other pangenomic studies have been performed in soybean (Li et al, 2014c) and Brassica oleracea (Golicz et al, 2016b) while exploratory studies have discovered and characterized gene PAV or CNV in important food crops like wheat (Saintenac et al, 2011), potato (Hardigan et al, 2016, Iovene et al, 2013 and sorghum .…”