Coming of age: orphan genes in plants

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…5b). This observed age dependence, also found in Arabidopsis 56,62 , may indicate that longer initial coding lengths are more likely to survive over time or that coding sequences that survive gradually lengthen over time through chance removal of stop codons 58 . Gene expression was also positively correlated with age, both when assessed qualitatively ( Supplementary Fig.…”

“…Despite some methodological concerns 54 , it is widely recognized that new genes arise continuously across all domains of life [55][56][57] . The fraction of Oryzeae-specific genes with syntenic orthologs in a second species was not substantially lower than for the two older groups, with 86% as compared to 93% and 97% for the Poaceae and angiosperm-derived families, respectively (Supplementary Table 38).…”

Deoxynivalenol resistance as a component of FHB resistance

“…There is increasing evidence that organisms have evolved taxonomically restricted 'orphan' genes to help them overcome environmental stress (Arendsee et al 2014;Perochon et al 2015). DON resistance research has contributed to our understanding of cereal evolution in that a Pooideae-restricted gene was discovered based on its responsiveness to the toxin.…”

Orthodox Seeds and Resurrection Plants: Two of a Kind?

“…A large fraction of the contigs assembled from hydrated, dehydrated, desiccated, and rehydrated samples of the resurrection species Sporobolus stapfianus (Yobi et al, 2017), Craterostigma plantagineum (Giarola and Bartels, 2015), and Haberlea rhodopensis (Gechev et al, 2013) predict the presence of protein sequences that bear little or no similarity to proteins in public databanks. Orphan or taxonomically restricted genes are genes without known homologs that either evolved de novo from noncoding sequences or were derived from older coding material (Arendsee et al, 2014). Whereas ;29% of annotated genes in B. hygrometrica are orphan genes (Xiao et al, 2015), only 5.4% in X. viscosa are orphan genes, with 5% to 15% being fairly typical in various species (Arendsee et al, 2014).…”

“…Orphan or taxonomically restricted genes are genes without known homologs that either evolved de novo from noncoding sequences or were derived from older coding material (Arendsee et al, 2014). Whereas ;29% of annotated genes in B. hygrometrica are orphan genes (Xiao et al, 2015), only 5.4% in X. viscosa are orphan genes, with 5% to 15% being fairly typical in various species (Arendsee et al, 2014). These findings suggest that the acquisition of vegetative DT in X. viscosa relied more on the redirection of genetic information than on the genesis of novel genes.…”