Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics

Abstract

BackgroundLong-established protein-coding genes may lose their coding potential during evolution (“unitary gene loss”). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated and remain largely elusive.ResultsUsing a locally developed pipeline, we identified 129 unitary gene loss events for long-established protein-coding genes from four representative species of Poaceae, i.e. brachypodium, rice, sorghum and maize. Functional annotation suggested that the lost genes in all or most of Poaceae species are enriched for genes involved in development and response to endogenous stimulus. We also found that 44 mutated genomic loci of lost genes, which we referred as relics, were still actively transcribed, and of which 84% (37 of 44) showed significantly differential expression across different tissues. More interestingly, we found that there were totally five expressed relics may function as competitive endogenous RNA in brachypodium, rice and sorghum genome.ConclusionsBased on comparative genomics and transcriptome data, we firstly compiled a comprehensive catalogue of unitary gene loss events in Poaceae species and characterized a statistically significant functional preference for these lost genes as well showed the potential of relics functioning as competitive endogenous RNAs in Poaceae genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0345-x) contains supplementary material, which is available to authorized users.

Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome

“…Orphan genes are sometimes considered as de novo genes originating from ancestral non‐coding sequences (Chen et al, 1997; Knowles & McLysaght, 2009; Li et al, 2010; Murphy & McLysaght, 2012; Xie et al, 2012). In fact, de novo formation is just one way by which orphan genes can form, as many orphan genes are derived from other distinct evolutionary processes, such as the duplication‐divergence mechanism (Schlotterer, 2015; Moyers & Zhang, 2016), TE exaptation (Toll‐Riera et al, 2009), loss of homologous genes in related species (Zhao et al, 2015), repetition of low‐complexity short peptides (Chen et al, 1997; Cheng & Chen, 1999), and horizontal gene transfer from fast‐evolving donors (Keeling & Palmer, 2008; Husnik & McCutcheon, 2018). An orphan gene can also originate through a combination of several origin mechanisms, such as the mixed origin mechanism in nematodes (Prabh & Rödelsperger, 2019).…”

A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes

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Estudos cromossômicos e reprodutivos em espécies de Mesosetum Steud. (Poaceae: Paspaleae)

“…A evolução das espécies de Poaceae seguiu uma sequência de eventos de aumento e redução do genoma Soreng et al 2015;Wang et al 2015). Enquanto o aumento do genoma ocorreu relacionado à poliploidia, a redução do genoma processou-se paralela à diploidização Kellog & Benetzen 2004;Parteson et al 2004;Zhao et al 2015;Wang et al 2015;.…”