Nowhere in the gene model definition of a gene is there a need that the gene play a role in specifying the characteristics of an organism. Small differences in which evidence is used to identify genes or how different evidence is weighted can produce big differences in how many genes are identified in a genome (Schnable et al., 2009 Kawahara et al., 2013 Jiao et al., 2017). The sequence may be identified by machine learning algorithms trained on other annotated genes. The sequence may show homology to a previously annotated gene either in the same species or a different one. There may be direct evidence of transcription and/or translation in the target species. The evidence for a gene model can come from one of several sources (Yandell & Ence, 2012 Mudge & Harrow, 2016).
A gene model is a region of the genome which is thought to be transcribed into RNA, and that RNA is, in turn, believed to be either translated into protein, or belong to one of a number of defined classes of noncoding RNA genes (Gerstein et al., 2007).
The second concept is the ‘gene model’ definition of a gene. In this original definition, a gene is defined by its impact on the characteristics of an organism. A few years later he explained the origin of the word gene like this: ‘the word Gene is completely free from any hypothesis, it only expresses the assured fact that, at any rate, many characteristics of the organism are conditioned by special, separable, and therefore self-existent fundamentals that occur in the gametes. I am embarrassed to admit how long it took me to realize that there are two very different concepts that are each represented by the word ‘gene.’ The first concept is the definition of a gene that comes from Wilhelm Ludvig Johannsen, who first coined the word gene in 1905. Which genes move around over evolutionary time. Which genes stay in the same place in the genome. As a plant geneticist, I spend a lot of time thinking about genes.
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