[According to Ensembl86] the human genome encodes 58,037 genes, of which approximately one-third are protein-coding (19,950), and yields 198,093 transcripts. By comparison, the mouse genome encodes 48,709 genes, of which half are protein-coding (22,018 genes), and yields 118,925 transcripts overall.The very latest Ensembl estimates (April 2017) for Homo sapiens and Mus musculus are similar. The difference in gene numbers between mouse and human is not significant according to the authors ...
The discrepancy in total number of annotated genes between the two species is unlikely to reflect differences in underlying biology, and can be attributed to the less advanced state of the mouse annotation.This is correct but it doesn't explain the other numbers. There's general agreement on the number of protein-coding genes in mammals. They all have about 20,000 genes. There is no agreement on the number of genes for functional noncoding RNAs. In its latest build, Ensemble says there are 14,727 lncRNA genes, 5,362 genes for small noncoding RNAs, and 2,222 other genes for nocoding RNAs. The total number of non-protein-coding genes is 22,311.
There is no solid evidence to support this claim. It's true there are many transcripts resembling functional noncoding RNAs but claiming these identify true genes requires evidence that they have a biological function. It would be okay to call them "potential" genes or "possible" genes but the annotators are going beyond the data when they decide that these are actually genes.
Breschi et al. mention the number of transcripts. I don't know what method Ensembl uses to identify a functional transcript. Are these splice variants of protein-coding genes?
The rest of the review discusses the similarities between human and mouse genes. They point out, correctly, that about 16,000 protein-coding genes are orthologous. With respect to lncRNAs they discuss all the problems in comparing human and mouse lncRNA and conclude that "... the current catalogues of orthologous lncRNAs are still highly incomplete and inaccurate." There are several studies suggesting that only 1,000-2,000 lncRNAs are orthologous. Unfortunately, there's very little overlap between the two most comprehensive studies (189 lncRNAs in common).
There are two obvious possibilities. First, it's possible that these RNAs are just due to transcriptional noise and that's why the ones in the mouse and human genomes are different. Second, all these RNAs are functional but the genes have arisen separately in the two lineages. This means that about 10,000 genes for biologically functional lncRNAs have arisen in each of the genomes over the past 100 million years.
Breschi et al. don't discuss the first possibility.
Breschi, A., Gingeras, T.R., and Guigó, R. (2017) Comparative transcriptomics in human and mouse. Nature Reviews Genetics [doi: 10.1038/nrg.2017.19]