Transcriptome innovations in primates revealed by single-molecule long-read sequencing

Abstract

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Around half of the captured isoforms are not annotated in their reference genomes, significantly expanding the gene models in primates. Furthermore, our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these evolutionary innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.

Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes

“…However, except for one RBMY2 transcript from gorilla, no ampliconic transcripts were reported as a cell-type marker for any of the analyzed species. Additionally, it would be of interest to confirm all the transcripts we discovered in our study at the protein level, as was done in (Ferrández-Peral et al 2022).…”

Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations

“…Ferrandez-Peral et al 12 found a correlation between fast-evolving immune genes and high isoform diversity in their analysis of isoform diversity in lymphoblastoid cell lines from primates. They suggested that this could point to an adaptive role for isoforms, but this inference is too indirect to provide a direct link.…”

“…Another strength of our dataset lies in the possibility of systematic comparisons of fixation probabilities between natural populations, subspecies, and species. Within such a framework, one can make inferences on microevolutionary patterns that were not possible in previous comparative studies on alternative splicing in more or less distantly related species 11,12,[46][47][48][49][50][51][52] . In particular, our data allow us to directly assess whether the large isoform diversity generated through alternative splicing could be a major mechanism to create adaptive genetic novelty [2][3][4] .…”

“…The recent development of long-read single-molecule sequencing technologies has enabled the capture of the full-length isoform diversity 10 , further facilitating the comparative analysis of alternative isoforms at the global transcript level in different species 11,12 . This has revealed a very high diversity of isoforms but it remains open how much of this is due to noise in the splicing machinery.…”

“…They showed not only a similar global pattern of isoform diversity between human and mouse, but also striking differences on certain genes between these two species. Another recent study from Ferrandez-Peral L (Ferrandez-Peral et al 2022) generated an extensive full-length isoform catalog in primates, and found that a high isoform diversity in immune genes correlates with signals of positive selection in the coding regions of the genes. These between-species comparison studies have provided insights into the complexity of alternative isoforms at a deep evolutionary time scale.…”