NL Barbosa-Morais, M Irimia, Q Pan, HY Xiong, S Gueroussov, LJ Lee, V Slobodeniuc, C Kutter, S Watt, R Colak, T Kim, CM Misquitta-Ali, MD Wilson, PM Kim, DT Odom, BJ Frey, BJ Blencowe
How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.