Evolution of tissue-specific expression of ancestral genes across vertebrates and insects

Abstract

Regulation of gene expression is arguably the main mechanism contributing to tissue phenotypic diversity within and between species. Here, we assembled a vast RNA-seq dataset covering twenty bilaterian species and eight tissues, selecting a specular phylogeny that allowed both the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-differential genes but even larger groups that diverged to define vertebrate and insect tissues. Consistently, systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with numerous gains being associated with the emergence of unique phenotypes. Such pervasive evolution of tissue-specificity was boosted by gene duplication coupled with specialization, including an unappreciated prolonged effect of whole genome duplications during recent vertebrate evolution.

Large-scale genome analyses provide insights into Hymenoptera evolution

“…= 0.03) (Supplementary Table 1). In order to minimize the impact of potential gene annotation issues on subsequent analysis, we then employed an alignment-based approach to identify potential broken/chimeric genes 10 , correcting about 3.6% of total genes (Supplementary Table 2). After gene corrections, orthology inference produced 33,405 orthogroups (OGs, also referred to as gene families), with 25.1% of these present in over 70% of hymenopterans (Figure 1, Supplementary Figure 1, and Supplementary Table 3).…”

“…Genes assigned to two or more OGs by Broccoli v1.2 were considered chimeric genes, while those that belonged to the same OG, were sequenced on the same strand on the same chromosome, showed low sequence similarity (less than 30% calculated using MAFFT v7.310 90 ), and matched different portions of longest homolog protein in Nasonia vitripennis were considered broken genes. Detailed correction procedures for chimeric and broken genes were referenced in a previous study 10 .…”

Alternative splicing decouples local from global PRC2 activity

“…Quantification of the samples for human (Homo sapiens), mouse (Mus musculus), cow (Bos taurus), chicken (Gallus gallus), and zebrafish (Danio rerio) were retrieved from vastDB (vastdb.crg.eu). The samples of opossum (Monodelphis domestica) and elephant shark (Callorhinchus milli) were analysed previously 37 . The PSI of SUZ12 exon 4 for manatee (Trichechus manatus latirostris), elephant (Loxodonta africana), armadillo (Dasypus novemcinctus) and platypus (Ornithorhynchus anatinus) were quantified as follow: a 42nt exon-exon junction ebwt-library for SUZ12 exons 3, 4, and 5 was generated using bowtie-build v1.1.2.…”