Supplementary material from "Phosphotyrosine signaling and the origin of animal multicellularity"

The evolution of multicellular animals (i.e., metazoans) from a unicellular ancestor is one of the most important yet least understood evolutionary transitions. Historically, given its indispensable functions in intercellular communication and exclusive presence in metazoans, phosphotyrosine (pTyr) signaling was considered a metazoan-specific evolutionary innovation that might have contributed to the origin of metazoan multicellularity. However, recent studies have led to a new understanding of pTyr signaling evolution and its role in the metazoan origin. Sequence analyses have unraveled a much earlier emergence of pTyr signaling in eukaryotic evolution. Even so, several distinct properties of holozoan pTyr signaling may have paved the way for a hypothesized functional transition of pTyr signaling at the multicellular origin, from environmental sensing to intercellular communication, and for it to evolve as a powerful intercellular signaling system for multicellularity. Biochemical analyses of premetazoan pTyr signaling components have further revealed the premetazoan origin of many key features of metazoan pTyr signaling, and the metazoan establishment of others, including the Csk-mediated negative regulation of the activity of Src, a conserved tyrosine kinase in the Holozoa. Finally, potential future directions are discussed, with a stress on the biological functions of premetazoan pTyr signaling via newly developed gene manipulation tools in non-animal holozoans

The Evolutionary Panorama of Organ-Specifically Expressed or Repressed Orthologous Genes in Nine Vertebrate Species

<div><p>RNA sequencing (RNA-Seq) technology provides the detailed transcriptomic information for a biological sample. Using the RNA-Seq data of six organs from nine vertebrate species, we identified a number of organ-specifically expressed or repressed orthologous genes whose expression patterns are mostly conserved across nine species. Our analyses show the following results: (i) About 80% of these genes have a chordate or more ancient origin and more than half of them are the legacy of one or multiple rounds of large-scale gene duplication events. (ii) Their evolutionary rates are shaped by the organ in which they are expressed or repressed, e.g. the genes specially expressed in testis and liver generally evolve more than twice as fast as the ones specially expressed in brain and cerebellum. The organ-specific transcription factors were discriminated from these genes. The ChIP-seq data from the ENCODE project also revealed the transcription-related factors that might be involved in regulating human organ-specifically expressed or repressed genes. Some of them are shared by all six human organs. The comparison of ENCODE data with mouse/chicken ChIP-seq data proposes that organ-specifically expressed or repressed orthologous genes are regulated in various combinatorial fashions in different species, although their expression features are conserved among these species. We found that the duplication events in some gene families might help explain the quick organ/tissue divergence in vertebrate lineage. The phylogenetic analysis of testis-specifically expressed genes suggests that some of them are prone to develop new functions for other organs/tissues.</p></div

Phylogenetic tree of MACC1 gene family.

<p>A <i>Ciona intestinalis</i> gene was selected as the outgroup to root the tree and only the cladogram is shown. The tree node where a possible large-scale duplication event happened is marked with a filled black square ■. 7 means the gene’s expression level is higher than 95% of all genes expressed in the organ. 6 is between 95% and 85%. 5 is between 85% and 65%. 4 is between 65% and 35%. 3 is between 35% and 15%. 2 is between 15% and 5%. 1 is lower than 5%. 0 means no expression at all. N is not available.</p

Comparison of human ChIPseq data with mouse/chicken ChIPseq data.

<p>Comparison of human ChIPseq data with mouse/chicken ChIPseq data.</p

Distribution of the number orthologous clusters in the gene families containing OSER genes.

<p>Distribution of the number orthologous clusters in the gene families containing OSER genes.</p

Classification of OSER clusters according to their evolutionary origins.

<p>Classification of OSER clusters according to their evolutionary origins.</p

Organ-specifically expressed or repressed transcriptional factors.

<p>Organ-specifically expressed or repressed transcriptional factors.</p

Five most common transcription-related factors might be involved in regulating OSER genes.

<p>Five most common transcription-related factors might be involved in regulating OSER genes.</p

The evolutionary origins of OSER clusters in each organ/tissue.

<p>The evolutionary origins of OSER clusters in each organ/tissue.</p

The number of specifically expressed or repressed (OSER) orthologous clusters in each organ/tissue.

<p>*The OSER clusters in nervous tissue show no significant expression difference between brain and cerebellum while have a distinct expression pattern between nervous tissues and the other organs.</p><p>The number of specifically expressed or repressed (OSER) orthologous clusters in each organ/tissue.</p