De novo assembly and evolutionary analyses of liver-expressed genes in 16 mammal species
Seminar Room 1, Newton Institute
Changes in gene regulation have been proposed as critical in the evolution of phenotypic diversity of primates. However, the lack of high-quality reference genomes for most species and the limited number of independently derived transcripts for non-human primates has made it difficult to study gene regulation across multiple primates. To overcome these problems, we used massively-parallel sequencing to interrogate mRNA samples extracted from the livers of 16 species (12 primates including human, and 4 non-primate out groups; 4 samples per species). Of the 12 primate species, 8 do not have currently available reference genome sequences (vervet, galago, slow loris, and 5 lemur species), which means that we had to assemble the transcriptomes de novo for these species. This study design results in nucleotide sequence, quantitative expression, and gene structure data from thousands of genes, providing insight into gene regulation and sequence evolution across a broad spectrum of primate species.
In this talk, I will describe the considerable statistical and computational challenges that arose when assembling transcriptomes de novo and how we analyzed the data generated. I will also discuss sets of genes whose expression level patterns are consistent with the action of natural selection along individual or ancestral primate lineages, and describe the relationship between alternative splicing within species and complete exon gains and losses between species.