Completed on 15 Jun 2017 by Guillaume Cornelis. Sourced from http://biorxiv.org/content/early/2017/05/12/137554.
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Awesome paper on placental evolution and transcriptome!
It is always surprising to me to see the strong conservation of placental function despite the tremendous diversity of structure and development among species. The pre-eclampsia gene category is particularly interesting.
Regarding the syncytiotrophoblast category, I am surprised to see that you don't detect expression of syncytin genes in Bonobo and dog, as such genes have been previously described in those species. Those genes are derived from transposable elements (namely endogenous retroviruses) and are rarely annotated as cellular genes (e.g. the syncytin-car1 gene in Carnivora species is annotated on the UCSC genome database, but not Ensembl). In addition, identification of these genes is sometimes challenging because of their independent origin from different viruses that show only limited sequence conservation. I would suggest looking at the genomic regions corresponding to those genes in those species (contig JH650268 and JH650565 for ERV-W1 and ERV-FRD1 in Pan paniscus and Chr3 for Syncytin-car1 in dog) and see if you could detect reads in those genomic regions.
I am also curious about the differences between the Eutherian and marsupial lineages. What would be the genes specific to the marsupial lineage, and reciprocally the eutherian specific genes and do the highlight specific functions of the eutherian and marsupial placenta?
Anyway, amazing work. Congratulations!