Kaessmann Lab

The molecular and cellular origins and evolution of vertebrate organs

Our lab has been interested in a range of topics related to the origins and evolution of organs in mammals and other vertebrates as well as the various underlying genomic/molecular changes. In the framework of our research, we have generated and analyzed comprehensive genomics (e.g., RNA-seq) datasets based on samples from our large organ collections. We have thus illuminated the origins and functional evolution of protein-coding genes, alternative splicing, long noncoding RNAs, microRNAs, and sex chromosomes across organs and species, as well as associated phenotypic implications. More recently, we have begun to bring the work of our lab to the level of individual cells using state-of-the-art single-cell genomics technologies and bioinformatics procedures. In a major set of new projects, we seek to scrutinize the origins and evolution of the vertebrate brain and its constituent tissues and cell types based on samples from representatives of all major vertebrate lineages, ranging from jawless vertebrates (e.g., the sea lamprey) to mammals (e.g., platypus and human). In other current projects, we investigate the evolution and development of gonads, liver and intestine (dietary adaptations), and the placenta across representative mammals.

Selected publications

Original papers

Developmental origins and evolution of pallial cell types and structures in birds
Zaremba, B., Fallahshahroudi, A., Schneider, C. et al. (2024)
bioRXiv

A male-essential microRNA is key for avian sex chromosome dosage compensation
Fallahshahroudi, A., Rodriguez-Montes, L., Yousefi Taemeh, S. et al. (2024)
bioRxiv [Preprint]

Cellular development and evolution of the mammalian cerebellum
Sepp, M., Leiss, K., Murat, F. et al. (2023)
Nature 625: 788-796 URL

Sex-biased gene expression across mammalian organ development and evolution
Rodríguez-Montes, L., Ovchinnikova, S., Yuan, X. et al. (2023)
Science 382: URL

A lamprey neural cell type atlas illuminates the origins of the vertebrate brain
Lamanna, F., Hervas-Sotomayor, F., Oel, A.P. et al. (2023)
Nat Ecol Evol 7: 1714-1728 URL

The molecular evolution of spermatogenesis across mammals
Murat, F., Mbengue, N., Winge, S.B. et al. (2022)
Nature 613: 308-316 URL

Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells
Sarropoulos, I., Sepp, M., Frömel, R. et al. (2021)
Science 373: eabg4696 URL

Alternative splicing during mammalian organ development
Mazin, P.V., Khaitovich, P., Cardoso-Moreira, M. et al. (2021)
Nat Genet 53: 925-934 URL

Transcriptome and translatome co-evolution in mammals
Wang, Z., Leushkin, E., Liechti, A. et al. (2020)
Nature 588: 642-647 URL

Gene expression across mammalian organ development
Cardoso-Moreira, M., Halbert, J., Valloton, D. et al. (2019)
Nature 571: 505-509 URL

Developmental dynamics of lncRNAs across mammalian organs and species
Sarropoulos, I., Marin, R., Cardoso-Moreira, M. et al. (2019)
Nature 571: 510-514 URL

Origins and functional evolution of Y chromosomes across mammals
Cortez, D., Marin, R., Toledo-Flores, D. et al. (2014)
Nature 508: 488-493 URL

The evolution of lncRNA repertoires and expression patterns in tetrapods
Necsulea, A., Soumillon, M., Warnefors, M. et al. (2014)
Nature 505: 635-640 URL

The evolution of gene expression levels in mammalian organs
Brawand, D., Soumillon, M., Necsulea, A. et al. (2011)
Nature 478: 343-348 URL

Reviews

Evolutionary dynamics of coding and non-coding transcriptomes
Necsulea, A., Kaessmann, H. (2014)
Nat Rev Genet 15: 734-748 URL

Origins, evolution, and phenotypic impact of new genes
Kaessmann, H. (2010)
Genome Res. 20: 1313-1326 URL

RNA-based gene duplication: mechanistic and evolutionary insights
Kaessmann, H., Vinckenbosch, N., Long, M. (2008)
Nat Rev Genet 10: 19-31 URL