TBG-Project Michael Hiller

Comparative Genomics

Genomic basis of phenotypes with translational potential

Myotis myotis © Oliver Farcy

Institution: Senckenberg Gesellschaft für Naturforschung

Prof. Dr. Michael Hiller

Summary

Comparative genomics can yield novel insights into species’ biology and the genomic underpinnings of interesting traits. In this project, we study the genomic basis of traits that have translational potential. For example, bats live longer than most other mammals after correcting for body size, but they rarely get cancer and show few signs of senescence. Infections with viruses that are deadly for humans is often asymptomatic in bats. Thus, bats are important models for healthy aging, enhanced resistance to tumorigenesis and infectious diseases. Furthermore, we are interested in traits such as adaptations to sugar- or protein-rich diets that evolved in different groups of bats and birds, and dormancy phenotypes which are present in numerous independent mammalian and bird lineages. Following Max Planck’s famous statement “insight must precede application”, a better understanding of the genomic changes that are relevant for such traits is a first step to apply new knowledge in biomedicine and other areas. 

To study these traits, we are generating and analyzing high-quality genome assemblies of strategically-selected species in collaboration with the TBG lab center, annotate genes by combining homology-based methods with newly generated transcriptomics data, build multiple genome alignments and conduct systematic screens for evolutionary changes in genes and regulatory elements.

TBG Project team

  • Dimitrios-Georgios Kontopoulos
  • Ariadna Morales
  • Ekaterina Osipova
  • Leon Hilgers
  • Michael Hiller (PI)

Group expertise / Methods

    • Gene annotation integrating gene projections by our TOGA (Tool to infer Orthologs from Genome Alignments) method, with de novo and homology-based gene predictions and transcriptomics data
    • Pairwise and multiple genome alignments
    • Screens for gene lossgain, selection, parallel substitutions and differences in regulatory elements (REforge, TFforge)
    • Genome sequencing with PacBio HiFi and chromosome-conformation capture (Hi-C) reads
    • Genome assembly, chromosome-scale scaffolding and base error correction

      More information is here.

Publications:

Jebb D, Huang Z, Pippel M, Hughes GM, Lavrichenko K, Devanna P, Winkler S, Jermiin LS, Skirmuntt EC, Katzourakis A, Burkitt-Gray L, Ray DA, Sullivan KAM, Roscito JG, Kirilenko BM, Dávalos LM, Corthals AP, Power ML, Jones G, Ransome RD, Dechmann D, Locatelli AG, Puechmaille SJ, Fedrigo O, Jarvis ED, Hiller M, Vernes SC, Myers EW, Teeling EC.  Six reference-quality genomes reveal evolution of bat adaptations. Nature, 583, 578–584, 2020

Wang LF, Gamage AM, Chan WOY, Hiller M, Teeling EC. Decoding bat immunity: the need for a coordinated research approach. Nature Reviews Immunology, 21, 269–271, 2021

Blumer M, Brown T, Freitas MB, Destro AL, Oliveira JA, Morales A, Schell T, Greve C, Pippel M, Jebb D, Hecker N, Ahmed AW, Kirilenko BM, Foote M, Janke A, Lim BK, Hiller M. Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding. Science Advances, 2022

Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M #. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Reports, 38(3):110280, 2022