Genomic Biomonitoring

 

Meta-OMICS group

Institution: Senckenberg Society for Nature Research

In the Meta-OMICS group we use high-throughput sequencing approaches to study the diversity and evolution of a variety of animal taxa, with a particular interest in aquatic and semi-aquatic groups. Extreme environments such as the polar regions, and deep sea/subterranean habitats present excellent grounds for the study of eco-evolutionary interactions and mechanisms of environmental adaptation. Our work includes development of methodologies for environmental monitoring and genomic biomonitoring, such as protocol development and novel applications of eDNA metabarcoding, metagenomics, all the way to reference genome sequencing and comparative analysis. We use bioinformatics for analysis of large datasets and establishment of pipelines for HTS data processing.
Group page: www.ilianabista.com

Group members

  • Dr. Iliana  Bista  (PI)
  • Alexandra Lino
  • Jacopo Martelossi
  • Emma Goerres 
  • Allanah Prinssen 

Group expertise, Methods

  • Metabarcoding, metagenomics, aquatic environmental DNA (eDNA)
  • DNA extraction of challenging samples (eDNA, community, HMW DNA)
  • Reference genome sequencing (PacBio)
  • DNA based biodiversity monitoring
  • Genomic adaptation to extreme environments
  • Comparative genomics

Genomes sequenced (selected)

  • Antarctic notothenioid fish
  • Aristotle’s catfish
  • Isopod crustacean (Asellidae)

Asellus aquaticus – © CC01, Gbif

Notothenia rossii  – © British Antarctic Surve

Selected publications

 

Bista, I., Collins, M., Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium (2024). The genome sequence of the marbled rockcod, Notothenia rossii (Richardson, 1844). Wellcome Open Research, 9:227.

Perry, W.B., Seymour, M., Orsini, L., Jâms, I.B., Milner, N., Edwards, F., Harvey, R., de Bruyn, M., Bista, I., Walsh, K., Emmett, B., Blackman, R., Altermatt,, F., Lawson Handley, L., Mächler, E., Deiner, K., Bik, H.M., Carvalho, G., Colbourne, J., Cosby, B.J., Durance, I., Creer, S (2024). An integrated spatio-temporal view of riverine biodiversity using environmental DNA metabarcoding Nature Communications, 15, 4372.

Bista, I.*, Wood, J. M. D., Desvignes, T., McCarthy, S. A., Matschiner, M., Ning Z., Tracey A., Torrance J., Sims Y., Chow W., Smith M., Oliver K., Haggerty L., Salzburger W., Postlethwait J.H., Howe K., Clark M.S., Detrich III H.W., Cheng C.H.C., Miska E.A., Durbin R.*, (2023). Genomics of cold adaptations in the Antarctic notothenioid fish radiation, Nature Communications, 14, 3412. (*Corresponding author). https://doi.org/10.1038/s41467-023-38567-6

Formenti G., Theissinger K., Fernandes C., Bista I., Bombarely A., Bleidorn C., Ciofi C., Crottini A, Godoy J.A., Höglund J., Malukiewicz J., Mouton A., Oomen R. A., Paez S., Palsbøll P. J, Pampoulie C., Ruiz-López M.J, Svardal H., Theofanopoulou C., deVries J., Waldvogel A.M., Zhang G., Mazzoni C.J., Jarvis E.D., Bálint M., and The European Reference Genome Atlas (ERGA) Consortium. (2022). The era of reference genomes in conservation genomics. Trends in Ecology & Evolution, 37(3), 197–202.

Dahn H. A., Mountcastle J., Balacco J., Winkler S., Bista I., Schmitt A. D., Vinnere-Pettersson O., Formenti G., Oliver K., Smith M., Tan W., Kraus A., Mac S., Komoroske L. M., Lama T., Crawford A. J., Murphy R. W., Brown S., Scott A. F., Morin P. A, Jarvis A. D., Fedrigo O. (2022). Benchmarking ultra-high molecular weight DNA preservation protocols for long-read and long-range sequencing. GigaScience, Vol. 11, (2022), giac068.  

Rhie A., McCarthy S. A., Fedrigo O., Damas J., Formenti G., Koren, S., Uliano-Silva M., Chow W., Fungtammasan A., Kim J., Lee C., Ko B. J., Chaisson M., Gedman G. L., Cantin L. J., Thibaud-Nissen F., Haggerty L., Bista I., Smith M., … Jarvis E. D.  (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737–746.

Bohmann K., Elbrecht V., Carøe C., Bista I., Leese, F., Bunce M., Yu D.W, Seymour M., Dumbrell A.J., Creer S. (2022). Strategies for sample labelling and library preparation in DNA metabarcoding studies. Molecular Ecology Resources, 22(4), 1231–1246.

Bista I.*, Carvalho G. R., Tang M., Walsh K., Zhou X., Hajibabaei M., Shokralla S., Seymour M., Bradley D., Liu S., Christmas M., Creer S.* (2018). Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples. Molecular Ecology Resources, 1–15 (*Corresponding author).

Bista I. *, Carvalho G.R., Walsh K., Seymour M., Hajibabaei M., Lallias D., Christmas M., Creer S.* (2017). Annual time-series analysis of aqueous eDNA reveals ecologically relevant dynamics of lake ecosystem biodiversity. Nature Communications, 8, 14087 (*Corresponding author).