On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Howard, C.; Denton, A.; Jackson, B.; Bates, A.; Jay, J.; Yatsenko, H.; Raman, P. S.; Thomas, A.; Oatley, G.; do Amaral, R. V.; Göktan, Z. E.; Gomez, J. P. N.; Clayton Lucey, I.; Sinclair, E.; Quail, M. A.; Blaxter, M.; Howe, K.; Lawniczak, M.

doi:10.1101/2025.04.11.648334

bioRxiv · 10.1101/2025.04.11.648334

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Howard, C.·Denton, A.·Jackson, B.·Bates, A.·Jay, J.·Yatsenko, H.·Raman, P. S.·Thomas, A.·Oatley, G.·do Amaral, R. V.·Göktan, Z. E.·Gomez, J. P. N.·Clayton Lucey, I.·Sinclair, E.·Quail, M. A.·Blaxter, M.·Howe, K.·Lawniczak, M.

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Abstract

Since its inception in 2019, the Tree of Life programme at the Wellcome Sanger Institute has released high-quality, chromosomally-resolved reference genome assemblies for over 2000 species. Tree of Life has at its core multiple teams, each of which are responsible for key components of the genome engine. One of these teams is the Tree of Life core laboratory, which is responsible for processing tissues across a wide range of species into high quality, high molecular weight DNA and intact RNA, and preparing tissues for Hi-C. Here, we detail the different workflows we have developed to successfully process a wide variety of species, covering plants, fungi, chordates, protists, arthropods, meiofauna and other metazoa. We summarise our success rates and describe how to best apply and combine the suite of current protocols, which are all publicly available at protocols.io.

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Howard, C., Denton, A., Jackson, B., Bates, A., Jay, J., Yatsenko, H., Raman, P. S., Thomas, A., Oatley, G., do Amaral, R. V., Göktan, Z. E., Gomez, J. P. N., Clayton Lucey, I., Sinclair, E., Quail, M. A., Blaxter, M., Howe, K., Lawniczak, M.. 2025-04-11. On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species. https://doi.org/10.1101/2025.04.11.648334

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