The PGTB offers a de novo sequencing service or resequencing of small genomes:
- De novo sequencing involves determining the sequence of an organism for which no reference sequence exists in public databases.
- Resequencing enables the identification of genomic variations such as SNPs and indels by aligning the resequenced sequences with the reference sequence.
The preparation of libraries for Illumina sequencing involves fragmenting genomic DNA mechanically or enzymatically into pieces of approximately 200–300 bp. Adapters are then added to enable sequencing. For Oxford Nanopore sequencing, it is possible to perform size selection on the DNA to maximise the size of the sequenced molecules.
Services
Sequencing can be carried out using short reads with Illumina technology on the NextSeq 2000, or using long reads with the P2 Solo from Oxford Nanopore Technologies.
Requirements
Illumina sequencing : see our requirements.
Oxford Nanopore sequencing: a minimum of 2 µg of high-molecular-weight DNA (as determined by fluorescence), in at least 25 µL.
Results
Sent by email or uploaded to a server
Depending on the service requested:
Associated publications
Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, Wang C, Rajaraman S, Rastas P, Zheng C, Muñoz DS, Meidanis J, Paschoal AR, Bawin Y, Krabbenhoft TJ, Wang ZQ, Fleck SJ, Aussel R, Bellanger L, Charpagne A, Fournier C, Kassam M, Lefebvre G, Métairon S, Moine D, Rigoreau M, Stolte J, Hamon P, Couturon E, Tranchant-Dubreuil C, Mukherjee M, Lan T, Engelhardt J, Stadler P, Correia De Lemos SM, Suzuki SI, Sumirat U, Wai CM, Dauchot N, Orozco-Arias S, Garavito A, Kiwuka C, Musoli P, Nalukenge A, Guichoux E, et al., 2024. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet. DOI: 10.1038/s41588-024-01695-w
Baby, V., Ambroset, C., Gaurivaud, P., Falquet, L., Boury, C., Guichoux, E., Jores, J., Lartigue, C., Tardy, F., Sirand-Pugnet, P., 2023. Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae. Microb Genom 9, 001112. https://doi.org/10.1099/mgen.0.001112
Penaud, B., Laurent, B., Milhes, M., Noüs, C., Ehrenmann, F., Dutech, C. 2022. SNP4OrphanSpecies: A bioinformatics pipeline to isolate molecular markers for studying genetic diversity of orphan species. Biodiversity Data Journal 10: e85587. https://doi.org/10.3897/BDJ.10.e85587