Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes
| Autor: | Jourdier, Etienne, Baudry, Lyam, Poggi-Parodi, Dante, Vicq, Yoan, Koszul, Romain, Margeot, Antoine, Marbouty, Martial, Bidard, Frédérique |
|---|---|
| Přispěvatelé: | IFP Energies nouvelles (IFPEN), Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS) |
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: | |
| Zdroj: | Biotechnology for Biofuels, Vol 10, Iss 1, Pp 1-13 (2017) Biotechnology for Biofuels Biotechnology for Biofuels, 2017, 10 (1), pp.151. ⟨10.1186/s13068-017-0837-6⟩ Biotechnology for Biofuels, BioMed Central, 2017, 10 (1), pp.151. ⟨10.1186/s13068-017-0837-6⟩ |
| ISSN: | 1754-6834 |
| Popis: | International audience; Background: The presence of low complexity and repeated regions in genomes often results in difficulties to assemblesequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to severalinvestigations, regarding for instance the evolution of entire clades, the analysis of chromosome rearrangements,and is pivotal to sexual crossing studies. In non-conventional but industrially relevant model organisms, such as theascomycete Trichoderma reesei, a complete genome assembly is seldom available.Results: The chromosome scaffolds of T. reesei QM6a and Rut-C30 strains have been generated using a contactgenomic/proximity ligation genomic approach. The original reference assembly, encompassing dozens of scaffolds,was reorganized into two sets of seven chromosomes. Chromosomal contact data also allowed to characterize10–40 kb, gene-free, AT-rich (76%) regions corresponding to the T. reesei centromeres. Large chromosomal rearrangements(LCR) in Rut-C30 were then characterized, in agreement with former studies, and the position of LCRbreakpoints used to assess the likely chromosome structure of other T. reesei strains [QM9414, CBS999.97 (1-1, re), andQM9978]. In agreement with published results, we predict that the numerous chromosome rearrangements found inhighly mutated industrial strains may limit the efficiency of sexual reproduction for their improvement.Conclusions: The GRAAL program allowed us to generate the karyotype of the Rut-C30 strain, and from there topredict chromosome structure for most T. reesei strains for which sequence is available. This method that exploitsproximity ligation sequencing approach is a fast, cheap, and straightforward way to characterize both chromosomestructure and centromere sequences and is likely to represent a popular convenient alternative to expensive andwork-intensive resequencing projects. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|