Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes
Abstract Background The presence of low complexity and repeated regions in genomes often results in difficulties to assemble sequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to several investigations, regarding for instance the evolution of entir...
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| Format: | Article |
| Language: | English |
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BMC
2017-06-01
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| Series: | Biotechnology for Biofuels |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13068-017-0837-6 |
| _version_ | 1818265309551788032 |
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| author | Etienne Jourdier Lyam Baudry Dante Poggi-Parodi Yoan Vicq Romain Koszul Antoine Margeot Martial Marbouty Frédérique Bidard |
| author_facet | Etienne Jourdier Lyam Baudry Dante Poggi-Parodi Yoan Vicq Romain Koszul Antoine Margeot Martial Marbouty Frédérique Bidard |
| author_sort | Etienne Jourdier |
| collection | DOAJ |
| description | Abstract Background The presence of low complexity and repeated regions in genomes often results in difficulties to assemble sequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to several investigations, 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 the ascomycete 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 contact genomic/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 characterize 10–40 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 LCR breakpoints used to assess the likely chromosome structure of other T. reesei strains [QM9414, CBS999.97 (1-1, re), and QM9978]. In agreement with published results, we predict that the numerous chromosome rearrangements found in highly 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 to predict chromosome structure for most T. reesei strains for which sequence is available. This method that exploits proximity ligation sequencing approach is a fast, cheap, and straightforward way to characterize both chromosome structure and centromere sequences and is likely to represent a popular convenient alternative to expensive and work-intensive resequencing projects. |
| first_indexed | 2024-12-12T19:48:46Z |
| format | Article |
| id | doaj.art-de56ba30574b48b784f00c0fbca35024 |
| institution | Directory Open Access Journal |
| issn | 1754-6834 |
| language | English |
| last_indexed | 2024-12-12T19:48:46Z |
| publishDate | 2017-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Biotechnology for Biofuels |
| spelling | doaj.art-de56ba30574b48b784f00c0fbca350242022-12-22T00:14:01ZengBMCBiotechnology for Biofuels1754-68342017-06-0110111310.1186/s13068-017-0837-6Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomesEtienne Jourdier0Lyam Baudry1Dante Poggi-Parodi2Yoan Vicq3Romain Koszul4Antoine Margeot5Martial Marbouty6Frédérique Bidard7IFP Energies nouvellesGroupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut PasteurIFP Energies nouvellesIFP Energies nouvellesGroupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut PasteurIFP Energies nouvellesGroupe Régulation Spatiale des Génomes, Department Genomes and Genetics, Institut PasteurIFP Energies nouvellesAbstract Background The presence of low complexity and repeated regions in genomes often results in difficulties to assemble sequencing data into full chromosomes. However, the availability of full genome scaffolds is essential to several investigations, 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 the ascomycete 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 contact genomic/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 characterize 10–40 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 LCR breakpoints used to assess the likely chromosome structure of other T. reesei strains [QM9414, CBS999.97 (1-1, re), and QM9978]. In agreement with published results, we predict that the numerous chromosome rearrangements found in highly 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 to predict chromosome structure for most T. reesei strains for which sequence is available. This method that exploits proximity ligation sequencing approach is a fast, cheap, and straightforward way to characterize both chromosome structure and centromere sequences and is likely to represent a popular convenient alternative to expensive and work-intensive resequencing projects.http://link.springer.com/article/10.1186/s13068-017-0837-6Trichoderma reeseiGenome assemblyHi-CGRAALCentromereKaryotype |
| spellingShingle | Etienne Jourdier Lyam Baudry Dante Poggi-Parodi Yoan Vicq Romain Koszul Antoine Margeot Martial Marbouty Frédérique Bidard Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes Biotechnology for Biofuels Trichoderma reesei Genome assembly Hi-C GRAAL Centromere Karyotype |
| title | Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes |
| title_full | Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes |
| title_fullStr | Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes |
| title_full_unstemmed | Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes |
| title_short | Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomes |
| title_sort | proximity ligation scaffolding and comparison of two trichoderma reesei strains genomes |
| topic | Trichoderma reesei Genome assembly Hi-C GRAAL Centromere Karyotype |
| url | http://link.springer.com/article/10.1186/s13068-017-0837-6 |
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