Proximity ligation scaffolding and comparison of two Trichoderma reesei strains genomesReport as inadecuate

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Biotechnology for Biofuels

, 10:151

First Online: 12 June 2017Received: 17 December 2016Accepted: 31 May 2017DOI: 10.1186-s13068-017-0837-6

Cite this article as: Jourdier, E., Baudry, L., Poggi-Parodi, D. et al. Biotechnol Biofuels 2017 10: 151. doi:10.1186-s13068-017-0837-6


BackgroundThe 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.

ResultsThe 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.

ConclusionsThe 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.

KeywordsTrichoderma reesei Genome assembly Hi-C GRAAL Centromere Karyotype Translocation Chromosomal contact Chromosome conformation capture AbbreviationsPFGEpulse-field gel electrophoresis

3Cchromosome conformation capture

CDScoding sequence

Electronic supplementary materialThe online version of this article doi:10.1186-s13068-017-0837-6 contains supplementary material, which is available to authorized users.

Etienne Jourdier and Lyam Baudry contributed equally to this work

Martial Marbouty and Frédérique Bidard contributed equally to this work

Author: Etienne Jourdier - Lyam Baudry - Dante Poggi-Parodi - Yoan Vicq - Romain Koszul - Antoine Margeot - Martial Marbouty - Fré



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