Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

BMC Genomics

Research Article

Matthieu Hainaut¹  Bernard Henrissat²  Ki-Tae Kim³  Yong-Hwan Lee³  Michael R. Thon⁴  Alexander H. J. Wittenberg⁵  Olivier Lespinet⁶  David C. Schwartz⁷  Shiguo Zhou⁷  Marisa V. de Queiroz⁸  Annie Auger⁹  Jean-Félix Dallery⁹  Nicolas Lapalu⁹  Sandrine Pigné⁹  Guillaume P. Robin⁹  Richard J. O’Connell⁹  Antonios Zampounis^1,10  Joëlle Amselem^1,11  Isabelle Luyten^1,11 

[1] CNRS UMR 7257, Aix-Marseille University, Marseille, France;INRA, USC 1408 AFMB, Marseille, France;CNRS UMR 7257, Aix-Marseille University, Marseille, France;INRA, USC 1408 AFMB, Marseille, France;Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia;Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea;Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain;KeyGene N.V., Wageningen, The Netherlands;Laboratoire de Recherche en Informatique, CNRS, Université Paris-Sud, Orsay, France;Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Orsay, France;Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA;Laboratório de Genética Molecular de Fungos, Universidade Federal de Viçosa, Viçosa, Brazil;UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France;UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France;Present Address: Department of Deciduous Fruit Trees, Institute of Plant Breeding and Plant Genetic Resources, Hellenic Agricultural Organization ‘Demeter’, Naoussa, Greece;UR1164 URGI, INRA, Versailles, France;

关键词: Fungal genome;    SMRT sequencing;    optical map;    transposable elements;    secondary metabolism genes;    subtelomeres;    segmental duplication;    accessory chromosomes;    Colletotrichum higginsianum;   

DOI  :  10.1186/s12864-017-4083-x

 received in 2017-05-24, accepted in 2017-08-21,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture.ResultsHere, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications.ConclusionThe gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.

【 授权许可】

CC BY   
© The Author(s). 2017