1. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters
- Author
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Jean-Félix, Dallery, Nicolas, Lapalu, Antonios, Zampounis, Sandrine, Pigné, Isabelle, Luyten, Joëlle, Amselem, Alexander H J, Wittenberg, Shiguo, Zhou, Marisa V, de Queiroz, Guillaume P, Robin, Annie, Auger, Matthieu, Hainaut, Bernard, Henrissat, Ki-Tae, Kim, Yong-Hwan, Lee, Olivier, Lespinet, David C, Schwartz, Michael R, Thon, Richard J, O'Connell, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Keygene N.V., Dept Chem, Lab Genet, Lab Mol & Computat Genom, University of Wisconsin-Madison, Lab Genet Mol Fungos, Universidade Federal de Viçosa (UFC), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, Ctr Fungal Genet Resources, Dept Agr Biotechnol, Seoul National University [Seoul] (SNU), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, CNRS, Lab Rech Informat, Université Paris Sud (Paris 11), Dept Microbiol & Genet, Inst Hispanoluso Invest Agr CIALE, Universidad de Salamanca, ANR-12-CHEX-008-01, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Viçosa = Federal University of Viçosa (UFV), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), BIOlogie GEstion des Risques en agriculture - Champignons Pathogènes des Plantes ( BIOGER-CPP ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Unité de Recherche Génomique Info ( URGI ), Institut National de la Recherche Agronomique ( INRA ), University of Wisconsin-Madison [Madison], Universidade Federal de Viçosa ( UFC ), Architecture et fonction des macromolécules biologiques ( AFMB ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ), King Abdulaziz Univ, Dept Biol Sci, Jeddah, Saudi Arabia, Seoul National University, Institut de Biologie Intégrative de la Cellule ( I2BC ), and Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 )
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Fungal genome ,SMRT sequencing ,optical map ,transposable elements ,secondary metabolism genes ,subtelomeres ,segmental duplication ,accessory chromosomes ,Colletotrichum higginsianum ,lcsh:QH426-470 ,lcsh:Biotechnology ,[SDV]Life Sciences [q-bio] ,Segmental duplication ,lcsh:TP248.13-248.65 ,Colletotrichum ,Point Mutation ,Accessory chromosomes ,Homologous Recombination ,Subtelomeres ,Phylogeny ,[ SDV ] Life Sciences [q-bio] ,Molecular Sequence Annotation ,Genomics ,lcsh:Genetics ,Optical map ,Secondary metabolism genes ,Multigene Family ,DNA Transposable Elements ,Chromosomes, Fungal ,Transposable elements ,Research Article - Abstract
Background The 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. Results Here, 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. Conclusion The 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. Electronic supplementary material The online version of this article (10.1186/s12864-017-4083-x) contains supplementary material, which is available to authorized users.
- Published
- 2017
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