title: Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum.
abstract: Many species belonging to the genus Colletotrichum cause anthracnose disease on a wide range of plant species. In addition to their economic impact, the genus Colletotrichum is a useful model for the study of the evolution of host specificity, speciation and reproductive behaviors. Genome projects of Colletotrichum species have already opened a new era for studying the evolution of pathogenesis in fungi.
  
  
  
  We sequenced and annotated the genomes of four strains in the Colletotrichum acutatum species complex (CAsc), a clade of broad host range pathogens within the genus. The four CAsc proteomes and secretomes along with those representing an additional 13 species (six Colletotrichum spp. and seven other Sordariomycetes) were classified into protein families using a variety of tools. Hierarchical clustering of gene family and functional domain assignments, and phylogenetic analyses revealed lineage specific losses of carbohydrate-active enzymes (CAZymes) and proteases encoding genes in Colletotrichum species that have narrow host range as well as duplications of these families in the CAsc. We also found a lineage specific expansion of necrosis and ethylene-inducing peptide 1 (Nep1)-like protein (NLPs) families within the CAsc.
  
  
  
  This study illustrates the plasticity of Colletotrichum genomes, and shows that major changes in host range are associated with relatively recent changes in gene content.
authors: Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), University of Western Brittany, Technopôle Brest-Iroise, 29280, Plouzané, France. riccardobaroncelli@gmail.com.
authors: Riccardo
authors: R
authors: Baroncelli
authors: Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Frb. C, Copenhagen, Denmark.
authors: Daniel Buchvaldt
authors: DB
authors: Amby
authors: Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
authors: Antonio
authors: A
authors: Zapparata
authors: Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
authors: Sabrina
authors: S
authors: Sarrocco
authors: Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
authors: Giovanni
authors: G
authors: Vannacci
authors: Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), University of Western Brittany, Technopôle Brest-Iroise, 29280, Plouzané, France.
authors: Gaétan
authors: G
authors: Le Floch
authors: NIAB-EMR, New Road, East Malling, Kent, ME19 6BJ, UK.
authors: Richard J
authors: RJ
authors: Harrison
authors: School of Life Sciences, Warwick Crop Centre, University of Warwick, Wellesbourne, Warwickshire, CV35 9EF, UK.
authors: Eric
authors: E
authors: Holub
authors: Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca, Campus de Villamayor, C/Del Duero, 12, 37185, Villamayor, Salamanca, Spain.
authors: Serenella A
authors: SA
authors: Sukno
authors: Institute of Biomedical and Environmental Science and Technology (iBEST), University of Bedfordshire, University Square, Luton, Bedfordshire, LU1 3JU, UK.
authors: Surapareddy
authors: S
authors: Sreenivasaprasad
authors: Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca, Campus de Villamayor, C/Del Duero, 12, 37185, Villamayor, Salamanca, Spain. mthon@usal.es.
authors: Michael R
authors: MR
authors: Thon
mesh_terms: D016000:Cluster Analysis; D020231:Colletotrichum / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005800:Genes, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D058507:Host Specificity / Q000235:genetics*; D054884:Host-Pathogen Interactions; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D009336:Necrosis; D010802:Phylogeny
keywords: Anthracnose; CAZyme; Colletotrichum spp.; Fungal genomics; Plant pathogen