Improved genome sequence of Diplodia seriata, a tool for comparative genomics of Diplodia species

Autor: Guillaume Robert, Vallet, J., Eliane ABOU MANSOUR, Xu, J., Patrice Rey, Bertsch, C., Cecília Rego, Larignon, P., Fontaine, F., Marc-Henri Lebrun
Přispěvatelé: ProdInra, Archive Ouverte, BIOlogie et GEstion des Risques en agriculture (BIOGER), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université de Reims Champagne-Ardenne (URCA), Université de Fribourg, BGI-Shenzhen, Santé Végétale (SV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Institut supérieur d'Agronomie, Tapada da Ajuda, Institut Français de la Vigne et du Vin (IFV), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, University of Fribourg, BGIShenzhen, Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Institut Français de la Vigne et du Vin Pôle Rhône-Méditerranée, Unité de Recherche Vigne et Vins de Champagne Stress et Environnement - EA 4707 (URVVC), Université de Reims Champagne-Ardenne (URCA)-SFR Condorcet, Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)
Jazyk: angličtina
Rok vydání: 2017
Předmět:
Zdroj: 29. Fungal genetics conference Asilomar 17
29. Fungal genetics conference Asilomar 17, Mar 2017, Asilomar, United States. p.159
HAL
Popis: The Ascomycotina Diplodia seriata is one of the causal agent of grapevine trunk diseases. Here, we present an improved genome sequence of D. seriata isolate F98.1, isolated in 1998 at Perpignan (France) from the trunk of a diseased grapevine. D. seriata is one of the most common Botryosphaeriaceae species associated with grapevine trunk diseases. This species is also frequently isolated from woody tissues of trees such as Acer sp., Prunus sp. or Quercus sp.. Sequencing was performed using Illumina HiSeq 2500 at a coverage of 270 X. Assembly with SOAPdenovo 1.05 led to 512 contigs and 112 scaffolds (37.27 Mb, GC%: 56.8). This high quality genome (Scaffold N50, 2.9 Mb; Min scaffold length, 1.007 bp; gaps, 250 kb) has 13 scaffolds with a size higher than 1 Mb (90% of total sequence), likely corresponding to chromosomes. Using GLEAN, 8.087 CDS were identified, 93 % being supported by RNAseq (mycelium on PDB or MM for 4 days). Recently, the genome sequence of D. seriata isolate DS831 from an infected grapevine (USA, 2011) was released. The genome size of DS831 (37.13 Mb) is almost similar to F98.1. However, its assembly is 5 times more fragmented (1391 contigs, 695 scaffolds) and it carries 9398 CDS. Bidirectional best blast hit (BDBH) analysis revealed that 82% of F98.1 and DS831 CDS are similar, 1507 genes are specific to F98.1 strain, and 2763 are specific to DS831 strain. Using Blast, we showed that 2686 (97.2%) of DS831 apparently specific genes were present in F98.1 genome sequence, and reversely 1440 (95.6%) of F98.1 apparently specific genes are present in DS831 genome sequence. Therefore, the difference in CDS numbers between DS831 and F98.1 is likely a consequence of using different annotation software (Glean vs Augustus). Fusion of two annotation leads to a total of 10,500 genes. The genomes of the two species Diplodia sapinea and Diplodia scrobiculata closely related to D. seriata have been sequenced. These two genome have a size of, respectively, 36,97 and 35,85 Mb, and 13020 and 13624 genes respectively. These differences could reflect recent massive gene losses in D. seriata.
Databáze: OpenAIRE
Externí odkaz: