Literature DB >> 29969057

Draft Genome Resource for the Potato Powdery Scab Pathogen Spongospora subterranea.

Stefan Ciaghi1, Sigrid Neuhauser1, Arne Schwelm2.   

Abstract

The Plasmodiophorida (Phytomyxea, Rhizaria) are a group of protists that infect plants. Of this group, Spongospora subterranea causes major problems for the potato industry by causing powdery scab and root galling of potatoes and as vector for the Potato mop-top virus (PMTV) (genus Pomovirus, family Virgaviridae). A single tuber isolate (SSUBK13) of this uncultivable protist was used to generate DNA for Illumina sequencing. The data were assembled to a draft genome of 28.08 Mb consisting of 2,340 contigs and an L50 of 280. A total of 10,778 genes were predicted and 93% of the BUSCO genes were detected. The presented genome assembly is only the second genome of a plasmodiophorid. The data will accelerate functional genomics to study poorly understood interaction of plasmodiophorids and their hosts.

Entities:  

Mesh：

Year:  2018        PMID： 29969057      PMCID： PMC6443038          DOI： 10.1094/MPMI-06-18-0163-A

Source DB:  PubMed          Journal:  Mol Plant Microbe Interact        ISSN： 0894-0282            Impact factor:   4.171


  23 in total

1.  SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Authors:  Anton Bankevich; Sergey Nurk; Dmitry Antipov; Alexey A Gurevich; Mikhail Dvorkin; Alexander S Kulikov; Valery M Lesin; Sergey I Nikolenko; Son Pham; Andrey D Prjibelski; Alexey V Pyshkin; Alexander V Sirotkin; Nikolay Vyahhi; Glenn Tesler; Max A Alekseyev; Pavel A Pevzner
Journal:  J Comput Biol       Date:  2012-04-16       Impact factor: 1.479

2.  SignalP 4.0: discriminating signal peptides from transmembrane regions.

Authors:  Thomas Nordahl Petersen; Søren Brunak; Gunnar von Heijne; Henrik Nielsen
Journal:  Nat Methods       Date:  2011-09-29       Impact factor: 28.547

3.  Scaffolding pre-assembled contigs using SSPACE.

Authors:  Marten Boetzer; Christiaan V Henkel; Hans J Jansen; Derek Butler; Walter Pirovano
Journal:  Bioinformatics       Date:  2010-12-12       Impact factor: 6.937

4.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

5.  Fast gapped-read alignment with Bowtie 2.

Authors:  Ben Langmead; Steven L Salzberg
Journal:  Nat Methods       Date:  2012-03-04       Impact factor: 28.547

6.  Genome sequence and analysis of the tuber crop potato.

Authors:  Xun Xu; Shengkai Pan; Shifeng Cheng; Bo Zhang; Desheng Mu; Peixiang Ni; Gengyun Zhang; Shuang Yang; Ruiqiang Li; Jun Wang; Gisella Orjeda; Frank Guzman; Michael Torres; Roberto Lozano; Olga Ponce; Diana Martinez; Germán De la Cruz; S K Chakrabarti; Virupaksh U Patil; Konstantin G Skryabin; Boris B Kuznetsov; Nikolai V Ravin; Tatjana V Kolganova; Alexey V Beletsky; Andrei V Mardanov; Alex Di Genova; Daniel M Bolser; David M A Martin; Guangcun Li; Yu Yang; Hanhui Kuang; Qun Hu; Xingyao Xiong; Gerard J Bishop; Boris Sagredo; Nilo Mejía; Wlodzimierz Zagorski; Robert Gromadka; Jan Gawor; Pawel Szczesny; Sanwen Huang; Zhonghua Zhang; Chunbo Liang; Jun He; Ying Li; Ying He; Jianfei Xu; Youjun Zhang; Binyan Xie; Yongchen Du; Dongyu Qu; Merideth Bonierbale; Marc Ghislain; Maria del Rosario Herrera; Giovanni Giuliano; Marco Pietrella; Gaetano Perrotta; Paolo Facella; Kimberly O'Brien; Sergio E Feingold; Leandro E Barreiro; Gabriela A Massa; Luis Diambra; Brett R Whitty; Brieanne Vaillancourt; Haining Lin; Alicia N Massa; Michael Geoffroy; Steven Lundback; Dean DellaPenna; C Robin Buell; Sanjeev Kumar Sharma; David F Marshall; Robbie Waugh; Glenn J Bryan; Marialaura Destefanis; Istvan Nagy; Dan Milbourne; Susan J Thomson; Mark Fiers; Jeanne M E Jacobs; Kåre L Nielsen; Mads Sønderkær; Marina Iovene; Giovana A Torres; Jiming Jiang; Richard E Veilleux; Christian W B Bachem; Jan de Boer; Theo Borm; Bjorn Kloosterman; Herman van Eck; Erwin Datema; Bas te Lintel Hekkert; Aska Goverse; Roeland C H J van Ham; Richard G F Visser
Journal:  Nature       Date:  2011-07-10       Impact factor: 49.962

7.  Toward almost closed genomes with GapFiller.

Authors:  Marten Boetzer; Walter Pirovano
Journal:  Genome Biol       Date:  2012-06-25       Impact factor: 13.583

8.  dbCAN: a web resource for automated carbohydrate-active enzyme annotation.

Authors:  Yanbin Yin; Xizeng Mao; Jincai Yang; Xin Chen; Fenglou Mao; Ying Xu
Journal:  Nucleic Acids Res       Date:  2012-05-29       Impact factor: 16.971

9.  Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs.

Authors:  Bruce A Curtis; Goro Tanifuji; Fabien Burki; Ansgar Gruber; Manuel Irimia; Shinichiro Maruyama; Maria C Arias; Steven G Ball; Gillian H Gile; Yoshihisa Hirakawa; Julia F Hopkins; Alan Kuo; Stefan A Rensing; Jeremy Schmutz; Aikaterini Symeonidi; Marek Elias; Robert J M Eveleigh; Emily K Herman; Mary J Klute; Takuro Nakayama; Miroslav Oborník; Adrian Reyes-Prieto; E Virginia Armbrust; Stephen J Aves; Robert G Beiko; Pedro Coutinho; Joel B Dacks; Dion G Durnford; Naomi M Fast; Beverley R Green; Cameron J Grisdale; Franziska Hempel; Bernard Henrissat; Marc P Höppner; Ken-Ichiro Ishida; Eunsoo Kim; Luděk Kořený; Peter G Kroth; Yuan Liu; Shehre-Banoo Malik; Uwe G Maier; Darcy McRose; Thomas Mock; Jonathan A D Neilson; Naoko T Onodera; Anthony M Poole; Ellen J Pritham; Thomas A Richards; Gabrielle Rocap; Scott W Roy; Chihiro Sarai; Sarah Schaack; Shu Shirato; Claudio H Slamovits; David F Spencer; Shigekatsu Suzuki; Alexandra Z Worden; Stefan Zauner; Kerrie Barry; Callum Bell; Arvind K Bharti; John A Crow; Jane Grimwood; Robin Kramer; Erika Lindquist; Susan Lucas; Asaf Salamov; Geoffrey I McFadden; Christopher E Lane; Patrick J Keeling; Michael W Gray; Igor V Grigoriev; John M Archibald
Journal:  Nature       Date:  2012-11-28       Impact factor: 49.962

10.  KAAS: an automatic genome annotation and pathway reconstruction server.

Authors:  Yuki Moriya; Masumi Itoh; Shujiro Okuda; Akiyasu C Yoshizawa; Minoru Kanehisa
Journal:  Nucleic Acids Res       Date:  2007-05-25       Impact factor: 16.971
View more
  4 in total

Review 1.  What Can We Learn from -Omics Approaches to Understand Clubroot Disease?

Authors:  Jutta Ludwig-Müller
Journal:  Int J Mol Sci       Date:  2022-06-04       Impact factor: 6.208

2.  Large-Scale Protein and Phosphoprotein Profiling to Explore Potato Resistance Mechanisms to Spongospora subterranea Infection.

Authors:  Sadegh Balotf; Calum R Wilson; Robert S Tegg; David S Nichols; Richard Wilson
Journal:  Front Plant Sci       Date:  2022-04-14       Impact factor: 6.627

3.  The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.

Authors:  Suzana Stjelja; Johan Fogelqvist; Christian Tellgren-Roth; Christina Dixelius
Journal:  Sci Rep       Date:  2019-10-31       Impact factor: 4.379

4.  Revised Taxonomy and Expanded Biodiversity of the Phytomyxea (Rhizaria, Endomyxa).

Authors:  Michaela Hittorf; Susanne Letsch-Praxmarer; Alexandra Windegger; David Bass; Martin Kirchmair; Sigrid Neuhauser
Journal:  J Eukaryot Microbiol       Date:  2020-11-08       Impact factor: 3.346
  4 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.