Literature DB >> 31094147

Five life stage-specific transcriptome assemblies for the reniform nematode, Rotylenchulus reniformis Linford & Oliveira.

Kurt C Showmaker1, William S Sanders2, Sebastian Eves-van den Akker3, Brigitte E Martin4, Franklin E Callahan5, Daniel G Peterson6, Martin J Wubben7.   

Abstract

The reniform nematode (Rotylenchulus reniformis Linford and Oliveira) is a semi-endoparasitic nematode that is a pathogen of numerous major crops such as cotton and soybean. Here, the authors present transcriptome assemblies of the egg, second-stage juvenile (J2), J3, vermiform adult, and sedentary female life stages of this important plant pathogen. The reniform nematode (Rotylenchulus reniformis Linford and Oliveira) is a semi-endoparasitic nematode that is a pathogen of numerous major crops such as cotton and soybean. Here, the authors present transcriptome assemblies of the egg, second-stage juvenile (J2), J3, vermiform adult, and sedentary female life stages of this important plant pathogen.

Entities:  

Year:  2018        PMID： 31094147      PMCID： PMC6909322          DOI： 10.21307/jofnem-2018-053

Source DB:  PubMed          Journal:  J Nematol        ISSN： 0022-300X            Impact factor:   1.402


  13 in total

1.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.

Authors:  Genis Parra; Keith Bradnam; Ian Korf
Journal:  Bioinformatics       Date:  2007-03-01       Impact factor: 6.937

2.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.

Authors:  Felipe A Simão; Robert M Waterhouse; Panagiotis Ioannidis; Evgenia V Kriventseva; Evgeny M Zdobnov
Journal:  Bioinformatics       Date:  2015-06-09       Impact factor: 6.937

3.  Fast and sensitive protein alignment using DIAMOND.

Authors:  Benjamin Buchfink; Chao Xie; Daniel H Huson
Journal:  Nat Methods       Date:  2014-11-17       Impact factor: 28.547

4.  STAR: ultrafast universal RNA-seq aligner.

Authors:  Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal:  Bioinformatics       Date:  2012-10-25       Impact factor: 6.937

5.  A Screen for Arabidopsis thaliana Mutants with Altered Susceptibility to Heterodera schachtii.

Authors:  T J Baum; M J Wubben; K A Hardyy; H Su; S R Rodermel
Journal:  J Nematol       Date:  2000-06       Impact factor: 1.402

6.  Accelerated Profile HMM Searches.

Authors:  Sean R Eddy
Journal:  PLoS Comput Biol       Date:  2011-10-20       Impact factor: 4.475

7.  Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Authors:  Manfred G Grabherr; Brian J Haas; Moran Yassour; Joshua Z Levin; Dawn A Thompson; Ido Amit; Xian Adiconis; Lin Fan; Raktima Raychowdhury; Qiandong Zeng; Zehua Chen; Evan Mauceli; Nir Hacohen; Andreas Gnirke; Nicholas Rhind; Federica di Palma; Bruce W Birren; Chad Nusbaum; Kerstin Lindblad-Toh; Nir Friedman; Aviv Regev
Journal:  Nat Biotechnol       Date:  2011-05-15       Impact factor: 54.908

8.  Trimmomatic: a flexible trimmer for Illumina sequence data.

Authors:  Anthony M Bolger; Marc Lohse; Bjoern Usadel
Journal:  Bioinformatics       Date:  2014-04-01       Impact factor: 6.937

9.  The Pfam protein families database: towards a more sustainable future.

Authors:  Robert D Finn; Penelope Coggill; Ruth Y Eberhardt; Sean R Eddy; Jaina Mistry; Alex L Mitchell; Simon C Potter; Marco Punta; Matloob Qureshi; Amaia Sangrador-Vegas; Gustavo A Salazar; John Tate; Alex Bateman
Journal:  Nucleic Acids Res       Date:  2015-12-15       Impact factor: 16.971

10.  The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence.

Authors:  Sebastian Eves-van den Akker; Dominik R Laetsch; Peter Thorpe; Catherine J Lilley; Etienne G J Danchin; Martine Da Rocha; Corinne Rancurel; Nancy E Holroyd; James A Cotton; Amir Szitenberg; Eric Grenier; Josselin Montarry; Benjamin Mimee; Marc-Olivier Duceppe; Ian Boyes; Jessica M C Marvin; Laura M Jones; Hazijah B Yusup; Joël Lafond-Lapalme; Magali Esquibet; Michael Sabeh; Michael Rott; Hein Overmars; Anna Finkers-Tomczak; Geert Smant; Georgios Koutsovoulos; Vivian Blok; Sophie Mantelin; Peter J A Cock; Wendy Phillips; Bernard Henrissat; Peter E Urwin; Mark Blaxter; John T Jones
Journal:  Genome Biol       Date:  2016-06-10       Impact factor: 13.583
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.