Literature DB >> 35819611

Computational Analysis of HTS Data and Its Application in Plant Pathology.

Edoardo Piombo1, Mukesh Dubey2.   

Abstract

High-throughput sequencing is a basic tool of biological research, and it is extensively used in plant pathology projects. Here, we describe how to handle data coming from a variety of sequencing experiments, focusing on the analysis of Illumina reads. We describe how to perform genome assembly and annotation with DNA reads, correctly analyze RNA-seq data to discover differentially expressed genes, handle amplicon sequencing data from microbial communities, and utilize small RNA sequencing data to predict miRNA sequences and their putative targets.
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Differential expression; Functional annotation; Genome assembly; High-throughput sequencing; Metabarcoding; Small RNA; Target prediction; Transcriptomics; miRNA

Mesh：

Substances：

Year:  2022        PMID： 35819611     DOI： 10.1007/978-1-0716-2517-0_17

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  103 in total

Review 1.  Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology.

Authors:  Kar-Chun Tan; Simon V S Ipcho; Robert D Trengove; Richard P Oliver; Peter S Solomon
Journal:  Mol Plant Pathol       Date:  2009-09       Impact factor: 5.663

Review 2.  High Throughput Sequencing For Plant Virus Detection and Discovery.

Authors:  D E V Villamor; T Ho; M Al Rwahnih; R R Martin; I E Tzanetakis
Journal:  Phytopathology       Date:  2019-04-01       Impact factor: 4.025

3.  Verticillium dahliae transcription factor VdFTF1 regulates the expression of multiple secreted virulence factors and is required for full virulence in cotton.

Authors:  Wen-Qi Zhang; Yue-Jing Gui; Dylan P G Short; Ting-Gang Li; Dan-Dan Zhang; Lei Zhou; Chun Liu; Yu-Ming Bao; Krishna V Subbarao; Jie-Yin Chen; Xiao-Feng Dai
Journal:  Mol Plant Pathol       Date:  2017-07-31       Impact factor: 5.663

4.  Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.

Authors:  Philipp Wiemann; Christian M K Sieber; Katharina W von Bargen; Lena Studt; Eva-Maria Niehaus; Jose J Espino; Kathleen Huß; Caroline B Michielse; Sabine Albermann; Dominik Wagner; Sonja V Bergner; Lanelle R Connolly; Andreas Fischer; Gunter Reuter; Karin Kleigrewe; Till Bald; Brenda D Wingfield; Ron Ophir; Stanley Freeman; Michael Hippler; Kristina M Smith; Daren W Brown; Robert H Proctor; Martin Münsterkötter; Michael Freitag; Hans-Ulrich Humpf; Ulrich Güldener; Bettina Tudzynski
Journal:  PLoS Pathog       Date:  2013-06-27       Impact factor: 6.823

5.  Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea.

Authors:  Magnus Karlsson; Mikael Brandström Durling; Jaeyoung Choi; Chatchai Kosawang; Gerald Lackner; Georgios D Tzelepis; Kristiina Nygren; Mukesh K Dubey; Nathalie Kamou; Anthony Levasseur; Antonio Zapparata; Jinhui Wang; Daniel Buchvaldt Amby; Birgit Jensen; Sabrina Sarrocco; Emmanuel Panteris; Anastasia L Lagopodi; Stefanie Pöggeler; Giovanni Vannacci; David B Collinge; Dirk Hoffmeister; Bernard Henrissat; Yong-Hwan Lee; Dan Funck Jensen
Journal:  Genome Biol Evol       Date:  2015-01-08       Impact factor: 3.416

Review 6.  Oxford Nanopore MinION Sequencing and Genome Assembly.

Authors:  Hengyun Lu; Francesca Giordano; Zemin Ning
Journal:  Genomics Proteomics Bioinformatics       Date:  2016-09-17       Impact factor: 7.691

7.  The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey.

Authors:  Kristiina Nygren; Mukesh Dubey; Antonio Zapparata; Mudassir Iqbal; Georgios D Tzelepis; Mikael Brandström Durling; Dan Funck Jensen; Magnus Karlsson
Journal:  Evol Appl       Date:  2018-03-14       Impact factor: 5.183

Review 8.  PacBio Sequencing and Its Applications.

Authors:  Anthony Rhoads; Kin Fai Au
Journal:  Genomics Proteomics Bioinformatics       Date:  2015-11-02       Impact factor: 7.691

9.  Comparative transcriptome profiling of resistant and susceptible rice genotypes in response to the seedborne pathogen Fusarium fujikuroi.

Authors:  Slavica Matić; Paolo Bagnaresi; Chiara Biselli; Luigi Orru'; Greice Amaral Carneiro; Ilenia Siciliano; Giampiero Valé; Maria Lodovica Gullino; Davide Spadaro
Journal:  BMC Genomics       Date:  2016-08-11       Impact factor: 3.969

10.  De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes.

Authors:  Kentaro K Shimizu; Dario Copetti; Moeko Okada; Thomas Wicker; Toshiaki Tameshige; Masaomi Hatakeyama; Rie Shimizu-Inatsugi; Catharine Aquino; Kazusa Nishimura; Fuminori Kobayashi; Kazuki Murata; Tony Kuo; Emily Delorean; Jesse Poland; Georg Haberer; Manuel Spannagl; Klaus F X Mayer; Juan Gutierrez-Gonzalez; Gary J Muehlbauer; Cecile Monat; Axel Himmelbach; Sudharsan Padmarasu; Martin Mascher; Sean Walkowiak; Tetsuya Nakazaki; Tomohiro Ban; Kanako Kawaura; Hiroyuki Tsuji; Curtis Pozniak; Nils Stein; Jun Sese; Shuhei Nasuda; Hirokazu Handa
Journal:  Plant Cell Physiol       Date:  2021-03-25       Impact factor: 4.927
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.