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Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China

Wheat blue dwarf (WBD) disease is an important disease that has caused heavy losses in wheat production in northwestern China. This disease is caused by WBD phytoplasma, which is transmitted by Psammotettix striatus. Until now, no genome information about WBD phytoplasma has been published, seriousl...

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Autores principales: Chen, Wang, Li, Yan, Wang, Qiang, Wang, Nan, Wu, Yunfeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010473/
https://www.ncbi.nlm.nih.gov/pubmed/24798075
http://dx.doi.org/10.1371/journal.pone.0096436
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author Chen, Wang
Li, Yan
Wang, Qiang
Wang, Nan
Wu, Yunfeng
author_facet Chen, Wang
Li, Yan
Wang, Qiang
Wang, Nan
Wu, Yunfeng
author_sort Chen, Wang
collection PubMed
description Wheat blue dwarf (WBD) disease is an important disease that has caused heavy losses in wheat production in northwestern China. This disease is caused by WBD phytoplasma, which is transmitted by Psammotettix striatus. Until now, no genome information about WBD phytoplasma has been published, seriously restricting research on this obligate pathogen. In this paper, we report a new sequencing and assembling strategy for phytoplasma genome projects. This strategy involves differential centrifugation, pulsed-field gel electrophoresis, whole genome amplification, shotgun sequencing, de novo assembly, screening of contigs from phytoplasma and the connection of phytoplasma contigs. Using this scheme, the WBD phytoplasma draft genome was obtained. It was comprised of six contigs with a total size of 611,462 bp, covering ∼94% of the chromosome. Five-hundred-twenty-five protein-coding genes, two operons for rRNA genes and 32 tRNA genes were identified. Comparative genome analyses between WBD phytoplasma and other phytoplasmas were subsequently carried out. The results showed that extensive arrangements and inversions existed among the WBD, OY-M and AY-WB phytoplasma genomes. Most protein-coding genes in WBD phytoplasma were found to be homologous to genes from other phytoplasmas; only 22 WBD-specific genes were identified. KEGG pathway analysis indicated that WBD phytoplasma had strongly reduced metabolic capabilities. However, 46 transporters were identified, which were involved with dipeptides/oligopeptides, spermidine/putrescine, cobalt and Mn/Zn transport, and so on. A total of 37 secreted proteins were encoded in the WBD phytoplasma chromosome and plasmids. Of these, three secreted proteins were similar to the reported phytoplasma virulence factors TENGU, SAP11 and SAP54. In addition, WBD phytoplasma possessed several proteins that were predicted to play a role in its adaptation to diverse environments. These results will provide clues for research on the pathogenic mechanisms of WBD phytoplasma and will also provide a perspective about the genome sequencing of other phytoplasmas and obligate organisms.
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spelling pubmed-40104732014-05-09 Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China Chen, Wang Li, Yan Wang, Qiang Wang, Nan Wu, Yunfeng PLoS One Research Article Wheat blue dwarf (WBD) disease is an important disease that has caused heavy losses in wheat production in northwestern China. This disease is caused by WBD phytoplasma, which is transmitted by Psammotettix striatus. Until now, no genome information about WBD phytoplasma has been published, seriously restricting research on this obligate pathogen. In this paper, we report a new sequencing and assembling strategy for phytoplasma genome projects. This strategy involves differential centrifugation, pulsed-field gel electrophoresis, whole genome amplification, shotgun sequencing, de novo assembly, screening of contigs from phytoplasma and the connection of phytoplasma contigs. Using this scheme, the WBD phytoplasma draft genome was obtained. It was comprised of six contigs with a total size of 611,462 bp, covering ∼94% of the chromosome. Five-hundred-twenty-five protein-coding genes, two operons for rRNA genes and 32 tRNA genes were identified. Comparative genome analyses between WBD phytoplasma and other phytoplasmas were subsequently carried out. The results showed that extensive arrangements and inversions existed among the WBD, OY-M and AY-WB phytoplasma genomes. Most protein-coding genes in WBD phytoplasma were found to be homologous to genes from other phytoplasmas; only 22 WBD-specific genes were identified. KEGG pathway analysis indicated that WBD phytoplasma had strongly reduced metabolic capabilities. However, 46 transporters were identified, which were involved with dipeptides/oligopeptides, spermidine/putrescine, cobalt and Mn/Zn transport, and so on. A total of 37 secreted proteins were encoded in the WBD phytoplasma chromosome and plasmids. Of these, three secreted proteins were similar to the reported phytoplasma virulence factors TENGU, SAP11 and SAP54. In addition, WBD phytoplasma possessed several proteins that were predicted to play a role in its adaptation to diverse environments. These results will provide clues for research on the pathogenic mechanisms of WBD phytoplasma and will also provide a perspective about the genome sequencing of other phytoplasmas and obligate organisms. Public Library of Science 2014-05-05 /pmc/articles/PMC4010473/ /pubmed/24798075 http://dx.doi.org/10.1371/journal.pone.0096436 Text en © 2014 Chen et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Chen, Wang
Li, Yan
Wang, Qiang
Wang, Nan
Wu, Yunfeng
Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
title Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
title_full Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
title_fullStr Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
title_full_unstemmed Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
title_short Comparative Genome Analysis of Wheat Blue Dwarf Phytoplasma, an Obligate Pathogen That Causes Wheat Blue Dwarf Disease in China
title_sort comparative genome analysis of wheat blue dwarf phytoplasma, an obligate pathogen that causes wheat blue dwarf disease in china
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4010473/
https://www.ncbi.nlm.nih.gov/pubmed/24798075
http://dx.doi.org/10.1371/journal.pone.0096436
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