PhytophthoraV1, Main, Exploration, bibRecord, 000914

The 25-26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes.

Identifieur interne : 000914 ( Main/Exploration ); précédent : 000913; suivant : 000915

The 25-26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes.

Source :

Frontiers in microbiology [ 1664-302X ] ; 2017.

RBID : pubmed:28512457

Abstract

Small RNAs (sRNAs) are important non-coding RNA regulators, playing key roles in developmental regulation, transposon suppression, environmental response, host-pathogen interaction and other diverse biological processes. However, their roles in oomycetes are poorly understood. Here, we performed sRNA sequencing and RNA sequencing of Phytophthora parasitica at stages of vegetative growth and infection of Arabidopsis roots to examine diversity and function of sRNAs in P. parasitica, a model hemibiotrophic oomycete plant pathogen. Our results indicate that there are two distinct types of sRNA-generating loci in P. parasitica genome, giving rise to clusters of 25-26 nt and 21 nt sRNAs, respectively, with no significant strand-biases. The 25-26 nt sRNA loci lie predominantly in gene-sparse and repeat-rich regions, and overlap with over 7000 endogenous gene loci. These overlapped genes are typically P. parasitica species-specific, with no homologies to the sister species P. infestans. They include approximately 40% RXLR effector genes, 50% CRN effector genes and some elicitor genes. The transcripts of most of these genes could not be detected at both the vegetative mycelium and infection stages as revealed by RNA sequencing, indicating that the 25-26 nt sRNAs are associated with efficient silencing of these genes. The 21 nt sRNA loci typically overlap with the exon regions of highly expressed genes, suggesting that the biogenesis of the 21 nt sRNAs may be dependent on the level of gene transcription and that these sRNAs do not mediate efficient silencing of homologous genes. Analyses of the published P. infestans sRNA and mRNA sequencing data consistently show that the 25-26 nt sRNAs, but not the 21 nt sRNAs, may mediate efficient gene silencing in Phytophthora.

DOI: 10.3389/fmicb.2017.00773
PubMed: 28512457
PubMed Central: PMC5411455

Affiliations:

République populaire de Chine

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<front><div type="abstract" xml:lang="en">Small RNAs (sRNAs) are important non-coding RNA regulators, playing key roles in developmental regulation, transposon suppression, environmental response, host-pathogen interaction and other diverse biological processes. However, their roles in oomycetes are poorly understood. Here, we performed sRNA sequencing and RNA sequencing of <i>Phytophthora parasitica</i>
 at stages of vegetative growth and infection of <i>Arabidopsis</i>
 roots to examine diversity and function of sRNAs in <i>P. parasitica</i>
, a model hemibiotrophic oomycete plant pathogen. Our results indicate that there are two distinct types of sRNA-generating loci in <i>P. parasitica</i>
 genome, giving rise to clusters of 25-26 nt and 21 nt sRNAs, respectively, with no significant strand-biases. The 25-26 nt sRNA loci lie predominantly in gene-sparse and repeat-rich regions, and overlap with over 7000 endogenous gene loci. These overlapped genes are typically <i>P. parasitica</i>
 species-specific, with no homologies to the sister species <i>P. infestans</i>
. They include approximately 40% RXLR effector genes, 50% CRN effector genes and some elicitor genes. The transcripts of most of these genes could not be detected at both the vegetative mycelium and infection stages as revealed by RNA sequencing, indicating that the 25-26 nt sRNAs are associated with efficient silencing of these genes. The 21 nt sRNA loci typically overlap with the exon regions of highly expressed genes, suggesting that the biogenesis of the 21 nt sRNAs may be dependent on the level of gene transcription and that these sRNAs do not mediate efficient silencing of homologous genes. Analyses of the published <i>P. infestans</i>
 sRNA and mRNA sequencing data consistently show that the 25-26 nt sRNAs, but not the 21 nt sRNAs, may mediate efficient gene silencing in <i>Phytophthora</i>
.</div>
</front>
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<Abstract><AbstractText>Small RNAs (sRNAs) are important non-coding RNA regulators, playing key roles in developmental regulation, transposon suppression, environmental response, host-pathogen interaction and other diverse biological processes. However, their roles in oomycetes are poorly understood. Here, we performed sRNA sequencing and RNA sequencing of <i>Phytophthora parasitica</i>
 at stages of vegetative growth and infection of <i>Arabidopsis</i>
 roots to examine diversity and function of sRNAs in <i>P. parasitica</i>
, a model hemibiotrophic oomycete plant pathogen. Our results indicate that there are two distinct types of sRNA-generating loci in <i>P. parasitica</i>
 genome, giving rise to clusters of 25-26 nt and 21 nt sRNAs, respectively, with no significant strand-biases. The 25-26 nt sRNA loci lie predominantly in gene-sparse and repeat-rich regions, and overlap with over 7000 endogenous gene loci. These overlapped genes are typically <i>P. parasitica</i>
 species-specific, with no homologies to the sister species <i>P. infestans</i>
. They include approximately 40% RXLR effector genes, 50% CRN effector genes and some elicitor genes. The transcripts of most of these genes could not be detected at both the vegetative mycelium and infection stages as revealed by RNA sequencing, indicating that the 25-26 nt sRNAs are associated with efficient silencing of these genes. The 21 nt sRNA loci typically overlap with the exon regions of highly expressed genes, suggesting that the biogenesis of the 21 nt sRNAs may be dependent on the level of gene transcription and that these sRNAs do not mediate efficient silencing of homologous genes. Analyses of the published <i>P. infestans</i>
 sRNA and mRNA sequencing data consistently show that the 25-26 nt sRNAs, but not the 21 nt sRNAs, may mediate efficient gene silencing in <i>Phytophthora</i>
.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jia</LastName>
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<Author ValidYN="Y"><LastName>Lu</LastName>
<ForeName>Wenqin</ForeName>
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</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zhong</LastName>
<ForeName>Chengcheng</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zhou</LastName>
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<Initials>R</Initials>
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<Initials>J</Initials>
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</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Gou</LastName>
<ForeName>Xiuhong</ForeName>
<Initials>X</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Wang</LastName>
<ForeName>Qinhu</ForeName>
<Initials>Q</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Yin</LastName>
<ForeName>Junliang</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Xu</LastName>
<ForeName>Cheng</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>Chongqing Tobacco Research InstituteChongqing, China.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Shan</LastName>
<ForeName>Weixing</ForeName>
<Initials>W</Initials>
<AffiliationInfo><Affiliation>State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F UniversityYangling, China.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F UniversityYangling, China.</Affiliation>
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<Month>05</Month>
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The 25-26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes.

The 25-26 nt Small RNAs in Phytophthora parasitica Are Associated with Efficient Silencing of Homologous Endogenous Genes.

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