Cargando…

Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor

BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating post transcriptional gene expression. Gall midges encompass a large group of insects that are of economic importance and also possess fascinating biological traits. The gall midge Mayetiola destructor, co...

Descripción completa

Detalles Bibliográficos
Autores principales: Khajuria, Chitvan, Williams, Christie E, El Bouhssini, Mustapha, Whitworth, R Jeff, Richards, Stephen, Stuart, Jeffrey J, Chen, Ming-Shun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608969/
https://www.ncbi.nlm.nih.gov/pubmed/23496979
http://dx.doi.org/10.1186/1471-2164-14-187
_version_ 1782264297661923328
author Khajuria, Chitvan
Williams, Christie E
El Bouhssini, Mustapha
Whitworth, R Jeff
Richards, Stephen
Stuart, Jeffrey J
Chen, Ming-Shun
author_facet Khajuria, Chitvan
Williams, Christie E
El Bouhssini, Mustapha
Whitworth, R Jeff
Richards, Stephen
Stuart, Jeffrey J
Chen, Ming-Shun
author_sort Khajuria, Chitvan
collection PubMed
description BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating post transcriptional gene expression. Gall midges encompass a large group of insects that are of economic importance and also possess fascinating biological traits. The gall midge Mayetiola destructor, commonly known as the Hessian fly, is a destructive pest of wheat and model organism for studying gall midge biology and insect – host plant interactions. RESULTS: In this study, we systematically analyzed miRNAs from the Hessian fly. Deep-sequencing a Hessian fly larval transcriptome led to the identification of 89 miRNA species that are either identical or very similar to known miRNAs from other insects, and 184 novel miRNAs that have not been reported from other species. A genome-wide search through a draft Hessian fly genome sequence identified a total of 611 putative miRNA-encoding genes based on sequence similarity and the existence of a stem-loop structure for miRNA precursors. Analysis of the 611 putative genes revealed a striking feature: the dramatic expansion of several miRNA gene families. The largest family contained 91 genes that encoded 20 different miRNAs. Microarray analyses revealed the expression of miRNA genes was strictly regulated during Hessian fly larval development and abundance of many miRNA genes were affected by host genotypes. CONCLUSION: The identification of a large number of miRNAs for the first time from a gall midge provides a foundation for further studies of miRNA functions in gall midge biology and behavior. The dramatic expansion of identical or similar miRNAs provides a unique system to study functional relations among miRNA iso-genes as well as changes in sequence specificity due to small changes in miRNAs and in their mRNA targets. These results may also facilitate the identification of miRNA genes for potential pest control through transgenic approaches.
format Online
Article
Text
id pubmed-3608969
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-36089692013-03-28 Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor Khajuria, Chitvan Williams, Christie E El Bouhssini, Mustapha Whitworth, R Jeff Richards, Stephen Stuart, Jeffrey J Chen, Ming-Shun BMC Genomics Research Article BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNAs that play critical roles in regulating post transcriptional gene expression. Gall midges encompass a large group of insects that are of economic importance and also possess fascinating biological traits. The gall midge Mayetiola destructor, commonly known as the Hessian fly, is a destructive pest of wheat and model organism for studying gall midge biology and insect – host plant interactions. RESULTS: In this study, we systematically analyzed miRNAs from the Hessian fly. Deep-sequencing a Hessian fly larval transcriptome led to the identification of 89 miRNA species that are either identical or very similar to known miRNAs from other insects, and 184 novel miRNAs that have not been reported from other species. A genome-wide search through a draft Hessian fly genome sequence identified a total of 611 putative miRNA-encoding genes based on sequence similarity and the existence of a stem-loop structure for miRNA precursors. Analysis of the 611 putative genes revealed a striking feature: the dramatic expansion of several miRNA gene families. The largest family contained 91 genes that encoded 20 different miRNAs. Microarray analyses revealed the expression of miRNA genes was strictly regulated during Hessian fly larval development and abundance of many miRNA genes were affected by host genotypes. CONCLUSION: The identification of a large number of miRNAs for the first time from a gall midge provides a foundation for further studies of miRNA functions in gall midge biology and behavior. The dramatic expansion of identical or similar miRNAs provides a unique system to study functional relations among miRNA iso-genes as well as changes in sequence specificity due to small changes in miRNAs and in their mRNA targets. These results may also facilitate the identification of miRNA genes for potential pest control through transgenic approaches. BioMed Central 2013-03-18 /pmc/articles/PMC3608969/ /pubmed/23496979 http://dx.doi.org/10.1186/1471-2164-14-187 Text en Copyright ©2013 Khajuria et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Khajuria, Chitvan
Williams, Christie E
El Bouhssini, Mustapha
Whitworth, R Jeff
Richards, Stephen
Stuart, Jeffrey J
Chen, Ming-Shun
Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor
title Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor
title_full Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor
title_fullStr Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor
title_full_unstemmed Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor
title_short Deep sequencing and genome-wide analysis reveals the expansion of MicroRNA genes in the gall midge Mayetiola destructor
title_sort deep sequencing and genome-wide analysis reveals the expansion of microrna genes in the gall midge mayetiola destructor
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608969/
https://www.ncbi.nlm.nih.gov/pubmed/23496979
http://dx.doi.org/10.1186/1471-2164-14-187
work_keys_str_mv AT khajuriachitvan deepsequencingandgenomewideanalysisrevealstheexpansionofmicrornagenesinthegallmidgemayetioladestructor
AT williamschristiee deepsequencingandgenomewideanalysisrevealstheexpansionofmicrornagenesinthegallmidgemayetioladestructor
AT elbouhssinimustapha deepsequencingandgenomewideanalysisrevealstheexpansionofmicrornagenesinthegallmidgemayetioladestructor
AT whitworthrjeff deepsequencingandgenomewideanalysisrevealstheexpansionofmicrornagenesinthegallmidgemayetioladestructor
AT richardsstephen deepsequencingandgenomewideanalysisrevealstheexpansionofmicrornagenesinthegallmidgemayetioladestructor
AT stuartjeffreyj deepsequencingandgenomewideanalysisrevealstheexpansionofmicrornagenesinthegallmidgemayetioladestructor
AT chenmingshun deepsequencingandgenomewideanalysisrevealstheexpansionofmicrornagenesinthegallmidgemayetioladestructor