Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes

Abstract Background: Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to gu...

Descripción completa

Detalles Bibliográficos
Autores principales: Valdés Franco, José A., Wang, Yi, Huo, Naxin, Ponciano, Grisel, Colvin, Howard A., McMahan, Colleen M., Gu, Yong Q., Belknap, William R.
Formato: Artículo
Lenguaje:inglés
Publicado: BioMed Central 2018
Materias:
Acceso en línea:http://eprints.uanl.mx/16308/1/151.pdf
_version_ 1824414570852122624
author Valdés Franco, José A.
Wang, Yi
Huo, Naxin
Ponciano, Grisel
Colvin, Howard A.
McMahan, Colleen M.
Gu, Yong Q.
Belknap, William R.
author_facet Valdés Franco, José A.
Wang, Yi
Huo, Naxin
Ponciano, Grisel
Colvin, Howard A.
McMahan, Colleen M.
Gu, Yong Q.
Belknap, William R.
author_sort Valdés Franco, José A.
collection Repositorio Institucional
description Abstract Background: Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. Results: The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50 =22 kb), maps >95% of the shotgun reads and is essentially complete. Approximately 40,000 transcribed, protein encoding genes were annotated on the assembly. Further characterization of this genome revealed 15 families of small, microsatellite-associated, transposable elements (TEs) with unexpected chromosomal distribution profiles. These SaTar (Satellite Targeted) elements, which are non-autonomous Mu-like elements (MULEs), were frequently observed in multimeric linear arrays of unrelated individual elements within which no individual element is interrupted by another. This uniformly non-nested TE multimer architecture has not been previously described in either eukaryotic or prokaryotic genomes. Five families of similarly distributed non-autonomous MULEs (microsatellite associated, modularly assembled) were characterized in the rice genome. Families of TEs with similar structures and distribution profiles were identified in sorghum and citrus. Conclusion: The sequencing and assembly of the guayule genome provides a foundation for application of current crop improvement technologies to this plant. In addition, characterization of this genome revealed SaTar elements with distribution profiles unique among TEs. Satar targeting appears based on an alternative MULE recombination mechanism with the potential to impact gene evolution. Keywords: Natural rubber, Genome, Assembly, Annotation, Class II transposable element, Non-autonomous, Transposon
format Article
id eprints-16308
institution UANL
language English
publishDate 2018
publisher BioMed Central
record_format eprints
spelling eprints-163082023-04-25T17:39:34Z http://eprints.uanl.mx/16308/ Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes Valdés Franco, José A. Wang, Yi Huo, Naxin Ponciano, Grisel Colvin, Howard A. McMahan, Colleen M. Gu, Yong Q. Belknap, William R. QH Historia Natural, Biología Abstract Background: Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. Results: The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50 =22 kb), maps >95% of the shotgun reads and is essentially complete. Approximately 40,000 transcribed, protein encoding genes were annotated on the assembly. Further characterization of this genome revealed 15 families of small, microsatellite-associated, transposable elements (TEs) with unexpected chromosomal distribution profiles. These SaTar (Satellite Targeted) elements, which are non-autonomous Mu-like elements (MULEs), were frequently observed in multimeric linear arrays of unrelated individual elements within which no individual element is interrupted by another. This uniformly non-nested TE multimer architecture has not been previously described in either eukaryotic or prokaryotic genomes. Five families of similarly distributed non-autonomous MULEs (microsatellite associated, modularly assembled) were characterized in the rice genome. Families of TEs with similar structures and distribution profiles were identified in sorghum and citrus. Conclusion: The sequencing and assembly of the guayule genome provides a foundation for application of current crop improvement technologies to this plant. In addition, characterization of this genome revealed SaTar elements with distribution profiles unique among TEs. Satar targeting appears based on an alternative MULE recombination mechanism with the potential to impact gene evolution. Keywords: Natural rubber, Genome, Assembly, Annotation, Class II transposable element, Non-autonomous, Transposon BioMed Central 2018 Article PeerReviewed text en cc_by_nc_nd http://eprints.uanl.mx/16308/1/151.pdf http://eprints.uanl.mx/16308/1.haspreviewThumbnailVersion/151.pdf Valdés Franco, José A. y Wang, Yi y Huo, Naxin y Ponciano, Grisel y Colvin, Howard A. y McMahan, Colleen M. y Gu, Yong Q. y Belknap, William R. (2018) Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes. BMC Genomics, 19 (1). pp. 1-14. ISSN 1471-2164 doi:10.1186/s12864-018-4653-6
spellingShingle QH Historia Natural, Biología
Valdés Franco, José A.
Wang, Yi
Huo, Naxin
Ponciano, Grisel
Colvin, Howard A.
McMahan, Colleen M.
Gu, Yong Q.
Belknap, William R.
Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
thumbnail https://rediab.uanl.mx/themes/sandal5/images/online.png
title Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
title_full Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
title_fullStr Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
title_full_unstemmed Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
title_short Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
title_sort modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes
topic QH Historia Natural, Biología
url http://eprints.uanl.mx/16308/1/151.pdf
work_keys_str_mv AT valdesfrancojosea modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes
AT wangyi modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes
AT huonaxin modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes
AT poncianogrisel modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes
AT colvinhowarda modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes
AT mcmahancolleenm modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes
AT guyongq modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes
AT belknapwilliamr modularassemblyoftransposableelementarraysbymicrosatellitetargetingintheguayuleandricegenomes