SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica

Abstract Seagrass meadows are among the four most productive marine ecosystems in the world. Zostera japonica (Z. japonica) is the most widely distributed species of seagrass in China. However, there is no reference genome or transcriptome available for Z. japonica, impeding progress in functional g...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Siting Chen, Guanglong Qiu, Mingliu Yang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c37b9af137b2496c8b81c213da82b127
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c37b9af137b2496c8b81c213da82b127
record_format	dspace
spelling	oai:doaj.org-article:c37b9af137b2496c8b81c213da82b1272021-12-02T15:09:39ZSMRT sequencing of full-length transcriptome of seagrasses Zostera japonica10.1038/s41598-019-51176-y2045-2322https://doaj.org/article/c37b9af137b2496c8b81c213da82b1272019-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-51176-yhttps://doaj.org/toc/2045-2322Abstract Seagrass meadows are among the four most productive marine ecosystems in the world. Zostera japonica (Z. japonica) is the most widely distributed species of seagrass in China. However, there is no reference genome or transcriptome available for Z. japonica, impeding progress in functional genomic and molecular ecology studies in this species. Temperature is the main factor that controls the distribution and growth of seagrass around the world, yet how seagrass responds to heat stress remains poorly understood due to the lack of genomic and transcriptomic data. In this study, we applied a combination of second- and third-generation sequencing technologies to sequence full-length transcriptomes of Z. japonica. In total, we obtained 58,134 uniform transcripts, which included 46,070 high-quality full-length transcript sequences. We identified 15,411 simple sequence repeats, 258 long non-coding RNAs and 28,038 open reading frames. Exposure to heat elicited a complex transcriptional response in genes involved in posttranslational modification, protein turnover and chaperones. Overall, our study provides the first large-scale full-length trascriptome in Zostera japonica, allowing for structural, functional and comparative genomics studies in this important seagrass species. Although previous studies have focused specifically on heat shock proteins, we found that examination of other heat stress related genes is important for studying response to heat stress in seagrass. This study provides a genetic resource for the discovery of genes related to heat stress tolerance in this species. Our transcriptome can be further utilized in future studies to understand the molecular adaptation to heat stress in Zostera japonica.Siting ChenGuanglong QiuMingliu YangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-13 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Siting Chen Guanglong Qiu Mingliu Yang SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica
description	Abstract Seagrass meadows are among the four most productive marine ecosystems in the world. Zostera japonica (Z. japonica) is the most widely distributed species of seagrass in China. However, there is no reference genome or transcriptome available for Z. japonica, impeding progress in functional genomic and molecular ecology studies in this species. Temperature is the main factor that controls the distribution and growth of seagrass around the world, yet how seagrass responds to heat stress remains poorly understood due to the lack of genomic and transcriptomic data. In this study, we applied a combination of second- and third-generation sequencing technologies to sequence full-length transcriptomes of Z. japonica. In total, we obtained 58,134 uniform transcripts, which included 46,070 high-quality full-length transcript sequences. We identified 15,411 simple sequence repeats, 258 long non-coding RNAs and 28,038 open reading frames. Exposure to heat elicited a complex transcriptional response in genes involved in posttranslational modification, protein turnover and chaperones. Overall, our study provides the first large-scale full-length trascriptome in Zostera japonica, allowing for structural, functional and comparative genomics studies in this important seagrass species. Although previous studies have focused specifically on heat shock proteins, we found that examination of other heat stress related genes is important for studying response to heat stress in seagrass. This study provides a genetic resource for the discovery of genes related to heat stress tolerance in this species. Our transcriptome can be further utilized in future studies to understand the molecular adaptation to heat stress in Zostera japonica.
format	article
author	Siting Chen Guanglong Qiu Mingliu Yang
author_facet	Siting Chen Guanglong Qiu Mingliu Yang
author_sort	Siting Chen
title	SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica
title_short	SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica
title_full	SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica
title_fullStr	SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica
title_full_unstemmed	SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica
title_sort	smrt sequencing of full-length transcriptome of seagrasses zostera japonica
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/c37b9af137b2496c8b81c213da82b127
work_keys_str_mv	AT sitingchen smrtsequencingoffulllengthtranscriptomeofseagrasseszosterajaponica AT guanglongqiu smrtsequencingoffulllengthtranscriptomeofseagrasseszosterajaponica AT mingliuyang smrtsequencingoffulllengthtranscriptomeofseagrasseszosterajaponica
_version_	1718387838113808384

SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica

Ejemplares similares