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Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses

Cinnamomum chago, an endangered species endemic to Yunnan province, possesses large economic and phylogenetic values in Lauraceae. However, the genomic information of this species remains relatively unexplored. In this study, we used RNAseq technology to characterize and annotate the C. chago transc...

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Autores principales: Zhang, Xue, Zhang, Yue, Wang, Yue-Hua, Shen, Shi-Kang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231050/
https://www.ncbi.nlm.nih.gov/pubmed/30455715
http://dx.doi.org/10.3389/fgene.2018.00505
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author Zhang, Xue
Zhang, Yue
Wang, Yue-Hua
Shen, Shi-Kang
author_facet Zhang, Xue
Zhang, Yue
Wang, Yue-Hua
Shen, Shi-Kang
author_sort Zhang, Xue
collection PubMed
description Cinnamomum chago, an endangered species endemic to Yunnan province, possesses large economic and phylogenetic values in Lauraceae. However, the genomic information of this species remains relatively unexplored. In this study, we used RNAseq technology to characterize and annotate the C. chago transcriptome and identify candidate genes involved in special metabolic pathways and gene-associated simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP). A total of 129,097 unigenes, with a mean length of 667 bp and an N50 length of 1,062 bp, were assembled. Among these genes, 56,887 (44.07%) unigenes were successfully annotated using at least one database. Furthermore, 47 and 46 candidate genes were identified in terpenoid biosynthesis and fatty acid biosynthesis, respectively. A total of 22 candidate genes participated in at least one abiotic stress response of C. chago. Additionally, a total of 25,654 SSRs and 640 SNPs were also identified. Based on these potential loci, 55 novel expressed sequence tag (EST)-SSR primers were successfully developed. This work provides comprehensive transcriptomic data that can be used to establish a valuable information platform for gene prediction, signaling pathway investigation, and molecular marker development for C. chago and other related species. Such a platform can facilitate further studies on germplasm conservation and utilization of Lauraceae species.
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spelling pubmed-62310502018-11-19 Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses Zhang, Xue Zhang, Yue Wang, Yue-Hua Shen, Shi-Kang Front Genet Genetics Cinnamomum chago, an endangered species endemic to Yunnan province, possesses large economic and phylogenetic values in Lauraceae. However, the genomic information of this species remains relatively unexplored. In this study, we used RNAseq technology to characterize and annotate the C. chago transcriptome and identify candidate genes involved in special metabolic pathways and gene-associated simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP). A total of 129,097 unigenes, with a mean length of 667 bp and an N50 length of 1,062 bp, were assembled. Among these genes, 56,887 (44.07%) unigenes were successfully annotated using at least one database. Furthermore, 47 and 46 candidate genes were identified in terpenoid biosynthesis and fatty acid biosynthesis, respectively. A total of 22 candidate genes participated in at least one abiotic stress response of C. chago. Additionally, a total of 25,654 SSRs and 640 SNPs were also identified. Based on these potential loci, 55 novel expressed sequence tag (EST)-SSR primers were successfully developed. This work provides comprehensive transcriptomic data that can be used to establish a valuable information platform for gene prediction, signaling pathway investigation, and molecular marker development for C. chago and other related species. Such a platform can facilitate further studies on germplasm conservation and utilization of Lauraceae species. Frontiers Media S.A. 2018-11-05 /pmc/articles/PMC6231050/ /pubmed/30455715 http://dx.doi.org/10.3389/fgene.2018.00505 Text en Copyright © 2018 Zhang, Zhang, Wang and Shen. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Zhang, Xue
Zhang, Yue
Wang, Yue-Hua
Shen, Shi-Kang
Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses
title Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses
title_full Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses
title_fullStr Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses
title_full_unstemmed Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses
title_short Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses
title_sort transcriptome analysis of cinnamomum chago: a revelation of candidate genes for abiotic stress response and terpenoid and fatty acid biosyntheses
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6231050/
https://www.ncbi.nlm.nih.gov/pubmed/30455715
http://dx.doi.org/10.3389/fgene.2018.00505
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