About: De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing

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About: De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing
Creator	He, Jia Jiang, Jingwei Jiang, Yumei Li, Xiaodan Liang, Lijian Peng, Feng Wang, Ren Xia, Bing Xu, Sheng
Source	Medline; PMC
abstract	BACKGROUND: Lycoris aurea, also called Golden Magic Lily, is an ornamentally and medicinally important species of the Amaryllidaceae family. To date, the sequencing of its whole genome is unavailable as a non-model organism. Transcriptomic information is also scarce for this species. In this study, we performed de novo transcriptome sequencing to produce the first comprehensive expressed sequence tag (EST) dataset for L. aurea using high-throughput sequencing technology. METHODOLOGY AND PRINCIPAL FINDINGS: Total RNA was isolated from leaves with sodium nitroprusside (SNP), salicylic acid (SA), or methyl jasmonate (MeJA) treatment, stems, and flowers at the bud, blooming, and wilting stages. Equal quantities of RNA from each tissue and stage were pooled to construct a cDNA library. Using 454 pyrosequencing technology, a total of 937,990 high quality reads (308.63 Mb) with an average read length of 329 bp were generated. Clustering and assembly of these reads produced a non-redundant set of 141,111 unique sequences, comprising 24,604 contigs and 116,507 singletons. All of the unique sequences were involved in the biological process, cellular component and molecular function categories by GO analysis. Potential genes and their functions were predicted by KEGG pathway mapping and COG analysis. Based on our sequence analysis and published literatures, many putative genes involved in Amaryllidaceae alkaloids synthesis, including PAL, TYDC OMT, NMT, P450, and other potentially important candidate genes, were identified for the first time in this Lycoris. Furthermore, 6,386 SSRs and 18,107 high-confidence SNPs were identified in this EST dataset. CONCLUSIONS: The transcriptome provides an invaluable new data for a functional genomics resource and future biological research in L. aurea. The molecular markers identified in this study will provide a material basis for future genetic linkage and quantitative trait loci analyses, and will provide useful information for functional genomic research in future.
has issue date	2013-04-09(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0060449
bibo:pmid	23593220
has license	cc-by
sha1sum (hex)	cd06185d94b38abd3c8209a45897a589da964bf2
schema:url	https://doi.org/10.1371/journal.pone.0060449
resource representing a document's title	De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing
has PubMed Central identifier	PMC3621892
has PubMed identifier	23593220
schema:publication	PLoS One
resource representing a document's body	covid:cd06185d94b38abd3c8209a45897a589da964bf2#body_text
is schema:about of	named entity 'FLX' named entity 'de novo' named entity 'family' named entity 'sequencing' named entity 'Lycoris' named entity 'Pyrosequencing' named entity 'De novo' named entity 'LYCORIS AUREA' named entity 'AMARYLLIDACEAE' named entity 'HIGH-THROUGHPUT SEQUENCING' named entity 'DATE' named entity 'TRANSCRIPTOME SEQUENCING' named entity 'ORGANISM' named entity 'SPECIES' named entity 'PERFORMED' named entity 'SEQUENCING TECHNOLOGY' named entity 'FAMILY' named entity 'TO PRODUCE' named entity 'NON-' named entity 'LYCORIS AUREA' named entity 'IMPORTANT' named entity 'DATASET' named entity 'MAGIC' named entity 'ITS' named entity 'LILY' named entity 'STUDY' named entity 'UNAVAILABLE' named entity 'USING' named entity 'INFORMATION' named entity 'EXPRESSED SEQUENCE TAG' named entity 'DE NOVO' named entity '454' named entity 'TRANSCRIPTOME' named entity 'PYROSEQUENCING' named entity 'CHARACTERIZATION' named entity 'TITANIUM' named entity 'SEQUENCE ASSEMBLY' named entity 'DE NOVO' named entity 'COMPREHENSIVE' named entity 'BACKGROUND' named entity 'AUREA' named entity 'SEQUENCING' named entity 'GOLDEN' named entity 'USING' named entity 'PLATFORM' named entity 'WHOLE GENOME' named entity 'MODEL' covid:arg/cd06185d94b38abd3c8209a45897a589da964bf2 named entity 'ornamentally' named entity 'Lycoris' named entity 'species' named entity 'organism' named entity 'dataset' named entity 'Amaryllidaceae' named entity 'Characterization' named entity 'Transcriptomic' named entity 'model organism' named entity 'ornamentally' named entity 'high-throughput sequencing technology' named entity 'karyotypes' named entity 'China' named entity 'pathogen' named entity 'cell growth' named entity 'alkaloids' named entity 'global map' named entity 'cDNA library' named entity 'SNP' named entity 'SNPs' named entity 'pharmacology' named entity 'Transcription' named entity 'cytochrome P450' named entity 'NMT' named entity 'coupling reaction'

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