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Phalaenopsis equestris

ABSTRACT: Phalaenopsis equestris Genome sequencing and assembly

PROVIDER: PRJNA192198 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
		Other
	SRR827602_1.fastq.gz	Fastqsanger.gz
	SRR827602_2.fastq.gz	Fastqsanger.gz
	SRR827603_1.fastq.gz	Fastqsanger.gz
	SRR827603_2.fastq.gz	Fastqsanger.gz

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De novo transcriptome assembly databases in the butterfly orchid Phalaenopsis equestris

Project description:Orchidaceae are renowned for their spectacular flowers as well as other reproductive and ecological adaptations. After the genome of the tropical epiphytic orchid Phalaenopsis equestris was sequenced, we combined Trinity data for de novo assembly and Illumina HiSeq1500 data for RNA-Seq analysis to characterize the transcriptomes of four different organs for a better understanding of the molecular mechanisms driving these characteristics. We present four de novo assembled transcripts reconstructed from RNA collected from the root, stem, leaf, and flower of Phalaenopsis equestris. These sets of transcripts greatly enrich the available data for Phalaenopsis equestris. Here, we present two databases, and each dataset allows for a different type of search for candidate homologues. The first dataset consists of the sets of assembled unigenes, which enable a sequence-based search. A comprehensive analysis of the assembled unigenes revealed the unigenes from root, stem, leaf, and flower with high e-values aligned versus the Nr, Swiss-Port, KEGG, COG, and GO database, respectively. This analysis enabled the production of a second database, which includes sequences correlated with annotated transcript names as well as the confidence of the best hit from BLAST.

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High-density genetic map and genome-wide associaation studies of floral color traits in Phalaenopsis orchids

Project description:The F1 population of Phalaenopsis Intermedia, which established from the cross between P. equestris and P. aphrodite was applied to build a high-density genetic map based on SSRs and SNPs from GBS methodology, with the digestion of by Hinp1 I and Hae III. In addition, another GBS was performed with enzymes ApeK I and Hae II to increase the SNP number for the GWAS analysis. We identified 10 SNPs highly associated with floral aesthetic trait, and among them, 4 were associated with flower color related. Genes with function related to anthocyanin biosynthesis were identified as the candidate genes. In addition, the flowering time-related gene SOC1 may contribute to flower color regulation in our discovery.

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