Transcriptome sequencing and metabolite analysis reveals the role of delphinidin metabolism in flower colour in grape hyacinth

Lei, Qian; Liu, Yali; Qi, Yinyan; Jiao, Shungang; Tian, Feifei; Jiang, Ling; Wang, Yuejin

doi:10.1093/jxb/eru168

Cited by 200 publications

(181 citation statements)

References 25 publications

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“…A series of transcriptomes of colored plant tissues have been sequenced using high-throughput sequencing technology, leading to the identification of many anthocyanin-related genes, as has been done in grape hyacinth (Lou et al, 2014), Camellia chekiangoleosa , and in the pericarp of Litchi chinensis (Lai et al, 2015). In this study, the transcriptome of red leaf lettuce was sequenced using an Illumina HiSeq 2500 platform.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis and anthocyanin-related genes in red leaf lettuce

Zhang

Cheng

et al. 2016

Genet. Mol. Res.

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ABSTRACT.This study aimed to analyze the transcriptome profile of red lettuce and identify the genes involved in anthocyanin accumulation. Red leaf lettuce is a popular vegetable and popular due to its high anthocyanin content. However, there is limited information available about the genes involved in anthocyanin biosynthesis in this species. In this study, transcriptomes of 15-day-old seedlings and 40-day-old red lettuce leaves were analyzed using an Illuminia Hiseq TM 2500 platform. A total of 10.6 GB clean data were obtained and de novo assembled into 83,333 unigenes with an N50 of 1067. After annotation against public databases, 51,850 unigene sequences were identified, among which 46,087 were annotated in the NCBI non-redundant protein database, and 41,752 were annotated in the Swiss-Prot database. A total of 9125 unigenes were mapped into 163 pathways using the Kyoto Encyclopedia of Genes and Genomes database. Thirty-four structural genes were found to cover the main steps of the anthocyanin pathway, including chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, dihydroflavonol 4-reductase, and anthocyanidin synthase. Seven MYB, three bHLH, and two WD40 genes, considered anthocyanin regulatory genes, were also identified. In addition, 3607 simple sequence repeat (SSR) markers were identified from 2916 unigenes. This research uncovered the transcriptomic characteristics of red leaf lettuce seedlings and mature plants. The identified candidate genes related to anthocyanin biosynthesis and the detected SSRs provide useful tools for future molecular breeding studies.

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Section: Discussionmentioning

confidence: 99%

Transcriptome analysis and anthocyanin-related genes in red leaf lettuce

Zhang

Cheng

et al. 2016

Genet. Mol. Res.

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“…To date, studies based on increasingly available sequence data have detected numerous genes and expression profiles that occur during the development of plant tissues such as flowers, leaves, and fruits (Ando et al 2012;Sweetman et al 2012;Singh et al 2013;Lou et al 2014). The root provides the plant growth with water, nutrients, and anchorage (Rich and Watt 2013), and an understanding of how root growth is controlled by hormones is essential for crop production, especially for fleshy root plants such as the carrot (Herder et al 2010;Remans et al 2012).…”

Section: Discussionmentioning

confidence: 99%

Sequencing, assembly, annotation, and gene expression: novel insights into the hormonal control of carrot root development revealed by a high-throughput transcriptome

Wang

Jia

et al. 2015

Mol Genet Genomics

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Previous studies have indicated that hormonal control is essential for plant root growth. The root of the carrot is an edible vegetable with a high nutritional value. However, molecular mechanisms underlying hormone-mediated root growth of carrot have not been illustrated. Therefore, the present study collected carrot root samples from four developmental stages, and performed transcriptome sequencing to understand the molecular functions of plant hormones in carrot root growth. A total of 160,227 transcripts were generated from our transcriptome, which were assembled into 32,716 unigenes with an average length of 1,453 bp. A total of 4,818 unigenes were found to be differentially expressed between the four developmental stages. In total, 87 hormone-related differentially expressed genes were identified, and the roles of the hormones are extensively discussed. Our results suggest that plant hormones may regulate carrot root growth in a phase-dependent manner, and these findings will provide valuable resources for future research on carrot root development.

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“…Many metabolic pathways, physiological processes, and growth and development mechanisms of non-model plant have been revealed by de novo transcriptome sequencing (Wu et al, 2014;Lang et al, 2015). The analysis of differentially expressed genes based on transcriptomic data from several samples is a powerful tool for revealing the biological mechanisms underlying differences among individuals (Lou et al, 2014;Liu et al, 2015;Shi et al, 2015). In particular, differential gene expression analyses showed that GGPS and (-)-alpha/ beta-pinene synthase were up-regulated in the high oleoresin-yielding genotype of Pinus massoniana .…”

Section: Discussionmentioning

confidence: 99%

Transcriptome and gene expression analysis revealed mechanisms for producing high oleoresin yields from Simao pine (Pinus kesiya var. langbianensis)

Wang¹,

Yuan²,

Mei³

et al. 2018

Plant Omics

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Simao pine (Pinus kesiya Royle ex Gordon var. langbianensis (A. Chev.) Gaussen) is an important oleoresin source in Yunnan Province, China. However, the molecular mechanisms of high oleoresin yield from Simao pine remain unclear. In this study, RNA-Seq was used to investigate the transcriptome of the species and compare the gene expression profiles of wounded bark from high and low oleoresin-yielding individuals, and the expression levels of genes in the methyl-erythritol 4-phosphate (MEP) pathway were detected by qPCR. A total of 1.41 billion reads were obtained and assembled into 68,881 unigenes from samples of the wounded bark of Simao pine. The KEGG analysis of differentially expressed genes showed that MEP pathway genes were obviously differentially expressed, while most genes in the mevalonate (MVA) pathway were not. The qPCR analysis showed that the MEP pathway gene expression of wounded bark from high oleoresin-yielding genotypes was higher than that of low oleoresin-yielding genotypes. The gene expression differences of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), and geranylgeranyl pyrophosphate synthase (GGPPs) between high and low oleoresin-yielding genotypes were significant. This implies that DXS, HDR, and GGPPs play important roles in high oleoresin production in Simao pine.

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Transcriptome sequencing and metabolite analysis reveals the role of delphinidin metabolism in flower colour in grape hyacinth

Abstract: SummaryThrough a combination of metabolite analysis with transcriptome sequencing, a new hypothesis was proposed to explain the lack of colour phenotype of the white variant of the blue grape hyacinth.

Cited by 200 publications

References 25 publications

Transcriptome analysis and anthocyanin-related genes in red leaf lettuce

Transcriptome analysis and anthocyanin-related genes in red leaf lettuce

Sequencing, assembly, annotation, and gene expression: novel insights into the hormonal control of carrot root development revealed by a high-throughput transcriptome

Transcriptome and gene expression analysis revealed mechanisms for producing high oleoresin yields from Simao pine (Pinus kesiya var. langbianensis)

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