Transcriptome Comparison Reveals Key Candidate Genes Responsible for the Unusual Reblooming Trait in Tree Peonies

Zhou, Hua; Cheng, Fangyun; Wang, Rong; Zhong, Yuan; He, Chaoying

doi:10.1371/journal.pone.0079996

Cited by 30 publications

(33 citation statements)

References 69 publications

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“…Zhang et al (2013) identified 50,829 unigenes with an average length of 585 bp. Zhou et al (2013) generated 59,275 and 63,962 unigenes with mean sizes of 698 and 699 bp from 2 types of tree peonies, respectively. Compared with these 2 studies, we obtained a larger number of unigenes in the leaf transcriptome with longer or similar average lengths.…”

Section: Discussionmentioning

confidence: 99%

“…However, the short reads generated by the Illumina platform can currently be assembled for a lower price, and a series of transcriptomes from non-model organisms have been successfully sequenced and assembled de novo (Li et al, 2012;Toledo-Silva et al, 2013). For tree peony, transcriptomes of petals and flower buds have been sequenced and millions of transcripts were obtained (Zhang et al, 2013;Zhou et al, 2013). Therefore, the Illumina platform is a preferable method for the transcriptome sequencing of peony leaves.…”

Section: Introductionmentioning

confidence: 99%

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Identification of heat shock proteins via transcriptome profiling of tree peony leaf exposed to high temperature

Zhang¹,

Cheng²,

Ya³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The tree peony leaf is an important vegetative organ that is sensitive to abiotic stress and particularly to high temperature. This sensitivity affects plant growth and restricts tree peony distribution. However, the transcriptomic information currently available on the peony leaf in public databases is limited. In this study, we sequenced the transcriptomes of peony leaves subjected to high temperature using the Illumina HiSeq TM 2000 platform. We performed de novo assembly of 93,714 unigenes (average length of 639.7 bp). By searching the public databases, 22,323 unigenes and 13,107 unigenes showed significant similarities with proteins in the NCBI non-redundant protein database and SWISS-PROT database (E-value < 1e-5), respectively. We assigned 17,340 unigenes to Gene Ontology categories, and we assigned 7618 unigenes to clusters of orthologous groups for eukaryotic complete genomes. By searching the Kyoto Encyclopedia of Genes and Genomes Pathway database, 8014 unigenes were assigned to 6 main categories, including 290 KEGG pathways. To advance research on improving thermotolerance, we identified 24 potential heat shock protein genes with complete open reading frames from the transcriptomic sequences. 8431-8442 (2015) This is the first study to characterize the leaf transcriptome of tree peony leaf using high-throughput sequencing. The information obtained from the tree peony leaf is valuable for gene discovery, and the identified heat shock protein genes can be used to improve plant stress-tolerance.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of heat shock proteins via transcriptome profiling of tree peony leaf exposed to high temperature

Zhang¹,

Cheng²,

Ya³

et al. 2015

Genet. Mol. Res.

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“…It also identified a large number of novel long non-coding RNAs and fusion transcripts [39]. At present, only NGS and SLAF-seq technologies have been applied frequently in tree peonies [40][41][42][43]. It is the first attempt to explore the carpel quantitative variation by SMLRS.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

et al. 2019

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Background Quantitative variation of floral organs in plants is caused by an extremely complex process of transcriptional regulation. Despite progress in model plants, the molecular mechanisms of quantitative variation remain unknown in woody flower plants. The Paeonia rockii originated in China is a precious woody plant with ornamental, medicinal and oil properties. There is a wide variation in the number of carpel in P. rockii , but the molecular mechanism of the variation has rarely been studied. Then a comparative transcriptome was performed among two cultivars of P. rockii with different development patterns of carpel in this study. Results Through the next-generation and single-molecule long-read sequencing (NGS and SMLRS), 66,563 unigenes and 28,155 differentially expressed genes (DEGs) were identified in P. rockii . Then clustering pattern and weighted gene coexpression network analysis (WGCNA) indicated that 15 candidate genes were likely involved in the carpel quantitative variation, including floral organ development, transcriptional regulatory and enzyme-like factors. Moreover, transcription factors (TFs) from the MYB, WD, RING1 and LRR gene families suggested the important roles in the management of the upstream genes. Among them, PsMYB114-like , PsMYB12 and PsMYB61-like from the MYB gene family were probably the main characters that regulated the carpel quantitative variation. Further, a hypothetical model for the regulation pattern of carpel quantitative variation was proposed in which the candidate genes function synergistically the quantitative variation process. Conclusions We present the high-quality sequencing products in P. rockii . Our results summarize a valuable collective of gene expression profiles characterizing the carpel quantitative variation. The DEGs are candidate for functional analyses of genes regulating the carpel quantitative variation in tree peonies, which provide a precious resource that reveals the molecular mechanism of carpel quantitative variation in other woody flower crops. Electronic supplementary material The online version of this article (10.1186/s12864-019-6036-z) contains supplementary material, which is available to authorized users.

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“…RNA-Seq has been successfully applied to many species, including Takifugu rubripes [21], Streptococcus mutans [22], Streptococcus mutans [23], Soybean [24] and tree peonies [25]. Here, we used RNA-Seq technology to characterize and identify the expression of a large number of genes, especially those expressed differentially during vernalization phase.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome comparison reveals key candidate genes in response to vernalization of Oriental lily

Liu

2016

BMC Genomics

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BackgroundOriental hybrid lily ‘Sorbonne’, a very important cut flower for lily, is enjoyed great popularity in the world, but it must experience a period of low winter temperature to initiate or accelerate the flowering process. To gain a better understanding of the temperature signaling pathway and the molecular metabolic reactions involved in the vernalization response, a genome-wide transcriptional analysis using RNA-Seq was performed.Results188,447,956 sequencing reads was assembled into 66,327 unigenes and showed similarity to known proteins in the Swiss-Prot protein database, and 2,893, 30,406 and 60,737 unigenes aligned to existing sequences in the KEGG, COG, and GO databases. Based on qRT-PCR results, we studied the expression of three signal regulation pathways genes–the plant hormones signal transduction (LoAP2, LoIAA1, LoARF10), the DNA methylation (LoCMT, LoFLD), and vernalizatin pathway (LoFLC, LoVRN1, LoVRN2, LoFT, LoSOC1, LoLFY, LoSVP) in the immature flower buds of Oriental hybrid lily. In addition, we identified two vernalizaiton–related genes (LoSVP and LoVRN1) from the cDNA library, which appear to be promising candidates for playing key roles in the development and response of flowering in Oriental lily plants, and LoSVP had a function in delaying flowering but LoVRN1could promote flowering early.ConclusionsWe collected a sample for transcriptome sequencing and comparison when the bulb’s apical meristem was in the time of floral transition when the apical meristem had not converted into the morphological differentiation process, which helped to obtain more genes playing key roles in the floral induction pathways. The upstream and downstream relationship between different genes were forecasted by the analysis of genes’ expression levels in a wide range of time. Future research that is targeted towards how genes interact on each other, which will promote establishing and perfecting the molecular mechanisms of floral induction pathway by vernalization.

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Transcriptome Comparison Reveals Key Candidate Genes Responsible for the Unusual Reblooming Trait in Tree Peonies

Cited by 30 publications

References 69 publications

Identification of heat shock proteins via transcriptome profiling of tree peony leaf exposed to high temperature

Identification of heat shock proteins via transcriptome profiling of tree peony leaf exposed to high temperature

Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

Transcriptome comparison reveals key candidate genes in response to vernalization of Oriental lily

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