Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis

Han, Yu; Wan, Huihua; Cheng, Tangren; Wang, Jia; Yang, Weiru; Pan, Huitang; Zhang, Qixiang

doi:10.1038/srep43382

Cited by 51 publications

(60 citation statements)

References 62 publications

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“…However, it is still unknown whether this “ABCE” is also applicable in other plant species. Recently, several studies were performed using RNA-Seq to characterize the key genes controlling petal development in some non-model plant species, such as roses, Brassica rapa and chrysanthemum [ 21 – 23 ].…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

et al. 2018

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BackgroundFlower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying this phenomenon is still obscure.ResultsHere, the comparative transcriptomic analysis was performed among petal, stamen petaloid and stamen through RNA-seq. Using pairwise comparison analysis, a large number of genes involved in hormonal signal transduction pathways and transcription factors, especially the MADS-box genes, were identified as candidate genes for stamen petaloid in lotus.ConclusionsTaken together, these results provide an insight into the molecular networks underlying lotus floral organ development and stamen petaloid.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4950-0) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

et al. 2018

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“…This was much better than previously published data for these two species (Table 2 , Additional file 1 : Table S1, Additional file 2 : Table S2; Fig. 3 a) [ 18 , 20 , 26 , 27 ] and other species/materials in Rosa [ 19 , 21 , 22 , 28 ]. A further assembly with all available data for OB produced even better transcript N50 (2092 bp) and average length (1359 bp).…”

Section: Resultsmentioning

confidence: 47%

“… 46.46 61 M 887 Yan et al 2016 [ 20 ] OB na 85,663 na na. 70 M 814 Guo et al 2017 [ 26 ] OB c 208,039 111,954 1997 45.8 231M c 1111 Han et al 2017 [ 27 ] Core set 1 BT vs. OB; 90% identity na. 10,773 2282 na.…”

Section: Resultsmentioning

confidence: 99%

“… 5959 2326 na. 13 M 2161 This study a assembly based on data produced from this study; b , assembly based on data from this study and references Yan et al [ 20 ] and Han et al [ 27 ]; c , conceptual confusion in original text; d , data from Fei lab ( http://bioinfo.bti.cornell.edu/cgi-bin/rose_454/index.cgi ) with transcript N50 and average length recalculated

Fig. 3 The assembly of high quality transcriptomes for roses.…”

Section: Resultsmentioning

confidence: 99%

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Comparative transcriptomics identifies patterns of selection in roses

Zhong

Dong

et al. 2018

BMC Plant Biol

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BackgroundRoses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge.ResultsHere, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis ‘Old Blush’ (OB) and R. wichuriana ‘Basye’s Thornless’ (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes.ConclusionsWe expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1585-x) contains supplementary material, which is available to authorized users.

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“…Furthermore, ABA is known as a versatile regulator, and plays an important role in petal development (Lü et al , Li et al , Trivellini et al ). In Rosa chinensis , most ABA signaling pathway genes were also downregulated at the petal growth stage (Han et al ).…”

Section: Discussionmentioning

confidence: 99%

Homeotic transformation from stamen to petal in Eriobotrya japonica is associated with hormone signal transduction and reduction of the transcriptional activity of EjAG

Jing

Chen

Xia

et al. 2019

Physiologia Plantarum

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Double-flower loquat (Eriobotrya japonica) is a new germplasm with homeotic transformation of stamen into petal in whorl 3. However, little information is available on the molecular mechanism of this transformation. Herein, we analyzed the transcriptome, candidate genes and endogenous hormones to investigate the mechanisms underlying this homeotic transformation. Some transcription factors, such as MADS-box, TCP and MYB, were significantly differentially expressed. Importantly, we confirmed that one of these (DN39625_c0_g1), which encoded a C-class floral homeotic protein referred to as AGAMOUS ortholog (EjAG), was significantly downregulated. Subcellular localization of EjAG was found to be in the nucleus. Ectopic expression of EjAG rescued the development of stamens and carpels from the double-flower phenotype in an Arabidopsis ag mutant, suggesting that EjAG expression is associated with double-flower formation. Meanwhile, enrichment analyses showed that the differentially expressed genes (DEGs) were mainly involved in the metabolic pathways of hormone signal transduction. The DEGs of auxin, gibberellin A (GA) and cytokinin signaling pathways were mainly upregulated. However, the DEGs of abscisic acid (ABA) and the ethylene signaling pathway were mainly downregulated. Accordingly, the concentrations of indoleacetic acid, kinetin and GA 3 were high at the petaloid stamen stage, but the ABA concentration remained low. The identified genes and pathways provide abundant sequence resources for studying the mechanisms underlying the homeotic transformation in loquat and other Rosaceae species.

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Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis

Cited by 51 publications

References 62 publications

Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

Comparative transcriptomics identifies patterns of selection in roses

Homeotic transformation from stamen to petal in Eriobotrya japonica is associated with hormone signal transduction and reduction of the transcriptional activity of EjAG

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