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• W3062912011 abstract "Abstract Background The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-reads sequencing techniques revealed their potential to generate complete transcript assemblies even when a reference genome is lacking. Cynara cardunculus var. altilis (DC) (cultivated cardoon) is a perennial hardy crop adapted to dry environments with many industrial and nutraceutical applications due to the richness of secondary metabolites mostly produced in flower heads. The investigation of this species benefited from the recent release of a draft genome, but the transcriptome profile during the capitula formation still remains unexplored. In the present study we show a transcriptome analysis of vegetative and inflorescence organs of cultivated cardoon through a novel hybrid RNA-seq assembly approach utilizing both long and short RNA-seq reads. Results The inclusion of a single Nanopore flow-cell output in a hybrid sequencing approach determined an increase of 15% complete assembled genes and 18% transcript isoforms respect to short reads alone. Among 25,463 assembled unigenes, we identified 578 new genes and updated 13,039 gene models, 11,169 of which were alternatively spliced isoforms. During capitulum development, 3424 genes were differentially expressed and approximately two-thirds were identified as transcription factors including bHLH, MYB, NAC, C2H2 and MADS-box which were highly expressed especially after capitulum opening. We also show the expression dynamics of key genes involved in the production of valuable secondary metabolites of which capitulum is rich such as phenylpropanoids, flavonoids and sesquiterpene lactones. Most of their biosynthetic genes were strongly transcribed in the flower heads with alternative isoforms exhibiting differentially expression levels across the tissues. Conclusions This novel hybrid sequencing approach allowed to improve the transcriptome assembly, to update more than half of annotated genes and to identify many novel genes and different alternatively spliced isoforms. This study provides new insights on the flowering cycle in an Asteraceae plant, a valuable resource for plant biology and breeding in Cynara and an effective method for improving gene annotation." @default.
• W3062912011 created "2020-08-24" @default.
• W3062912011 creator A5002389692 @default.
• W3062912011 creator A5020845045 @default.
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• W3062912011 creator A5058087209 @default.
• W3062912011 creator A5074421892 @default.
• W3062912011 creator A5077023142 @default.
• W3062912011 date "2020-08-21" @default.
• W3062912011 modified "2023-10-10" @default.
• W3062912011 title "Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.)" @default.
• W3062912011 cites W1483984725 @default.
• W3062912011 cites W1519765314 @default.
• W3062912011 cites W1528794162 @default.
• W3062912011 cites W1533767717 @default.
• W3062912011 cites W1828956777 @default.
• W3062912011 cites W1944880632 @default.
• W3062912011 cites W1974116356 @default.
• W3062912011 cites W1980509967 @default.
• W3062912011 cites W1993111564 @default.
• W3062912011 cites W1993763119 @default.
• W3062912011 cites W2003652292 @default.
• W3062912011 cites W2004416209 @default.
• W3062912011 cites W2013128880 @default.
• W3062912011 cites W2013964001 @default.
• W3062912011 cites W2015038632 @default.
• W3062912011 cites W2019552331 @default.
• W3062912011 cites W2020421892 @default.
• W3062912011 cites W2023179728 @default.
• W3062912011 cites W2038245309 @default.
• W3062912011 cites W2038407052 @default.
• W3062912011 cites W2041874267 @default.
• W3062912011 cites W2047251302 @default.
• W3062912011 cites W2053034932 @default.
• W3062912011 cites W2061416939 @default.
• W3062912011 cites W2068767807 @default.
• W3062912011 cites W2069168352 @default.
• W3062912011 cites W2072596911 @default.
• W3062912011 cites W2074271189 @default.
• W3062912011 cites W2074951329 @default.
• W3062912011 cites W2077472070 @default.
• W3062912011 cites W2083586714 @default.
• W3062912011 cites W2084958970 @default.
• W3062912011 cites W2096771132 @default.
• W3062912011 cites W2097123946 @default.
• W3062912011 cites W2102278945 @default.
• W3062912011 cites W2103837125 @default.
• W3062912011 cites W2120902911 @default.
• W3062912011 cites W2124341242 @default.
• W3062912011 cites W2130116522 @default.
• W3062912011 cites W2131271579 @default.
• W3062912011 cites W2131518388 @default.
• W3062912011 cites W2134526812 @default.
• W3062912011 cites W2136400808 @default.
• W3062912011 cites W2139112836 @default.
• W3062912011 cites W2141165178 @default.
• W3062912011 cites W2145555148 @default.
• W3062912011 cites W2150926421 @default.
• W3062912011 cites W2155628349 @default.
• W3062912011 cites W2160443567 @default.
• W3062912011 cites W2160832949 @default.
• W3062912011 cites W2162098634 @default.
• W3062912011 cites W2169456326 @default.
• W3062912011 cites W2179507357 @default.
• W3062912011 cites W2194172909 @default.
• W3062912011 cites W2236822143 @default.
• W3062912011 cites W2248359350 @default.
• W3062912011 cites W2341599515 @default.
• W3062912011 cites W2399181677 @default.
• W3062912011 cites W2409002067 @default.
• W3062912011 cites W2438121023 @default.
• W3062912011 cites W2463761386 @default.
• W3062912011 cites W2521004200 @default.
• W3062912011 cites W2527988385 @default.
• W3062912011 cites W2533355719 @default.
• W3062912011 cites W2541674816 @default.
• W3062912011 cites W2565674822 @default.
• W3062912011 cites W2607170507 @default.
• W3062912011 cites W2611604995 @default.
• W3062912011 cites W2728605235 @default.
• W3062912011 cites W2736109964 @default.
• W3062912011 cites W2739303444 @default.
• W3062912011 cites W2752475749 @default.
• W3062912011 cites W2755196863 @default.
• W3062912011 cites W2769040703 @default.
• W3062912011 cites W2782611518 @default.
• W3062912011 cites W2783309530 @default.
• W3062912011 cites W2794241885 @default.
• W3062912011 cites W2804476515 @default.
• W3062912011 cites W2808150499 @default.
• W3062912011 cites W2809300385 @default.
• W3062912011 cites W2900984346 @default.
• W3062912011 cites W2912467062 @default.
• W3062912011 cites W2913454006 @default.
• W3062912011 cites W2932933039 @default.
• W3062912011 cites W2972131171 @default.
• W3062912011 cites W2989599894 @default.
• W3062912011 cites W3001760655 @default.
• W3062912011 doi "https://doi.org/10.1186/s12864-020-6670-5" @default.
• W3062912011 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7441626" @default.

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