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Comparative transcriptome analysis of genes involved in anthocyanin biosynthesis in the red and yellow fruits of sweet cherry (Prunus avium L.).

Wei H, Chen X, Zong X, Shu H, Gao D, Liu Q - PLoS ONE (2015)

Bottom Line: Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database.The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit.These results will provide a platform for further functional genomic research on this fruit crop.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China; Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong 271000, China.

ABSTRACT

Background: Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry.

Methodology/principal findings: In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).

Conclusions/significance: The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop.

No MeSH data available.


Fruits of P. avium L. ‘13–33’ and ‘Tieton’ used in deep sequencing.(A) ‘13–33’ fruit at 20 DAF (stage 1). (B) ‘13–33’ fruit at 35 DAF (stage 2). (C) ‘13–33’ fruit at 45 DAF (stage 3). (D) ‘13–33’ fruit at 55 DAF (stage 4). (E) ‘Tieton’ fruit at 20 DAF (stage 1). (F) ‘Tieton’ fruit at 35 DAF (stage 2). (G) ‘Tieton’ fruit at 45 DAF (stage 3). (H) ‘Tieton’ fruit at 55 DAF (stage 4).
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pone.0121164.g001: Fruits of P. avium L. ‘13–33’ and ‘Tieton’ used in deep sequencing.(A) ‘13–33’ fruit at 20 DAF (stage 1). (B) ‘13–33’ fruit at 35 DAF (stage 2). (C) ‘13–33’ fruit at 45 DAF (stage 3). (D) ‘13–33’ fruit at 55 DAF (stage 4). (E) ‘Tieton’ fruit at 20 DAF (stage 1). (F) ‘Tieton’ fruit at 35 DAF (stage 2). (G) ‘Tieton’ fruit at 45 DAF (stage 3). (H) ‘Tieton’ fruit at 55 DAF (stage 4).

Mentions: The pure yellow sweet cherry cultivar P. avium L. (‘13–33’) and the red sweet cherry cultivar P. avium L. (‘Tieton’) were used in this study [32]. The plants were grown in Shandong Institute of Pomology, Tai’an, Shandong Province, China. According to the data from our laboratory, the fruit development periods of the two cultivars were similar. The total sugar accumulation pattern was the same in the two cultivars, beginning at the early stages and accelerating during ripening. The total acid content first increased and then decreased until the fruit was ripe in both cultivars (S1 Table). Fruit samples were collected at four different ripening stages: 20 days after flowering (DAF) (stage 1), 35 DAF (stage 2), 45 DAF (stage 3) and 55 DAF (stage 4). Fig. 1 shows samples of fruits at the four different ripening stages. After collection, samples were flash-frozen in liquid nitrogen and stored at -80°C until further processing.


Comparative transcriptome analysis of genes involved in anthocyanin biosynthesis in the red and yellow fruits of sweet cherry (Prunus avium L.).

Wei H, Chen X, Zong X, Shu H, Gao D, Liu Q - PLoS ONE (2015)

Fruits of P. avium L. ‘13–33’ and ‘Tieton’ used in deep sequencing.(A) ‘13–33’ fruit at 20 DAF (stage 1). (B) ‘13–33’ fruit at 35 DAF (stage 2). (C) ‘13–33’ fruit at 45 DAF (stage 3). (D) ‘13–33’ fruit at 55 DAF (stage 4). (E) ‘Tieton’ fruit at 20 DAF (stage 1). (F) ‘Tieton’ fruit at 35 DAF (stage 2). (G) ‘Tieton’ fruit at 45 DAF (stage 3). (H) ‘Tieton’ fruit at 55 DAF (stage 4).
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4370391&req=5

pone.0121164.g001: Fruits of P. avium L. ‘13–33’ and ‘Tieton’ used in deep sequencing.(A) ‘13–33’ fruit at 20 DAF (stage 1). (B) ‘13–33’ fruit at 35 DAF (stage 2). (C) ‘13–33’ fruit at 45 DAF (stage 3). (D) ‘13–33’ fruit at 55 DAF (stage 4). (E) ‘Tieton’ fruit at 20 DAF (stage 1). (F) ‘Tieton’ fruit at 35 DAF (stage 2). (G) ‘Tieton’ fruit at 45 DAF (stage 3). (H) ‘Tieton’ fruit at 55 DAF (stage 4).
Mentions: The pure yellow sweet cherry cultivar P. avium L. (‘13–33’) and the red sweet cherry cultivar P. avium L. (‘Tieton’) were used in this study [32]. The plants were grown in Shandong Institute of Pomology, Tai’an, Shandong Province, China. According to the data from our laboratory, the fruit development periods of the two cultivars were similar. The total sugar accumulation pattern was the same in the two cultivars, beginning at the early stages and accelerating during ripening. The total acid content first increased and then decreased until the fruit was ripe in both cultivars (S1 Table). Fruit samples were collected at four different ripening stages: 20 days after flowering (DAF) (stage 1), 35 DAF (stage 2), 45 DAF (stage 3) and 55 DAF (stage 4). Fig. 1 shows samples of fruits at the four different ripening stages. After collection, samples were flash-frozen in liquid nitrogen and stored at -80°C until further processing.

Bottom Line: Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database.The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit.These results will provide a platform for further functional genomic research on this fruit crop.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China; Key Laboratory for Fruit Biotechnology Breeding of Shandong, Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, Tai'an, Shandong 271000, China.

ABSTRACT

Background: Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry.

Methodology/principal findings: In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3'-hydroxylase (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR).

Conclusions/significance: The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop.

No MeSH data available.