Alternative Splicing Regulation of Anthocyanin Biosynthesis in <i>Camellia sinensis</i> var. <i>assamica</i> Unveiled by PacBio Iso-Seq

Chen, Lijiao; Shi, Xin; Nian, Bo; Duan, Shuangmei; Jiang, Bin; Wang, Xinghua; Lv, Chen; Zhang, Guanghui; Ma, Yan; Zhao, Ming

doi:10.1534/g3.120.401451

Cited by 23 publications

(21 citation statements)

References 49 publications

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“…AS is a gene regulatory mechanism that has been shown to play an important role in plant growth and development and in responses to biotic and abiotic stresses [ 1 , 2 , 36 ]. In tea plants, AS is involved in gene expression associated with metabolism [ 37 ], response to low temperature [ 9 ], and drought stress [ 38 ]. However, there is a lack of data available for researchers regarding AS in tea plants.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, there have been several reports identifying genes related to anthocyanin synthesis in tea plants [ 40 , 41 ]. In fact, the synthesis of anthocyanin was not only regulated by the full-length transcripts, but also by AS isoforms of genes such as anthocyanidin reductase (ANR) and anthocyanidin synthase (ANS) [ 37 ]. These results indicated that AS plays an important role in regulating metabolism and stress responses of tea plants.…”

Section: Discussionmentioning

confidence: 99%

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TeaAS: a comprehensive database for alternative splicing in tea plants (Camellia sinensis)

Yue

Tang

et al. 2021

BMC Plant Biol

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Alternative splicing (AS) increases the diversity of transcripts and proteins through the selection of different splice sites and plays an important role in the growth, development and stress tolerance of plants. With the release of the reference genome of the tea plant (Camellia sinensis) and the development of transcriptome sequencing, researchers have reported the existence of AS in tea plants. However, there is a lack of a platform, centered on different RNA-seq datasets, that provides comprehensive information on AS.To facilitate access to information on AS and reveal the molecular function of AS in tea plants, we established the first comprehensive AS database for tea plants (TeaAS, http://www.teaas.cn/index.php). In this study, 3.96 Tb reads from 66 different RNA-seq datasets were collected to identify AS events. TeaAS supports four methods of retrieval of AS information based on gene ID, gene name, annotation (non-redundant/Kyoto encyclopedia of genes and genomes/gene ontology annotation or chromosomal location) and RNA-seq data. It integrates data pertaining to genome annotation, type of AS event, transcript sequence, and isoforms expression levels from 66 RNA-seq datasets. The AS events resulting from different environmental conditions and that occurring in varied tissue types, and the expression levels of specific transcripts can be clearly identified through this online database. Moreover, it also provides two useful tools, Basic Local Alignment Search Tool and Generic Genome Browser, for sequence alignment and visualization of gene structure.The features of the TeaAS database make it a comprehensive AS bioinformatics platform for researchers, as well as a reference for studying AS events in woody crops. It could also be helpful for revealing the novel biological functions of AS in gene regulation in tea plants.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

TeaAS: a comprehensive database for alternative splicing in tea plants (Camellia sinensis)

Yue

Tang

et al. 2021

BMC Plant Biol

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“…The biosynthetic pathways to anthocyanins are well known, starting with the shikimate pathway, followed by the phenylpropanoid pathway and different possible related routes within the flavonoids biosynthetic pathways leading to the anthocyanidins cyanidin, pelargonidin, and delphinidin and to their respective anthocyanin glycosides [29][30][31] (Fig. 4A).…”

Section: Resultsmentioning

confidence: 99%

Proof of anthocyanins in the carnivorous plant genus Nepenthes

et al. 2021

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Yellow to red colored betalains are a chemotaxonomic feature of Caryophyllales, while in most other plant taxa, anthocyanins are responsible for these colors. The carnivorous plant family Nepenthaceae belongs to Caryophyllales; here, red-pigmented tissues seem to attract insect prey. Strikingly, the chemical nature of red color in Nepenthes has never been elucidated. Although belonging to Caryophyllales, in Nepenthes, some molecular evidence supports the presence of anthocyanins rather than betalains. However, there was previously no direct chemical proof of this. Using UHPLC-ESI-HRMS, we identified cyanidin glycosides in Nepenthes species and tissues. Further, we reveal the existence of a complete set of constitutively expressed anthocyanin biosynthetic genes in Nepenthes.Thus, here we finally conclude the long-term open question regarding red pigmentation in Nepenthaceae.

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“…Single molecule sequencing on Pacbio Iso-seq or Oxford Nanopore platforms should in principle overcome issues with 5’ and 3’ end determination and phasing of AS events. Iso-seq has been used to sequence cDNAs of up to 10kb and has been applied to a number of crop species including maize (23), sorghum (24), cotton (8, 25), rubber (26) and tea (27) crops. However, depending on the number of sequencing cycles, some Iso-seq reads suffer from a high sequencing error rate.…”

Section: Introductionmentioning

confidence: 99%

BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Coulter

Entizne

Guo

et al. 2021

Preprint

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Accurate characterization of splice junctions as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data and enable detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset (RTD) from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the splice junctions and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared to an earlier version, BaRTv1.0. The accuracy of transcript level quantification, splice junctions and transcript start and end sites has been validated extensively using parallel technologies and analysis, including high resolution RT PCR and 5 prime RACE. BaRTv2.18 contains 39,434 genes and 148,260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.

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Alternative Splicing Regulation of Anthocyanin Biosynthesis in Camellia sinensis var. assamica Unveiled by PacBio Iso-Seq

Cited by 23 publications

References 49 publications

TeaAS: a comprehensive database for alternative splicing in tea plants (Camellia sinensis)

TeaAS: a comprehensive database for alternative splicing in tea plants (Camellia sinensis)

Proof of anthocyanins in the carnivorous plant genus Nepenthes

BaRTv2: A highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

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