Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut

Flower bud development is a defining feature of walnut, which contributes to the kernel yield, yield stability, fruit quality and commodity value. However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divid...

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Published in:PloS one 2021-11, Vol.16 (11), p.e0260017-e0260017
Main Authors: Ma, Kai, Luo, Xiang, Han, Liqun, Zhao, Yu, Mamat, Aisajan, Li, Ning, Mei, Chuang, Yan, Peng, Zhang, Rui, Hu, Jianfang, Wang, Jixun
Format: Article
Language:English
Subjects:
Alternative Splicing
Analysis
Annotations
Base Sequence - genetics
Biological clocks
Biology and Life Sciences
Circadian Clocks - genetics
Circadian rhythm
Circadian Rhythm - genetics
Circadian rhythms
Crops
Domestication
Error correction & detection
Flowers
Flowers - genetics
Fruits
Gene Expression - genetics
Gene Expression Profiling - methods
Gene Expression Regulation, Plant - genetics
Gene sequencing
Genes
Genes, Plant - genetics
Genetic aspects
Genomes
High-Throughput Nucleotide Sequencing
Horticulture
Isoforms
Juglans - genetics
Juglans - growth & development
Laboratories
Metabolism
Metabolites
Non-coding RNA
Protocol
Reproduction
Research and analysis methods
Ribonucleic acid
RNA
RNA sequencing
RNA, Long Noncoding
RNA-Seq - methods
Sequence Analysis, DNA
Sequence Analysis, RNA
Software
Transcription factors
Transcriptome - genetics
Transcriptomes
Walnut
Walnuts
Whole Exome Sequencing
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container_end_page e0260017
container_issue 11
container_start_page e0260017
container_title PloS one
container_volume 16
creator Ma, Kai
Luo, Xiang
Han, Liqun
Zhao, Yu
Mamat, Aisajan
Li, Ning
Mei, Chuang
Yan, Peng
Zhang, Rui
Hu, Jianfang
Wang, Jixun
description Flower bud development is a defining feature of walnut, which contributes to the kernel yield, yield stability, fruit quality and commodity value. However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divided into five period (P01-05) by using histological observation. They were further studied through PacBio Iso-Seq and RNA-seq analysis. Accordingly, we obtained 52,875 full-length transcripts, where 4,579 were new transcripts, 3,065 were novel genes, 1,437 were consensus lncRNAs and 20,813 were alternatively spliced isoforms. These transcripts greatly improved the current genome annotation and enhanced our understanding of the walnut transcriptome. Next, RNA sequencing of female flower buds at five periods revealed that circadian rhythm-plant was commonly enriched along with the flower bud developmental gradient. A total of 14 differentially expressed genes (DEGs) were identified, and six of them were confirmed by real-time quantitative analysis. Additionally, six and two differentially expressed clock genes were detected to be regulated by AS events and lncRNAs, respectively. All these detected plant circadian genes form a complex interconnected network to regulate the flower bud development. Thus, investigation of key genes associated with the circadian clock could clarify the process of flower bud development in walnut.
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However, little is known about the mechanism of the flower bud development in walnut. Here, the stages of walnut female flower bud development were divided into five period (P01-05) by using histological observation. They were further studied through PacBio Iso-Seq and RNA-seq analysis. Accordingly, we obtained 52,875 full-length transcripts, where 4,579 were new transcripts, 3,065 were novel genes, 1,437 were consensus lncRNAs and 20,813 were alternatively spliced isoforms. These transcripts greatly improved the current genome annotation and enhanced our understanding of the walnut transcriptome. Next, RNA sequencing of female flower buds at five periods revealed that circadian rhythm-plant was commonly enriched along with the flower bud developmental gradient. A total of 14 differentially expressed genes (DEGs) were identified, and six of them were confirmed by real-time quantitative analysis. Additionally, six and two differentially expressed clock genes were detected to be regulated by AS events and lncRNAs, respectively. All these detected plant circadian genes form a complex interconnected network to regulate the flower bud development. Thus, investigation of key genes associated with the circadian clock could clarify the process of flower bud development in walnut.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>34793486</pmid><doi>10.1371/journal.pone.0260017</doi><orcidid>https://orcid.org/0000-0002-3811-2740</orcidid><oa>free_for_read</oa></addata></record>
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source Publicly Available Content Database; PubMed Central
subjects Alternative Splicing
Analysis
Annotations
Base Sequence - genetics
Biological clocks
Biology and Life Sciences
Circadian Clocks - genetics
Circadian rhythm
Circadian Rhythm - genetics
Circadian rhythms
Crops
Domestication
Error correction & detection
Flowers
Flowers - genetics
Fruits
Gene Expression - genetics
Gene Expression Profiling - methods
Gene Expression Regulation, Plant - genetics
Gene sequencing
Genes
Genes, Plant - genetics
Genetic aspects
Genomes
High-Throughput Nucleotide Sequencing
Horticulture
Isoforms
Juglans - genetics
Juglans - growth & development
Laboratories
Metabolism
Metabolites
Non-coding RNA
Protocol
Reproduction
Research and analysis methods
Ribonucleic acid
RNA
RNA sequencing
RNA, Long Noncoding
RNA-Seq - methods
Sequence Analysis, DNA
Sequence Analysis, RNA
Software
Transcription factors
Transcriptome - genetics
Transcriptomes
Walnut
Walnuts
Whole Exome Sequencing
title Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut
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