Regulatory mechanisms of fatty acids biosynthesis in Armeniaca sibirica seed kernel oil at different developmental stages

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Plant Biology

Main article text

 

Introduction

Materials & Methods

Plant materials and study design

Analysis of FAs composition in seed kernels

RNA extraction, library construction and sequencing

Transcriptome annotation and pathway enrichment analysis

Identification of differentially expressed genes (DEGs)

Validation of transcriptome data by qRT-PCR

Results

Changes in FAs composition in developing seed kernels

Seed kernels transcriptome analysis

Transcriptome functional annotation

Hierarchical cluster analysis of DEGs associated with FAs accumulation

Expression analysis of genes encoding key enzymes involved in FAs biosynthesis

Differential expression of transcription factors involved in FAs biosynthesis

Identification of lncRNAs involved in oil accumulation

Validation of RNA-Seq data by qRT-PCR

Discussion

Conclusions

Supplemental Information

Sequence information of primers for RT-qPCR

DOI: 10.7717/peerj.14125/supp-1

The raw data for fatty acid content in Armeniaca sibirica seed kernel oil at different developmental stages

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The contents of various saturated fatty acids (SFAs) and unsaturated fatty acids (UFAs) in Armeniaca sibirica seed kernels at different developmental stages ( μg/g)

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The content of total fatty acids in Armeniaca sibirica seed kernels at different developmental stages ( μg/g)

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The relative proportion of saturated fatty acids (SFAs) and unsaturated fatty acids (UFAs) in Armeniaca sibirica seed kernels at different developmental stages

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The content of main unsaturated fatty acids in Armeniaca sibirica seed kernels at different developmental stages. (ug/g)

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The content of main saturated fatty acids in Armeniaca sibirica seed kernels at different developmental stages. (ug/g)

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Quality statistics for transcriptome sequencing (RNA-seq) data

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The summary statistics ofthe assembled transcripts and unigenes

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Detailed information of unigenes in the transcriptome of Armeniaca sibirica matching the 20 top species using BLAST against the Nr database

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Detailed information of KOG annotation of Armeniaca sibirica transcriptome

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Detailed information of GO annotation of Armeniaca sibirica transcriptome

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Detailed information of KEGG functional classification and pathway enrichment analysis of unigenes of Armeniaca sibirica seed kernels

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FPKM values of differentially expressed genes (DEGs) associated with FAs accumulation in Armeniaca sibirica seed kernels at different developmental stages

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FPKM of genes encoding enzymes involved in the biosynthesis of fatty acids in Armeniaca sibirica seed kernels at different developmental stages

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The identification result of transcription factor families and transcription factor numbers in Armeniaca sibirica seed kernels at different developmental stages

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Overview of differentially expressed transcription factors co-expressed with the major lipid-related genes in Armeniaca sibirica seed kernels

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LncRNA prediction results of CNCI software in Armeniaca sibirica seed kernels at different developmental stages

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Overview of the differentially expressed lncRNAs co-expressed with the major lipid-related genes in Armeniaca sibirica seed kernels

DOI: 10.7717/peerj.14125/supp-19

The Ct value of sample

DOI: 10.7717/peerj.14125/supp-20

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Yueliang Wu conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Wenya Gao performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Xinli Li performed the experiments, prepared figures and/or tables, and approved the final draft.

Shilin Sun conceived and designed the experiments, performed the experiments, prepared figures and/or tables, and approved the final draft.

Jian Xu performed the experiments, prepared figures and/or tables, and approved the final draft.

Xiaoqiong Shi performed the experiments, prepared figures and/or tables, and approved the final draft.

Huiyan Guo conceived and designed the experiments, performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The transcript sequence data is available at NCBI: PRJNA799670, PRJNA799941, PRJNA803801.

The assembled data is available at NCBI: GJXS00000000.

Data Availability

The following information was supplied regarding data availability:

The raw data are available in the Supplementary Files.

Funding

This work was supported by the National Key Research and Development Program of China (2018YFD1000606-4-1) and the Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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