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马齿苋的单分子长读长测序及与不饱和脂肪酸生物合成相关的差异基因表达

Single-Molecule Long-Read Sequencing of Purslane () and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids.

作者信息

Du Hongmei, Zaman Shah, Hu Shuiqingqing, Che Shengquan

机构信息

School of Design, Shanghai Jiao Tong University, Shanghai 200240, China.

School of Agricultural and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.

出版信息

Plants (Basel). 2021 Mar 30;10(4):655. doi: 10.3390/plants10040655.

DOI:10.3390/plants10040655
PMID:33808162
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8066459/
Abstract

This study aimed to obtain the full-length transcriptome of purslane (); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT-PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

摘要

本研究旨在获得马齿苋的全长转录组；使用了各种植物样本进行单分子实时（SMRT）测序。基于SMRT，完成了转录本的功能注释、转录因子（TFs）分析、简单序列重复分析和长链非编码RNA（LncRNAs）预测。共产生了15.33GB的读数；有9350222条子读数，子读数的平均长度为1640bp。聚类后，以99.99%的准确率检测到132536个转录本和78559个基因。所有独特的SMART转录本都在七个功能数据库中进行了注释。预测了4180个TFs（包括转录调节因子）和7289个LncRNAs。RNA-seq的结果通过qRT-PCR分析得到了证实。对两种马齿苋基因型的叶片和根系进行了Illumina测序。发现了差异表达基因的数量和相关的KEGG途径。分析了两种基因型马齿苋叶片和根系中不饱和脂肪酸生物合成途径中相关基因的表达谱。该途径中基因的差异表达为马齿苋不同器官和基因型中ω-3脂肪酸的积累奠定了基础。上述结果提供了序列信息，可能为未来马齿苋的全基因组测序提供有价值的资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/14d226f6a5e0/plants-10-00655-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/e02aff069dfe/plants-10-00655-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/669a01b36120/plants-10-00655-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/f9e286d789d9/plants-10-00655-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/4e4efc997c49/plants-10-00655-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/1cbf0dbc8e97/plants-10-00655-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/35fd5ac65e60/plants-10-00655-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/51c742b0ff78/plants-10-00655-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/77dff8e9764b/plants-10-00655-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/14d226f6a5e0/plants-10-00655-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/e02aff069dfe/plants-10-00655-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/669a01b36120/plants-10-00655-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/f9e286d789d9/plants-10-00655-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/4e4efc997c49/plants-10-00655-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/1cbf0dbc8e97/plants-10-00655-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/35fd5ac65e60/plants-10-00655-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/51c742b0ff78/plants-10-00655-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/77dff8e9764b/plants-10-00655-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ffba/8066459/14d226f6a5e0/plants-10-00655-g009.jpg

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