Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall

Abstract

Background Prunus pedunculata Pall, the deciduous shrub of Amygdalus subgenus in Rosaceae, is a new kind of desert oil-bearing tree. It has a long story of being planted in the West and North of China for sand fixation and desert control. In addition, the seeds of P. pedunculata are rich of oil, especially the monounsaturated fatty acid and polyunsaturated fatty acid. However, little is known about the molecular mechanisms of oil accumulation during the seed development of P. pedunculata. Results The seeds of P. pedunculata from three independent plants at 10, 18, 24, 31, 39, 45, 59 and 73 days after flowering (DAF) were obtained and the oil compositions were evaluated. It showed that oleic acid was the dominant type of oil content in the mature seeds (from 32.724% at 10DAF to 72.06% at 73DAF). Next, transcriptome sequencing for the developing seeds produced 988.795 million high quality reads and TRINITY assembled 326,271 genes for the first transcriptome for P. pedunculata. After the assembled transcriptome was evaluated by BUSCO with 85.9% completeness, we identified 195,342, 109,850 and 121,897 P. pedunculata genes aligned to NR, GO and KEGG pathway databases, respectively. Then, we predicted 23,229 likely proteins from the assembled transcriptome and identified 1917 signal peptides and 5512 transmembrane related proteins. In the developing seeds we detected 91,362 genes (average FPKM > 5) and correlation analysis indicated three possible development stages – early (10 ~ 24DAF), middle (31 ~ 45DAF) and late (59 ~ 73DAF). We next analyzed the differentially expressed genes (DEGs) in the developing seeds. Interestingly, compared to 10DAF the number of DEGs was increased from 4406 in 18DAF to 27,623 in 73DAF. Based on the gene annotation, we identified 753, 33, 8 and 645 DEGs related to the fatty acid biosynthesis, lipid biosynthesis, oil body and transcription factors. Notably, GPAT, DGD1, LACS2, UBC and RINO were highly expressed at the early development stage, ω6-FAD, SAD, ACP, ACCA and AHG1 were highly expressed at the middle development stage, and LACS6, DGD1, ACAT1, AGPAT, WSD1, EGY2 and oleosin genes were highly expressed at the late development stage. Conclusions This is the first time to study the developing seed transcriptome of P. pedunculata and our findings will provide a valuable resource for future studies. More importantly, it will improve our understanding of molecular mechanisms of oil accumulation in P. pedunculata.

Integrated Lipidomic and Transcriptomic Analysis Reveals Lipid Metabolism in Foxtail Millet (Setaria italica)

“… Feng et al (2016) identified 10 KAS genes involved in fatty acid synthesis in eucommia ulmoides seeds by transcriptome sequencing. Bao et al (2021) found that fatty acid biosynthesis related genes LACS6, DGD1 , ACAT1 , AGPAT , WSD1 , EGY2 , and oleosin were highly expressed during late development of Prunus Pedunculata Pall seeds. Xiu et al (2018) found key genes in oil biosynthesis of Paenpnia , containing ACCase , LPCAT , FADs , DGAT.…”

Complete mitochondrial genome of the endangered Prunus pedunculata (Prunoideae, Rosaceae) in China: characterization and phylogenetic analysis

“…Based on three RNA-seq datasets of P. pedunculata deposited in the SRA database ( https://www.ncbi.nlm.nih.gov/sra/ ; accession numbers: SRR13261917, SRR13261918 and SRR13261919) ( Bao et al., 2021 ), we identified the putative RNA editing sites in mitochondrial PCGs. Mapping the RNA-seq data onto the sequences of mitochondrial PCGs by using BWA v0.7.15 ( Li and Durbin, 2010 ) software.…”

“…In addition, P. pedunculata was classified as a national near-threatened species by the China Biodiversity Red List – Higher Plants ( Ministry of Ecology and Environment of the People's Republic of China and Science, 2020 ) and been assessed by the IUCN Red List of Threatened Species ( Rhodes and Maxted, 2016 ). Extensive investigations have focused on chloroplast (cp) genome analysis ( Duan et al., 2020 ; Du et al., 2021 ), chemical compounds ( Ma, 2013 ; Lu et al., 2018 ; Yao et al., 2018 ; Li et al., 2020 ), genetic diversity ( Zuo, 2016 ; Bao et al., 2021 ), resistance to various abiotic stress ( Ma, 2006 ; Jiang, 2008 ; Luo, 2009 ; Guo, 2014 ), cultivation technology ( Li, 2017 ; Wang et al., 2020b ; Wang et al., 2021b ), protection and utilization ( Chu et al., 2015 ; Liu, 2017 ; Xiong et al., 2018 ; Bao et al., 2021 ) of P. pedunculata . Previous studies have indicated that P. pedunculata possesses many resistance genes.…”

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“…Feng et al (2016) identified 10 KAS genes involved in fatty acid synthesis in eucommia ulmoides seeds by transcriptome sequencing. Bao et al (2021) found that fatty acid biosynthesis related genes LACS6, DGD1, ACAT1, AGPAT, WSD1, EGY2, and oleosin were highly expressed during late development of Prunus Pedunculata Pall seeds. Xiu et al (2018) found key genes in oil biosynthesis of Paenpnia, containing ACCase, LPCAT, FADs, DGAT.…”