Transcriptome Analysis and Identification of Lipid Genes in Physaria lindheimeri, a Genetic Resource for Hydroxy Fatty Acids in Seed Oil

Abstract

Hydroxy fatty acids (HFAs) have numerous industrial applications but are absent in most vegetable oils. Physaria lindheimeri accumulating 85% HFA in its seed oil makes it a valuable resource for engineering oilseed crops for HFA production. To discover lipid genes involved in HFA synthesis in P. lindheimeri, transcripts from developing seeds at various stages, as well as leaf and flower buds, were sequenced. Ninety-seven percent clean reads from 552,614,582 raw reads were assembled to 129,633 contigs (or transcripts) which represented 85,948 unique genes. Gene Ontology analysis indicated that 60% of the contigs matched proteins involved in biological process, cellular component or molecular function, while the remaining matched unknown proteins. We identified 42 P. lindheimeri genes involved in fatty acid and seed oil biosynthesis, and 39 of them shared 78–100% nucleotide identity with Arabidopsis orthologs. We manually annotated 16 key genes and 14 of them contained full-length protein sequences, indicating high coverage of clean reads to the assembled contigs. A detailed profiling of the 16 genes revealed various spatial and temporal expression patterns. The further comparison of their protein sequences uncovered amino acids conserved among HFA-producing species, but these varied among non-HFA-producing species. Our findings provide essential information for basic and applied research on HFA biosynthesis.

Transcriptomic analysis of seed development in Paysonia auriculata (Brassicaceae) identifies genes involved in hydroxy fatty acid biosynthesis and seed maturation

“…The greatest rate of production of the major HFA in all three species was at approximately similar times: 20:2-OH in P. auriculata between 21 and 28 DAP, and 20:1-OH in Physaria fendleri and P. lindheimeri between 21 and 28 DAP (Chen et al, 2011;Chen et al, 2017). The accumulation of 20:2-OH HFA in P. auriculata also coincided with the upregulation of PaFAH12, PaFAD3 and PaKCS18 expression, as was also reported in P. fendleri (Chen et al, 2011;Kim and Chen, 2015;Horn et al, 2016) and P. lindheimeri (Chen et al, 2021). Both P. auriculata and P. fendleri maintain relatively high and constant levels of 18:1 unsaturated FA during seed development (32.4-37.8% and 28.2-37.0% respectively), whereas P. lindheimeri is reported to have lower levels that peak when HFA production first accelerates at 19.3% and then fall in subsequent sampling periods to 5.6%.…”

Genetic Engineering of Lesquerella with Increased Ricinoleic Acid Content in Seed Oil

“…As such, efforts have been made through plant breeding to develop lesquerella as a new oilseed crop that is a safe source of HFA [12,13]. With the success of lesquerella biotechnology [14,15] and the deep knowledge of genes for fatty acid and seed oil biosynthesis [16][17][18], lesquerella oil can be improved through metabolic engineering [15].…”

“…Suppressing KCS18 reduces 20:1OH and subsequently increases 18:1OH for TAG assembly. PfFAD2, PfFAD3, and PfKCS18 share high sequence homology with camelina CsFAD2, CsFAD3, and arabidopsis AtKCS18, showing 93.6%, 95.6%, and 82.3%, respectively [18]. RNAi constructs, CsFAD2 RNAi, CsFAD3 RNAi and AtFEA1 RNAi, are effective in silencing corresponding gene expression in camelina [56][57][58].…”