The developmental transcriptome atlas of the biofuel crop Camelina sativa

Abstract

SUMMARYCamelina sativa is currently being embraced as a viable industrial bio-platform crop due to a number of desirable agronomic attributes and the unique fatty acid profile of the seed oil that has applications for food, feed and biofuel. The recent completion of the reference genome sequence of C. sativa identified a young hexaploid genome. To complement this work, we have generated a genome-wide developmental transcriptome map by RNA sequencing of 12 different tissues covering major developmental stages during the life cycle of C. sativa. We have generated a digital atlas of this comprehensive transcriptome resource that enables interactive visualization of expression data through a searchable database of electronic fluorescent pictographs (eFP browser). An analysis of this dataset supported expression of 88% of the annotated genes in C. sativa and provided a global overview of the complex architecture of temporal and spatial gene expression patterns active during development. Conventional differential gene expression analysis combined with weighted gene expression network analysis uncovered similarities as well as differences in gene expression patterns between different tissues and identified tissue-specific genes and network modules. A high-quality census of transcription factors, analysis of alternative splicing and tissue-specific genome dominance provided insight into the transcriptional dynamics and sub-genome interplay among the well-preserved triplicated repertoire of homeologous loci. The comprehensive transcriptome atlas in combination with the reference genome sequence provides a powerful resource for genomics research which can be leveraged to identify functional associations between genes and understand the regulatory networks underlying developmental processes.

Selective gene dosage by CRISPR‐Cas9 genome editing in hexaploid Camelina sativa

“…Unlike wheat, Camelina has three similar subgenomes that are generally expressed, indicating the existence of an important functional gene redundancy (Kagale et al, 2014(Kagale et al, , 2016. Our work shows that CRISPR-Cas9 could efficiently bypass this limitation by quickly isolating triple homozygous mutants.…”

“…The effect of csfad2-2 mutation on OAI could even be observed in the heterozygous state, indicating the importance of allele dosage for FAD2 activity ( Figure S4). It was reported that Camelina subgenome 3 (CsG3) was globally more expressed than the two other subgenomes (Kagale et al, 2016). CsFAD2-2 belongs to CsG3, and indeed, its expression is higher in maturing seeds compared to the two other homeologous genes ( Figure S5).…”

“…The genomic sequence of Camelina sativa cv. C eline CsFAD2-1, CsFAD2-2 and CsFAD2-3 was named according to the previous work (Kang et al, 2011) and was respectively related to the accessions Csa19 g016350, Csa01 g013220 and Csa15 g016000 (Kagale et al, 2016) and CsFAD2A, CsFAD2B and CsFAD2C (Hutcheon et al, 2010).…”

“…The Camelina genome is composed of three subgenomes, two of which are extremely similar to each other and may be derived from an event of autopolyploidy, while the third one is slightly more divergent (Kagale et al, 2014). Subgenome-specific transcriptomic studies showed a remarkably low degree of gene loss and gene functional differentiation among the three subgenomes (Kagale et al, 2014(Kagale et al, , 2016Mudalkar et al, 2014;Nguyen et al, 2013). The different homeologous genes were most often expressed with a slight enhanced expression level for genes from the most divergent subgenome (Kagale et al, 2014(Kagale et al, , 2016.…”

“…Subgenome-specific transcriptomic studies showed a remarkably low degree of gene loss and gene functional differentiation among the three subgenomes (Kagale et al, 2014(Kagale et al, , 2016Mudalkar et al, 2014;Nguyen et al, 2013). The different homeologous genes were most often expressed with a slight enhanced expression level for genes from the most divergent subgenome (Kagale et al, 2014(Kagale et al, , 2016. Obtaining recessive mutants in Camelina is therefore limited by the high genetic redundancy.…”