Dataset Information

Cold stress induces differential gene expression of retained homeologs in Camelina sativa cv Suneson.

ABSTRACT: Camelina sativa (L.) Crantz, a member of the Brassicaceae, has potential as a biofuel feedstock which is attributable to the production of fatty acids in its seeds, its fast growth cycle, and low input requirements. While a genome assembly is available for camelina, it was generated from short sequence reads and is thus highly fragmented in nature. Using long read sequences, we generated a chromosome-scale, highly contiguous genome assembly (644,491,969 bp) for the spring biotype cultivar 'Suneson' with an N50 contig length of 12,031,512 bp and a scaffold N50 length of 32,184,682 bp. Annotation of protein-coding genes revealed 91,877 genes that encode 133,355 gene models. We identified a total of 4,467 genes that were significantly up-regulated under cold stress which were enriched in gene ontology terms associated with "response to cold" and "response to abiotic stress". Coexpression analyses revealed multiple coexpression modules that were enriched in genes differentially expressed following cold stress that had putative functions involved in stress adaptation, specifically within the plastid. With access to a highly contiguous genome assembly, comparative analyses with Arabidopsis thaliana revealed 23,625 A. thaliana genes syntenic with 45,453 Suneson genes. Of these, 24,960 Suneson genes were syntenic to 8,320 A. thaliana genes reflecting a 3 camelina homeolog to 1 Arabidopsis gene relationship and retention of all three homeologs. Some of the retained triplicated homeologs showed conserved gene expression patterns under control and cold-stressed conditions whereas other triplicated homeologs displayed diverged expression patterns revealing sub- and neo-functionalization of the homeologs at the transcription level. Access to the chromosome-scale assembly of Suneson will enable both basic and applied research efforts in the improvement of camelina as a sustainable biofuel feedstock.

SUBMITTER: Fang C

PROVIDER: S-EPMC10687638 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Cold stress induces differential gene expression of retained homeologs in <i>Camelina sativa</i> cv Suneson.

Fang Chao C Hamilton John P JP Vaillancourt Brieanne B Wang Yi-Wen YW Wood Joshua C JC Deans Natalie C NC Scroggs Taylor T Carlton Lemor L Mailloux Kathrine K Douches David S DS Nadakuduti Satya Swathi SS Jiang Jiming J Buell C Robin CR

Frontiers in plant science 20231116

<i>Camelina sativa</i> (L.) Crantz, a member of the Brassicaceae, has potential as a biofuel feedstock which is attributable to the production of fatty acids in its seeds, its fast growth cycle, and low input requirements. While a genome assembly is available for camelina, it was generated from short sequence reads and is thus highly fragmented in nature. Using long read sequences, we generated a chromosome-scale, highly contiguous genome assembly (644,491,969 bp) for the spring biotype cultivar ...[more]

PMID: 38034564

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Project description:Camelina sativa stands out among oilseed crops due to its remarkable resilience to challenging environmental conditions and its significant potential for biodiesel production. The MADS-box transcription factors play a pivotal role in numerous biological processes within plants, encompassing growth, development, and responses to environmental stressors. In this research, by employing the BLAST, we have successfully identified 325 MADS-box genes within Camelina sativa genome. These genes were systematically categorized into two principal groups: type I (comprising Mα, Mβ, and Mγ) and type II (including MI-KCC and MIKC*) predicated upon their phylogenetic relationships, structural protein motifs, and exon-intron configurations. Our findings reveal that type II MADS-box genes have, in general, experienced a more profound expansion relative to type I genes. Specifically, the TM3 subgroup within type II MADS-box genes exhibited the highest degree of gene expansion, comprising 21 TM3 genes. The amino acid sequences encoded by these genes exhibited a length variation ranging from 150 to 820 aa. The predicted molecular weights (MW) of the CsMADS-box proteins displayed a range from 17.01 to 94.06 kDa, while the isoelectric points (pI) were observed to span from 4.13 to 10.09. Evolutionary analysis predicated on the Ka/Ks ratios indicates that the evolutionary pathway of MADS-box genes in Camelina sativa has been predominantly driven by the mechanisms of purifying selection. Moreover, an investigation of cis-acting elements has elucidated the participation of MADS-box genes in the adaptive responses to abiotic stressors. The expression profiles of six Type I and three MIKCC genes across diverse organs and under varying drought treatment conditions demonstrated that these genes are expressed in both reproductive and vegetative structures, displaying uniform expression patterns throughout several developmental phases of flowering. The expression levels of CsMADS035, CsMADS115, CsMADS131, and CsMADS181 were notably modified in reaction to drought stress conditions. The detailed annotation and comprehensive transcriptome profiling provided in this research yield essential insights into the functional roles that MADS-box genes perform in stress resistance, as well as their contributions to growth and developmental processes. This acquired understanding establishes a foundational framework for the functional characterization and potential genetic engineering initiatives pertaining to Camelina sativa, thereby augmenting the prospective application of these candidate genes.

Project description:As an important oilseed worldwide, Camelina sativa is being increasingly explored for its use in production of food, feed, biofuel and industrial chemicals. However, detailed mechanisms of camelina oil biosynthesis and accumulation, particularly in vegetative tissues, are understood to a very small extent. Here, we present genome-wide identification, cloning and functional analysis of phospholipid diacylglycerol acyltransferase (PDAT) in C. sativa, which catalyses the final acylation step in triacylglycerol (TAG) biosynthesis by transferring a fatty acyl moiety from a phospholipid to diacylglycerol (DAG). We identified five genes (namely CsPDAT1-A, B, and C and CsPDAT2-A and B) encoding PDATs from the camelina genome. CsPDAT1-A is mainly expressed in seeds, whereas CsPDAT1-C preferentially accumulates in flower and leaf tissues. High expression of CsPDAT2-A and CsPDAT2-B was detected in stem and root tissues, respectively. Cold stress induced upregulation of CsPDAT1-A and CsPDAT1-C expression by 3.5- and 2.5-fold, respectively, compared to the control. Salt stress led to an increase in CsPDAT2-B transcripts by 5.1-fold. Drought treatment resulted in an enhancement of CsPDAT2-A mRNAs by twofold and a reduction of CsPDAT2-B expression. Osmotic stress upregulated the expression of CsPDAT1-C by 3.3-fold. Furthermore, the cDNA clones of these CsPDAT genes were isolated for transient expression in tobacco leaves. All five genes showed PDAT enzymatic activity and substantially increased TAG accumulation in the leaves, with CsPDAT1-A showing a higher preference for ɑ-linolenic acid (18:3 ω-3). Overall, this study demonstrated that different members of CsPDAT family contribute to TAG synthesis in different tissues. More importantly, they are involved in different types of stress responses in camelina seedlings, providing new evidence of their roles in oil biosynthesis and regulation in camelina vegetative tissue. The identified CsPDATs may have practical applications in increasing oil accumulation and enhancing stress tolerance in other plants as well.

Dataset Information

Cold stress induces differential gene expression of retained homeologs in Camelina sativa cv Suneson.

Publications

Cold stress induces differential gene expression of retained homeologs in <i>Camelina sativa</i> cv Suneson.

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