Genome-Scale Transcriptome Analysis of the Desert Shrub Artemisia sphaerocephala

Abstract

BackgroundArtemisia sphaerocephala, a semi-shrub belonging to the Artemisia genus of the Compositae family, is an important pioneer plant that inhabits moving and semi-stable sand dunes in the deserts and steppes of northwest and north-central China. It is very resilient in extreme environments. Additionally, its seeds have excellent nutritional value, and the abundant lipids and polysaccharides in the seeds make this plant a potential valuable source of bio-energy. However, partly due to the scarcity of genetic information, the genetic mechanisms controlling the traits and environmental adaptation capacity of A. sphaerocephala are unknown.ResultsHere, we present the first in-depth transcriptomic analysis of A. sphaerocephala. To maximize the representation of conditional transcripts, mRNA was obtained from 17 samples, including living tissues of desert-growing A. sphaerocephala, seeds germinated in the laboratory, and calli subjected to no stress (control) and high and low temperature, high and low osmotic, and salt stresses. De novo transcriptome assembly performed using an Illumina HiSeq 2500 platform resulted in the generation of 68,373 unigenes. We analyzed the key genes involved in the unsaturated fatty acid synthesis pathway and identified 26 A. sphaerocephala fad2 genes, which is the largest fad2 gene family reported to date. Furthermore, a set of genes responsible for resistance to extreme temperatures, salt, drought and a combination of stresses was identified.ConclusionThe present work provides abundant genomic information for functional dissection of the important traits of A. sphaerocephala and contributes to the current understanding of molecular adaptive mechanisms of A. sphaerocephala in the desert environment. Identification of the key genes in the unsaturated fatty acid synthesis pathway could increase understanding of the biological regulatory mechanisms of fatty acid composition traits in plants and facilitate genetic manipulation of the fatty acid composition of oil crops.

Cloning and Functional Analysis of the FAD2 Gene Family from Desert Shrub Artemisia sphaerocephala

“…In addition, seeds after 3 and 7 days of germination, seedlings, and six different callus tissues were collected from the laboratory. These samples were taken as same as our previous work [ 16], and the formal identification of these samples based on the flora of China [ 23]. The collection of all samples completely complies with local and national legislation permission.…”

“…Total RNA was extracted from each plant sample using the UNlQ-10 Column Trizol Total RNA Isolation Kit (Sangon, China) and analyzed for concentration and quality using NanoDrop ND1000 (Thermo Fisher Scientific, USA) and gel electrophoresis. Based on our previous study [ 16], nucleotide sequences of twenty-six AsFAD2 genes determined by RNA-seq (Additional file 1: Table S1). 5′/3′ RACE (Rapid Amplification of cDNA Ends) gene-specific primers for each AsFAD2 gene were designed by Primer 5.0 and synthesized by the Sangon Company (Additional file 2: Table S2 and Additional file 3: Table S3).…”

“…With the exception of Arabidopsis thaliana, which has only one FAD2 gene [ 11], while most plants have multiple FAD2 genes. Thus, olive (Olea europaea) has two FAD2 genes [ 12], Oilseed rape (Brassica napus) has four [ 13], peanut (Arachis hypogaea) has six [ 14], safflower (Carthamus tinctorius) has eleven [ 15], and Artemisia sphaerocephala has twenty-six [ 16]. Gene families usually occur through gene duplication and mutations, and the variations in the number of gene family members is an important evolutionary mechanism underlying functional diversity and shaping genomic adaptation in various species [ 17].…”

“…Artemisia sphaerocephalKraschen, which belongs to the Artemisia genus of the Compositae family, is a perennial wild shrub widely distributed in the moving and semi-stable sand dunes in the deserts of northern China [ 23].Artemisia sphaerocephal seeds contain 21.5% oil and can be used to produce biodiesel [ 24], nearly 90% of seeds oil are unsaturated fatty acids, especially LA, constituting over 78% of total fatty acids [ 25]. Comparing with other plants, such as sunflower, soybean, and peanut, A. sphaerocephal seeds and leaves can accumulate much more LA [ 16]. The maintenance of high degree of membrane lipid unsaturation under stress conditions is one of the important stress adaptation mechanisms in plants, previous studies showed that A. sphaerocephala is resistant to drought and salt by maintaining high LA content [ 26,27].…”

Native Plants to Arid Areas: A Genetic Reservoir for Drought-Tolerant Crops

“…These had homology to 17 kinases, 2 potential chaperones, 52 enzymes, 6 transporters and channels, and 3 aquaporins. Even though, transcription factor were not identified, 25 out of the 108 unigenes were among the 1000 most highly expressed genes [87].…”