Jerusalem artichoke (Helianthus tuberosus L.) is widely cultivated in Northwest China which has become an emerging economic crop with rapid development. Because of its elevated inulin content and high resistance, it is widely used in functional food, inulin processing, feed, and ecological management. In this study, Illumina sequencing technology was utilized to assemble and annotate the complete chloroplast genome sequences of Jerusalem artichoke. The total length was 151,431 bp, including four conserved regions: A pair of reverse repeat regions (IRa 24,568 bp and IRb 24,603 bp), a large single-copy region (LSC, 83,981 bp), and a small single-copy region (SSC, 18,279 bp). The genome had a total of 115 genes, with 19 present in the reverse direction in the IR region. 36 simple sequence repeats (SSRs) were identified in the coding and non-coding regions, most of which were biased towards A/T bases. 32 SSRs were distributed in the non-coding regions. Comparative analysis of the chloroplast genome sequence of Jerusalem artichoke and other species of the composite family revealed the chloroplast genome sequences of plants of the composite family to be highly conserved. Differences were observed in 24 gene loci in the coding region, with the degree of differentiation of the ycf2 gene being the most obvious. Phylogenetic analysis showed Helianthus petiolaris subsp. fallax had the closest relationship with Jerusalem artichoke, both members of the Helianthus genus. Selective locus detection of the ycf2 gene in eight species of the composite family was performed to explore adaptive evolution traits of the ycf2 gene in Jerusalem artichoke. The results show that there are significant and extremely significant positive selection sites at the 1239N and 1518R loci, respectively, indicating that the ycf2 gene has been subject to adaptive evolution and has the potential to be used as a phylogenetic reconstruction locus in the composite family. Insights from our assessment of the complete chloroplast genome sequences of Jerusalem artichoke will aid in the in-depth study of the evolutionary relationship of the composite family, and provide significant sequencing information for the genetic improvement of Jerusalem artichoke.

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Background Jerusalem artichoke (Helianthus tuberosus L.) is a highly stress-resistant crop, especially it grows normally in the desertified land of Qinghai-Tibet Plateau in the past two years, and has become a crop with agricultural, industrial and ecological functions. However, there are few studies on drought resistance of Jerusalem artichoke at present, and studies on the mechanisms of stress resistance of Jerusalem artichoke breeding and fructan are seriously lagging behind. In this study, we selected two differentially resistant cultivars for drought stress experiments with different concentration gradients, the aim was finding DEGs and metabolic pathways associated with drought stress. Results Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. It was suggested that flavonoids could help Jerusalem artichoke to resist drought stress and maintain normal metabolic activities. In addition, the gene analysis of the abscisic acid (ABA) key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1, but QY1 had more genes in response to drought stress as a whole. By combining RNA-Seq and WGCNA, a weighted gene co-expression network was constructed and divided into modules. By analyzing specifically the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase had the highest significance in these pathways. Conclusions These findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the excavation of related genes.