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• A total of 119 WRKY genes were identified in Helianthus annuus L. • WRKYs present genetic diversity among oil crops. • Segmental and tandem duplications contribute to the expansion of sunflower WRKYs. • Expression analysis shows neo- or subfunctionalization after WRKY duplications. • Some HaWRKY genes play critical roles response to biotic and abiotic stresses. WRKY proteins constitute a large family of transcription factors that play important roles in many aspects of physiological processes and adaptation to environmental challenge. Although previous studies have identified and characterized WRKY genes from sunflower (Helianthus annuus L.) expressed sequence tag and genomic databases, the phylogenetic diversity of WRKY repertoires of oil crop species and the responses of sunflower WRKY proteins to various stressors have not been elucidated. In this study, a total of 860 WRKY members from seven oil crop species, namely, sunflower, sesame, castor bean, soybean, canola, Arachis duranensis , and Arachis ipaensis , were subjected to comparative genomic analysis. Genetic diversity within the WRKY family among these oil crop species was revealed through pairwise comparisons of orthologous groups and phylogenetic analysis. Sequence features and phylogenetic analysis revealed that the WRKY genes of oil crop species belong to well-defined groups or subgroups, and different oil plant species exhibit obvious expansion or loss to different degrees. One hundred nineteen sunflower WRKY (HaWRKY) genes were found to be unevenly distributed across each chromosome. Segmental and tandem duplications contributed to the expansion of group II and III WRKY genes in sunflower, respectively. The duplicated genes generally exhibit divergent expression patterns, which may indicate that neofunctionalization or subfunctionalization of these genes tends to occur after duplication. Moreover, expression profiles derived from transcriptomic data exhibited distinct expression patterns of HaWRKY genes in various tissues and in response to different stress treatments, including hormone treatments, salt and drought stress, infection by the fungus Verticillium dahliae , and colonization by the fungus Rhizoglomus irregulare. According to these results, WRKY genes may be involved in the strong adaptability of sunflower to various environments, thereby contributing to the importance of sunflower as a widely cultivated oil resource. This systematic analysis provides a foundation for further functional characterization of WRKY genes among oil crop species for the improvement of stress resistance. [ABSTRACT FROM AUTHOR]

CONSTANS-like (COL) genes play crucial roles in the regulation of photoperiodic flowering and responses to biotic and abiotic stresses; however, COL genes in sunflower (HaCOL) have not been extensively studied. In the present study, we identified 22 putative HaCOL genes in the whole genome sequence of sunflower, which were unevenly distributed on 10 chromosomes. The phylogenetic analysis showed that the HaCOLs could be divided into three well-defined groups (groups I, II and III). Group III had the highest number of COL genes among the three tested monocots, while the highest number of COL genes were observed in group I among the five tested dicots. Among all eight species, group II had the fewest COL family members. Segmental duplications contributed greatly to the expansion of this gene family. Furthermore, 11 tissue expression profiles of 22 HaCOL genes were analyzed through RNA-seq, which displayed their tissue-specific expression profiles. In addition, the expression levels of these HaCOL genes were analyzed under hormone, cadmium (Cd), heat, and drought stresses, and the results showed that HaCOL3 , HaCOL6 , and HaCOL19 were more sensitive than other HaCOLs to certain abiotic stresses. Moreover, the duplicated genes conferred important neofunctionalization in response to abiotic stresses. On the basis of our findings, we speculate that this conserved, duplicated and neofunctionalized COL gene family may play pivotal roles in the adaptation of sunflower to adverse environments. • A total of 22 putative CONSTANS-like genes identified in sunflower genome. • Sunflower CONSTANS-like genes could be divided into three well defined groups. • Segmental duplications contribute greatly to the expansion of this gene family. • Duplicated genes confer their novel functions in response to abiotic stresses. • The neofunctionalized sunflower COLs involved in environmental adaptation. [ABSTRACT FROM AUTHOR]

• Root flavonoid contents were higher in triennial S. flavescens than biennial S. flavescens. • Taproot and lateral root expression profiles were clustered by cultivation period. • Genes involved in flavonoid biosynthesis in S. flavescens were identified. • Transcription factors are involved in flavonoid biosynthesis in S. flavescens. Flavonoids are a primary bioactive component of Sophora flavescens , which is widely used in traditional Chinese medicine. Understanding flavonoid biosynthesis is of great importance for improving the production of active compounds. In this study, both the total flavonoid content and the contents of six main flavonoid (namely, genistin, trifolirhizin, maackiain, kushenol I, kurarinone, and nor-kurarinone) were significantly higher in triennial S. flavescens than in biennial plants, and the flavonoid content of lateral roots was higher than that of taproots. We attempted to generate exhaustive molecular information on the flavonoid secondary metabolite pathway and to increase the genomic resources for S. flavescens. De novo transcriptome data provided 643,251 unigenes, and 365,572 (56.83 %) were successfully annotated in five public protein databases. The gene expression profiles of taproots and lateral roots clustered with each other and were separated by the cultivation period; the other expression profiles were clustered according to tissue pattern. The differentially expressed unigenes (DEGs) in the lateral roots, taproots and stems between biennial and triennial S. flavescens were identified and subjected to functional annotation enrichment. A total of 92 unigenes encoding well-known enzymes involved in flavonoid biosynthesis were found to show differential expression between biennial and triennial S. flavescens. Furthermore, the comparative expression results of eight unigenes were validated by real-time quantitative PCR (qRT-PCR). The most abundant transcription factors (TFs) that were differentially expressed in S. flavescens were those belonging to the bHLH-, NAC-, ERF- and MYB-related families, and these TFs were identified regardless of the tissue or cultivation period. Our study provides important resources of gene sequences and expression and insights into the molecular mechanism of flavonoid biosynthesis during S. flavescens cultivation. [ABSTRACT FROM AUTHOR]