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Summary Safflower (Carthamus tinctorius L.), a member of the Asteraceae, is a popular crop due to its high linoleic acid (LA) and flavonoid (such as hydroxysafflor yellow A) contents. Here, we report the first high‐quality genome assembly (contig N50 of 21.23 Mb) for the 12 pseudochromosomes of safflower using single‐molecule real‐time sequencing, Hi‐C mapping technologies and a genetic linkage map. Phyloge nomic analysis showed that safflower diverged from artichoke (Cynara cardunculus) and sunflower (Helianthus annuus) approximately 30.7 and 60.5 million years ago, respectively. Comparative genomic analyses revealed that uniquely expanded gene families in safflower were enriched for those predicted to be involved in lipid metabolism and transport and abscisic acid signalling. Notably, the fatty acid desaturase 2 (FAD2) and chalcone synthase (CHS) families, which function in the LA and flavonoid biosynthesis pathways, respectively, were expanded via tandem duplications in safflower. CarFAD2‐12 was specifically expressed in seeds and was vital for high‐LA content in seeds, while tandemly duplicated CarFAD2 genes were up‐regulated in ovaries compared to CarFAD2‐12, which indicates regulatory divergence of FAD2 in seeds and ovaries. CarCHS1, CarCHS4 and tandem‐duplicated CarCHS5˜CarCHS6, which were up‐regulated compared to other CarCHS members at early stages, contribute to the accumulation of major flavonoids in flowers. In addition, our data reveal multiple alternative splicing events in gene families related to fatty acid and flavonoid biosynthesis. Together, these results provide a high‐quality reference genome and evolutionary insights into the molecular basis of fatty acid and flavonoid biosynthesis in safflower.

Alhagi sparsifolia Shap. is a perennial herbaceous plant belonging to the genus Alhagi, Leguminosae. This species is of high nutritional, medicinal and ecological values. The complete chloroplast genome was 128,418 bp and lost an IR (inverted repeat) region. Further annotation revealed the chloroplast genome contains 108 genes, including 75 protein coding genes, 29 tRNA genes, and 4 rRNA genes. A total of 103 simple sequence repeats (SSRs) were identified in the chloroplast genome. This chloroplast genome resource will be useful for study on the evolution and genetic diversity of A. sparsifolia in the future.

Meiotic recombination (MR) drives novel combinations of alleles and contributes to genomic diversity in eukaryotes. In this study, we showed that heat stress (36°C–38°C) over the fertile threshold fully abolished crossover formation in Arabidopsis (Arabidopsis thaliana). Cytological and genetic studies in wild-type plants and syn1 and rad51 mutants suggested that heat stress reduces generation of SPO11-dependent double-strand breaks (DSBs). In support, the abundance of recombinase DMC1, which is required for MR-specific DSB repair, was significantly reduced under heat stress. In addition, high temperatures induced disassembly and/or instability of the ASY4- but not the SYN1-mediated chromosome axis. At the same time, the ASY1-associated lateral element of the synaptonemal complex (SC) was partially affected, while the ZYP1-dependent central element of SC was disrupted, indicating that heat stress impairs SC formation. Moreover, expression of genes involved in DSB formation; e.g. SPO11-1, PRD1, 2, and 3 was not impacted; however, recombinase RAD51 and chromosome axis factors ASY3 and ASY4 were significantly downregulated under heat stress. Taken together, these findings revealed that heat stress inhibits MR via compromised DSB formation and homolog synapsis, which are possible downstream effects of the impacted chromosome axis. Our study thus provides evidence shedding light on how increasing environmental temperature influences MR in Arabidopsis.

RWP-RK is a plant-specific family of transcription factors, involved in nitrate response, gametogenesis, and nodulation. However, genome-wide characterization, phylogeny, and the regulation of RWP-RK genes in the nodulating and non-nodulating plant species of nitrogen-fixing clade (NFC) are widely unknown. Therefore, we identified a total of 292 RWP-RKs, including 278 RWP-RKs from 25 NFC species and 14 RWP-RKs from the outgroup, Arabidopsis thaliana. We classified the 292 RWP-RKs in two subfamilies: the NIN-like proteins (NLPs) and the RWP-RK domain proteins (RKDs). The transcriptome and phylogenetic analysis of RWP-RKs suggested that, compared to RKD genes, the NLP genes were just upregulated in nitrate response and nodulation. Moreover, nodule-specific NLP genes of some nodulating NFC species may have a common ancestor (OG0002084) with AtNLP genes in A. thaliana. Further, co-expression networks of A.thaliana under N-starvation and N-supplementation conditions revealed that there is a higher correlation between expression of AtNLP genes and symbiotic genes during N-starvation. In P. vulgaris, we confirmed that N-starvation stimulated nodulation by regulating expression of PvNLP2, closely related to AtNLP6 and AtNLP7 with another common origin (OG0004041). Taken together, we concluded that different origins of the NLP genes involved in both N-starvation response and specific expression of nodulation would contribute to the evolution of nodulation in NFC plant species. Our results shed light on the phylogenetic relationships of NLP genes and their differential regulation in nitrate response of A. thaliana and nodulation of NFC.

Background Nitrogen, as a constituent of amino acids and nucleic acids, is an essential macronutrient for all living organisms. The nitrogen-fixation clade (NFC) is a clade, consisting of Fabales, Fagales, Cucurbitales, and Rosales, where all nodulating plants have been originated. The plant-specific RWP-RK family of transcription factors are involved in nitrate responses and play specific roles in nodule inception. In the present study, by investigation of RWP-RKs at genome-wide level and comparative coexpression networks, the roles of RWP-RKs involved in nitrate response and nodulation were analyzed to reveal evolution of RWP-RKs and a possible relationship between nitrogen signaling and nodulation.Results Here, we systematically investigated 292 RWP-RKs from 26 species of legumes and non-legumes of NFC by whole-genomic analysis and characterized their evolutionary relationships, protein motifs, and gene structures. We compared RWP-RK networks from Arabidopsis thaliana under N-starvation and N-supplementation conditions, as well as transcriptome atlases from Phaseolus vulgaris and Glycine max . This revealed that N starvation, which is essential for nodulation, alters the connectivity of RWP-RKs to other genes, including symbiosis-related genes. Meanwhile, appropriately low concentrations of nitrates stimulate nodulation by regulating RWP-RK expression in P. vulgaris .Conclusions Our comparative evolutionary analysis of RWP-RKs between A. thaliana and legumes revealed the evolutionary features and the relationship between the nitrate signaling pathway in a model organism and nodulation in legumes.

Background Nitrogen, as a constituent of amino acids and nucleic acids, is an essential macronutrient for all living organisms. The nitrogen-fixation clade (NFC) is a clade, consisting of Fabales, Fagales, Cucurbitales, and Rosales, where all nodulating plants have been originated. The plant-specific RWP-RK family of transcription factors are involved in nitrate responses and play specific roles in nodule inception. In the present study, by investigation of RWP-RKs at genome-wide level and comparative coexpression networks, the roles of RWP-RKs involved in nitrate response and nodulation were analyzed to reveal evolution of RWP-RKs and a relationship between nitrogen signaling and nodulation.Results Here, we systematically investigated 292 RWP-RKs from 26 species of legumes and non-legumes of NFC by whole-genomic analysis and characterized their evolutionary relationships, protein motifs, and gene structures. We compared RWP-RK networks from Arabidopsis thaliana under N-starvation and N-supplementation conditions, as well as transcriptome atlases from Phaseolus vulgaris and Glycine max. This revealed that N starvation, which is essential for nodulation, alters the connectivity of RWP-RKs to other genes, including symbiosis-related genes. Meanwhile, appropriately low concentrations of nitrates stimulate nodulation by regulating RWP-RK expression in P. vulgaris.Conclusions Our comparative evolutionary analysis of RWP-RKs between A. thaliana and legumes revealed the evolutionary features and the relationship between the nitrate signaling pathway in a model organism and nodulation in legumes.