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Summary High‐quality genome of rosemary (Salvia rosmarinus) represents a valuable resource and tool for understanding genome evolution and environmental adaptation as well as its genetic improvement. However, the existing rosemary genome did not provide insights into the relationship between antioxidant components and environmental adaptability. In this study, by employing Nanopore sequencing and Hi‐C technologies, a total of 1.17 Gb (97.96%) genome sequences were mapped to 12 chromosomes with 46 121 protein‐coding genes and 1265 non‐coding RNA genes. Comparative genome analysis reveals that rosemary had a closely genetic relationship withSalvia splendensandSalvia miltiorrhiza, and it diverged from them approximately 33.7 million years ago (MYA), and one whole‐genome duplication occurred around 28.3 MYA in rosemary genome. Among all identified rosemary genes, 1918 gene families were expanded, 35 of which are involved in the biosynthesis of antioxidant components. These expanded gene families enhance the ability of rosemary adaptation to adverse environments. Multi‐omics (integrated transcriptome and metabolome) analysis showed the tissue‐specific distribution of antioxidant components related to environmental adaptation. During the drought, heat and salt stress treatments, 36 genes in the biosynthesis pathways of carnosic acid, rosmarinic acid and flavonoids were up‐regulated, illustrating the important role of these antioxidant components in responding to abiotic stresses by adjusting ROS homeostasis. Moreover, cooperating with the photosynthesis, substance and energy metabolism, protein and ion balance, the collaborative system maintained cell stability and improved the ability of rosemary against harsh environment. This study provides a genomic data platform for gene discovery and precision breeding in rosemary. Our results also provide new insights into the adaptive evolution of rosemary and the contribution of antioxidant components in resistance to harsh environments. 

Understanding the mechanism of crop response to nitrogen (N) deficiency is very important for developing sustainable agriculture. In addition, it is unclear if the microRNA-mediated mechanism related to root growth complies with a common mechanism in monocots and dicots under N deficiency. Therefore, the root morpho-physiological characteristics and microRNA-mediated mechanisms were studied under N deficiency in wheat (Triticum aestivumL.) and cotton (Gossypium hirsutumL.). For both crops, shoot dry weight, plant dry weight and total leaf area as well as some physiological traits, i.e., the oxygen consuming rate in leaf and root, the performance index based on light energy absorption were significantly decreased after 8 days of N deficiency. Although N deficiency did not significantly impact the root biomass, an obvious change on the root morphological traits was observed in both wheat and cotton. After 8 days of treatment with N deficiency, the total root length, root surface area, root volume of both crops showed an opposite trend with significantly decreasing in wheat but significantly increasing in cotton, while the lateral root density was significantly increased in wheat but significantly decreased in cotton. At the same time, the seminal root length in wheat and the primary root length in cotton were increased after 8 days of N deficiency treatment. Additionally, the two crops had different root regulatory mechanisms of microRNAs (miRNAs) to N deficiency. In wheat, the expressions of miR167, miR319, miR390, miR827, miR847, and miR165/166 were induced by N treatment; these miRNAs inhibited the total root growth but promoted the seminal roots growth and lateral root formation to tolerate N deficiency. In cotton, the expressions of miR156, miR167, miR171, miR172, miR390, miR396 were induced and the expressions of miR162 and miR393 were inhibited; which contributed to increasing in the total root length and primary root growth and to decreasing in the lateral root formation to adapt the N deficiency. In conclusion, N deficiency significantly affected the morpho-physiological characteristics of roots that were regulated by miRNAs, but the miRNA-mediated mechanisms were different in wheat and cotton. 

Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton (Gossypium hirsutumandGossypium barbadense, AADD) and its extant AA (Gossypium arboreum) and DD (Gossypium raimondii) progenitors. We observed distinct DHS distributions betweenG. arboreumandG. raimondii. In contrast, the DHSs of the two subgenomes ofG. hirsutumandG. barbadenseshowed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploidsGossypium darwiniiandG. hirsutumvar.yucatanense, but absent from a resynthesized hybrid ofG. arboreumandG. raimondii, suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putativecis-regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization. 

The mechanism of miRNA-mediated root growth and development in response to nutrient deficiency in peanut (Arachis hypogaeaL.) is still unclear. In the present study, we found that both nitrogen (N) and potassium (K) deficiency resulted in a significant reduction in plant growth, as indicated by the significantly decreased dry weight of both shoot and root tissues under N or K deficiency. Both N and K deficiency significantly reduced the root length, root surface area, root volume, root vitality, and weakened root respiration, as indicated by the reduced O₂consuming rate. N deficiency significantly decreased primary root length and lateral root number, which might be associated with the upregulation of miR160, miR167, miR393, and miR396, and the downregulation of AFB3 and GRF. The primary and lateral root responses to K deficiency were opposite to that of the N deficiency condition. The upregulated miR156, miR390, NAC4, ARF2, and AFB3, and the downregulated miR160, miR164, miR393, and SPL10 may have contributed to the growth of primary roots and lateral roots under K deficiency. Overall, roots responded differently to the N or K deficiency stresses in peanuts, potentially due to the miRNA-mediated pathway and mechanism.