Bioscience Methods 2024, Vol.15, No.5, 244-254 http://bioscipublisher.com/index.php/bm 249 5 Genomic Analysis 5.1 Overview of genomic studies onAtractylodes macrocephala Atractylodes macrocephala, a prominent medicinal herb in traditional Chinese medicine, has been the subject of various genomic studies aimed at understanding its genetic makeup and medicinal properties. These studies have provided insights into the plant's genetic diversity, phylogenetic relationships, and the molecular basis of its pharmacological activities. For instance, the complete plastome sequence of A. macrocephala has been analyzed, revealing a genome length of 153 265 bp with typical quadripartite structures common to Asteraceae species (Cai et al., 2020). Additionally, phylogenetic analyses have been conducted to explore the relationships between A. macrocephala and other species within the Atractylodes genus, highlighting the complex evolutionary history and potential hybridization events (Wang et al., 2020; Liu et al., 2022). 5.2 Genome sequencing and assembly The genome sequencing of Atractylodes macrocephala has been a significant milestone in understanding its genetic framework. The complete plastome sequence was determined to be 153,265 bp in length, comprising a large single-copy (LSC) region of 84,311 bp, a small single-copy (SSC) region of 18,674 bp, and a pair of inverted repeat (IR) regions of 25,140 bp each (Cai et al., 2020). This sequencing effort has provided a comprehensive view of the genetic structure, including 107 unique genes, which consist of 80 protein-coding genes, 23 tRNA genes, and 4 rRNA genes. The overall GC content of the genome is 37.7%, which is consistent with other members of the Asteraceae family (Cai et al., 2020). 5.3 Annotation of functional genes Functional annotation of the Atractylodes macrocephala genome has identified numerous genes associated with its medicinal properties. For example, high-throughput RNA sequencing has revealed 114 572 unigenes, with 3 570 differentially expressed genes (DEGs) between one-year and three-year growth rhizomes. These DEGs include genes involved in terpenoid synthesis, which are crucial for the plant's pharmacological activities (Fang et al., 2022). Additionally, the identification of autotoxic compounds such as 2,4-Ditertbutyl phenol (2,4-DP) and their impact on the plant's immune system has been explored, providing insights into the molecular mechanisms underlying autotoxicity and systemic acquired resistance (SAR) (Zheng et al., 2018). 5.4 Comparative genomics with related species Comparative genomic studies have been instrumental in elucidating the evolutionary relationships between Atractylodes macrocephala and related species. Phylogenetic analyses using plastome and nuclear gene sequences have shown that A. macrocephala shares a high degree of genetic similarity with A. lancea and A. chinensis, suggesting potential hybridization events (Figure 3) (Wang et al., 2020; Liu et al., 2022). The identification of molecular markers has facilitated the differentiation of these species, despite their morphological similarities (Wang et al., 2020). Furthermore, the cytonuclear discordance observed in the genus Atractylodes highlights the complex phylogenetic history and the role of interspecific hybridization in shaping the genetic landscape of these medicinal plants (Liu et al., 2022). In summary, the genomic analysis of Atractylodes macrocephala has provided valuable insights into its genetic composition, functional genes, and evolutionary relationships. These findings not only enhance our understanding of the plant's medicinal properties but also pave the way for future research aimed at improving its cultivation and therapeutic applications. 6 Genetic Basis of Medicinal Properties 6.1 Identification of key genes and pathways Atractylodes macrocephala, a traditional Chinese medicinal herb, has been extensively studied to identify the genetic basis underlying its medicinal properties. Recent genomic analyses have revealed several key genes and pathways that contribute to its pharmacological activities. For instance, the complete plastome sequence of A. macrocephala has been characterized, providing insights into its genetic makeup and evolutionary relationships with other species in the Atractylodes genus (Cai et al., 2020). Additionally, studies have identified differentially expressed genes (DEGs) in A. macrocephalarhizomes from different growth years, highlighting genes involved in terpenoid synthesis, which are crucial for its medicinal properties (Fang et al., 2022). Network pharmacology
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