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Haplotype-resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution.
Lu, Yongbin; Chen, Xiao; Yu, Hang; Zhang, Chao; Xue, Yajie; Zhang, Qiang; Wang, Haifeng.
Afiliación
  • Lu Y; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
  • Chen X; Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and the Chinese Academy of Sciences, Yanshan, Guilin, 541006, China.
  • Yu H; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
  • Zhang C; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
  • Xue Y; Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China.
  • Zhang Q; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, China.
  • Wang H; Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning, 530004, China.
Plant J ; 118(2): 488-505, 2024 Apr.
Article en En | MEDLINE | ID: mdl-38173092
ABSTRACT
Phanera championii is a medicinal liana plant that has successfully adapted to hostile karst habitats. Despite extensive research on its medicinal components and pharmacological effects, the molecular mechanisms underlying the biosynthesis of critical flavonoids and its adaptation to karst habitats remain elusive. In this study, we performed high-coverage PacBio and Hi-C sequencing of P. championii, which revealed its high heterozygosity and phased the genome into two haplotypes Hap1 (384.60 Mb) and Hap2 (383.70 Mb), encompassing a total of 58 612 annotated genes. Comparative genomes analysis revealed that P. championii experienced two whole-genome duplications (WGDs), with approximately 59.59% of genes originating from WGD events, thereby providing a valuable genetic resource for P. championii. Moreover, we identified a total of 112 genes that were strongly positively selected. Additionally, about 81.60 Mb of structural variations between the two haplotypes. The allele-specific expression patterns suggested that the dominant effect of P. championii was the elimination of deleterious mutations and the promotion of beneficial mutations to enhance fitness. Moreover, our transcriptome and metabolome analysis revealed alleles in different tissues or different haplotypes collectively regulate the synthesis of flavonoid metabolites. In summary, our comprehensive study highlights the significance of genomic and morphological adaptation in the successful adaptation of P. championii to karst habitats. The high-quality phased genomes obtained in this study serve as invaluable genomic resources for various applications, including germplasm conservation, breeding, evolutionary studies, and elucidation of pathways governing key biological traits of P. championii.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genoma de Planta / Genómica Idioma: En Revista: Plant J Asunto de la revista: BIOLOGIA MOLECULAR / BOTANICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Genoma de Planta / Genómica Idioma: En Revista: Plant J Asunto de la revista: BIOLOGIA MOLECULAR / BOTANICA Año: 2024 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido