首页|A chromosome-level genome assembly of Agave hybrid NO.11648 provides insights into the CAM photosynthesis

A chromosome-level genome assembly of Agave hybrid NO.11648 provides insights into the CAM photosynthesis

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The subfamily Agavoideae comprises crassulacean acid metabolism(CAM),C3,and C4 plants with a young age of speciation and slower mutation accumulation,making it a model crop for studying CAM evolution.However,the genetic mechanism underlying CAM evolution remains unclear because of lacking genomic information.This study assembled the genome of Agave hybrid NO.11648,a constitutive CAM plant belonging to subfamily Agavoideae,at the chromosome level using data generated from high-throughput chromosome conformation capture,Nanopore,and Illumina techniques,resulting in 30 pseudo-chromosomes with a size of 4.87 Gb and scaffold N50 of 186.42 Mb.The genome annotation revealed 58 841 protein-coding genes and 76.91％repetitive sequences,with the dominant repetitive sequences being the I-type repeats(Copia and Gypsy accounting for 18.34％and 13.5％of the genome,respectively).Our findings also provide support for a whole genome duplication event in the lineage leading to A.hybrid,which occurred after its divergence from subfamily Asparagoideae.Moreover,we identified a gene duplication event in the phosphoenolpyruvate carboxylase kinase(PEPCK)gene family and revealed that three PEPCK genes(PEPCK3,PEPCK5,and PEPCK12)were involved in the CAM pathway.More importantly,we identified transcription factors enriched in the circadian rhythm,MAPK signaling,and plant hormone signal pathway that regulate the PEPCK3 expression by analysing the transcriptome and using yeast one-hybrid assays.Our results shed light on CAM evolution and offer an essential resource for the molecular breeding program of Agave spp.

Ziping Yang、Qian Yang、Qi Liu、Xiaolong Li、Luli Wang、Yanmei Zhang、Zhi Ke、Zhiwei Lu、Huibang Shen、Junfeng Li、Wenzhao Zhou

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Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement,South Subtropical Crops Research Institute,Chinese Academy of Tropical Agricultural Sciences,524091 Zhanjiang,Guangdong,China

Wuhan Onemore-tech Co.,Ltd,430076 Wuhan,Hubei,China

Biomarker Technologies Corporation,101300 Beijing,China

Earmarked Fund for the China Agriculture Research System国家自然科学基金Guangdong Provincial Team of Technical System Innovation for Sugarcane Sisal Hemp IndustryGuangdong Basic and Applied Basic Research FoundationGuangdong Basic and Applied Basic Research Foundation海南省自然科学基金海南省自然科学基金Central Publicinterest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural SciencesCentral Publicinterest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural SciencesCentral Publicinterest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural SciencesCentral Publicinterest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences

CARS-19318016792023KJ104-032021A15150124212022A1515011841321QN300323MS0991630062019016163006202001516300620220021630062021015

2024

10.1093/hr/uhad269

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(2)
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