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

被引:3
作者
Yang, Ziping [1 ]
Yang, Qian [1 ]
Liu, Qi [2 ]
Li, Xiaolong [3 ]
Wang, Luli [1 ]
Zhang, Yanmei [1 ]
Ke, Zhi [1 ]
Lu, Zhiwei [1 ]
Shen, Huibang [1 ]
Li, Junfeng [1 ]
Zhou, Wenzhao [1 ]
机构
[1] Chinese Acad Trop Agr Sci, South Subtrop Crops Res Inst, Zhanjiang Key Lab Trop Crop Genet Improvement, Zhanjiang 524091, Guangdong, Peoples R China
[2] Wuhan Onemore Tech Co Ltd, Wuhan 430076, Hubei, Peoples R China
[3] Biomarker Technol Corp, Beijing 101300, Peoples R China
基金
中国国家自然科学基金; 海南省自然科学基金;
关键词
CRASSULACEAN ACID METABOLISM; ALIGNMENT; ANNOTATION; EVOLUTION; SEQUENCE; GENES; DATABASE; PROGRAM; TRANSCRIPTOME; DUPLICATIONS;
D O I
10.1093/hr/uhad269
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
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.
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页数:15
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