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

Abstract

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.

Acknowledgements

This study was sponsored by the Earmarked fund for the China Agriculture Research System (grant No. CARS-19), the National Natural Science Foundation of China (grant No. 31801679), Guangdong Provincial Team of Technical System Innovation for Sugarcane Sisal Hemp Industry (grant No. 2023KJ104-03), Guangdong Basic and Applied Basic Research Foundation (grant Nos 2021A1515012421 and 2022A1515011841), Hainan Provincial Natural Science Foundation of China (321QN300 and 323MS099), and Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences (grant Nos. 1630062019016, 1630062020015, 1630062022002, and 1630062021015).

Author contributions

Z.Y. and W.Z. designed and coordinated the whole project. Z.Y. and Q.Y. led and performed the whole project. Q.L., X.L., L.W., and Y.Z. analysed the data. Z.K., Z.L., and H.S. collected and processed the samples. Z.Y. and Q.Y. drafted the manuscript. W.Z. revised the manuscript. Z.K., Z.L., H.S., and J.L. contributed to the manuscript preparation. All authors read and approved the final manuscript.

Data availability

Data generated during this study have been deposited into National Genomics Data Center under the project accession number PRJCA016359 (https://ngdc.cncb.ac.cn/gsub/).

Conflict of interest statement

The authors declare that they have no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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