The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales

Song, X and Sun, P and Yuan, J and Gong, K and Li, N and Meng, F and Zhang, Z and Li, X and Hu, J and Wang, J and Yang, Q and Jiao, B and Nie, F and Liu, T and Chen, W and Feng, S and Pei, Q and Yu, T and Kang, X and Zhao, W and Cui, C and Yu, Y and Wu, T and Shan, L and Liu, M and Qin, Z and Lin, H and Varshney, R K and Li, X Q and Paterson, A H and Wang, X (2020) The celery genome sequence reveals sequential paleo‐polyploidizations, karyotype evolution and resistance gene reduction in apiales. Plant Biotechnology Journal (TSI). pp. 1-14. ISSN 1467-7644

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Abstract

Celery (Apium graveolens L. 2n = 2x = 22), a member of the Apiaceae family, is among the most important and globally grown vegetables. Here, we report a high-quality genome sequence assembly, anchored to 11 chromosomes, with total length of 3.33 Gb and N50 scaffold length of 289.78 Mb. Most (92.91%) of the genome is composed of repetitive sequences, with 62.12% of 31 326 annotated genes confined to the terminal 20% of chromosomes. Simultaneous bursts of shared long-terminal repeats (LTRs) in different Apiaceae plants suggest inter-specific exchanges. Two ancestral polyploidizations were inferred, one shared by Apiales taxa and the other confined to Apiaceae. We reconstructed 8 Apiales proto-chromosomes, inferring their evolutionary trajectories from the eudicot common ancestor to extant plants. Transcriptome sequencing in three tissues (roots, leaves and petioles), and varieties with different-coloured petioles, revealed 4 and 2 key genes in pathways regulating anthocyanin and coumarin biosynthesis, respectively. A remarkable paucity of NBS disease-resistant genes in celery (62) and other Apiales was explained by extensive loss and limited production of these genes during the last ~10 million years, raising questions about their biotic defence mechanisms and motivating research into effects of chemicals, for example coumarins, that give off distinctive odours. Celery genome sequencing and annotation facilitates further research into important gene functions and breeding, and comparative genomic analyses in Apiales.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Celery genome, Paleopolyploidizations, Karyotype Reconstruction, Resistance gene, Coumarins.
Subjects:	Others > Vegetable and Field crops Others > Genetics and Genomics
Depositing User:	Mr Arun S
Date Deposited:	31 Dec 2020 04:55
Last Modified:	31 Dec 2020 04:55
URI:	http://oar.icrisat.org/id/eprint/11685
Official URL:	https://doi.org/10.1111/pbi.13499
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	This work was supported by the National Natural Science Foundation of China (31801856 to X.S, 31371282, 2016YFD0101001 to X.W), the Hebei Province Higher Education Youth Talents Program (BJ2018016 to X.S), China-Hebei 100 Scholars Supporting Project to X.W. (E2013100003), and the China Postdoctoral Science Foundation (2020M673188 to X.S). The genome sequencing, Hi-C sequencing and primary assembly were performed with the help of Novogene.
Links:	Google Scholar

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