TY - JOUR
T1 - Insights from the first genome assembly of Onion (Allium cepa)
AU - Finkers, Richard
AU - van Kaauwen, Martijn
AU - Ament, Kai
AU - Burger-Meijer, Karin
AU - Egging, Raymond
AU - Huits, Henk
AU - Kodde, Linda
AU - Kroon, Laurens
AU - Shigyo, Masayoshi
AU - Sato, Shusei
AU - Vosman, Ben
AU - van Workum, Wilbert
AU - Scholten, Olga
N1 - Funding Information:
The authors would like to thank Dr Marta Mutschler for providing the DH line and Dr Alexey Zimin for his help in debugging the MaSurCa assembly pipeline. This work was, in part, carried out on the Dutch national e-infrastructure with the support of SURF Cooperative.
Funding Information:
This research was supported by a grant from the Top Sector Horticulture & Propagation Materials (H279-SEQUON) and by the companies Bejo Zaden B.V., De Groot en Slot B.V., and GenomeScan. Within the Top Sector, the business community, knowledge institutions and the government work together on innovations in the field of sustainable production of healthy and safe food and the development of a healthy, green living environment.
Publisher Copyright:
© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.
PY - 2021
Y1 - 2021
N2 - Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
AB - Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Of this, 2.4 Gb was ordered into eight pseudomolecules using four genetic linkage maps. The remainder of the genome is available in 89.6 K scaffolds. Only 72.4% of the genome could be identified as repetitive sequences and consist, to a large extent, of (retro) transposons. In addition, an estimated 20% of the putative (retro) transposons had accumulated a large number of mutations, hampering their identification, but facilitating their assembly. These elements are probably already quite old. The ab initio gene prediction indicated 540,925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. Of these models, 47,066 showed RNASeq support. No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with Allium sativum (garlic) showed collinearity but also major rearrangements between both species. This assembly is the first high-quality genome sequence available for the study of onion and will be a valuable resource for further research.
KW - DHCU066619
KW - Gene space
KW - Large genome
KW - Repeats
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U2 - 10.1093/g3journal/jkab243
DO - 10.1093/g3journal/jkab243
M3 - Article
C2 - 34544132
AN - SCOPUS:85114422765
VL - 11
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
SN - 2160-1836
IS - 9
M1 - jkab243
ER -