Location: Vegetable Crops ResearchTitle: Genome survey sequencing of Ailanthus altissima and identification of simple sequence repeat (SSR) markers
|YAPING, MA - Ningxia University
|LIHUA, SONG - Nanjing Forestry University
|GAO, HANDONG - Nanjing Forestry University
|BING, CAO - Nanjing Forestry University
Submitted to: SILVAE GENETICA
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/12/2022
Publication Date: 8/7/2022
Citation: Yaping, M., Mura, J.D., Lihua, S., Gao, H., Bing, C. 2022. Genome survey sequencing of Ailanthus altissima and identification of simple sequence repeat (SSR) markers. SILVAE GENETICA. 70(1):47-53. https://doi.org/10.2478/sg-2022-0006.
Interpretive Summary: Ailanthus altissima, commonly known as the tree of heaven, is a deciduous tree native to China and considered an invasive species in North America. Besides allelopathy, it has a wide range of medical applications. However, there is a lack of whole-genome data of this species for its research development. The current study was focused on conducting a genomic survey of A. altissima and determine its whole-genome sequencing scheme. We used Next-generation sequencing and k-mer analysis to measure the genome size of A. altissima. We identified a total of 735,179 high-quality genomic simple sequence repeat markers based on genome survey sequences. This study could serve as a reference for the future whole-genomic sequence of A. altissima. This information is useful in studying the biology of invasion, key genes for effective medicinal components, and genetic diversity of A. altissima.
Technical Abstract: Ailanthus altissima is a deciduous tree native to China and introduced to other parts of the world as an ornamental plant. It exhibits resistance to both abiotic and biotic stress factors. A. altissima has various pharmacological effects and strong allelopathy, creating wide research interests. However, there have been no reports of the whole genome in this species, limiting the research development. The current study's objective was to conduct a first genomic survey of A. altissima to determine the genomic profile. Next-generation sequencing and K-mer analysis were employed to measure the genome size of A. altissima and establish genomic profile. A total of 61.93 high-quality clean data was obtained, representing approximately 64.09× coverage of the A. altissima genome. The genomic characteristics of A. altissima include a genome size of 966.38 Mbp, a heterozygosis rate of 0.78%, and a repeat rate of 41.22%. A total of 735,179 high-quality genomic SSRs markers were identified based on genome survey sequences. Alignment analysis showed that Citrus sinensis and Leitneria floridana were closely related to A. altissima. This is the first report of genome survey of Ailanthus altissima. This study could serve as a reference for future whole-genomic sequence and molecular breeding of A. altissima.