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Centromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance
National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
National Engineering Laboratory for Tree Breeding, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
Protected Agricultural Technology, R&D Center, Shanxi Datong University, Datong, China.
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2021 (English)In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 12, article id 766389Article in journal (Refereed) Published
Abstract [en]

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2021. Vol. 12, article id 766389
Keywords [en]
centromere, Gypsy, LINE1, very-long-chain fatty acid, yellowhorn
National Category
Botany Biochemistry and Molecular Biology
Research subject
biology
Identifiers
URN: urn:nbn:se:umu:diva-190416DOI: 10.3389/fpls.2021.766389ISI: 000726943000001PubMedID: 34880890Scopus ID: 2-s2.0-85120747893OAI: oai:DiVA.org:umu-190416DiVA, id: diva2:1620663
Available from: 2021-12-16 Created: 2021-12-16 Last updated: 2024-01-17Bibliographically approved

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Mannapperuma, ChanakaVan Zalen, ElenaStreet, Nathaniel R.Zhao, WeiWang, Xiao-Ru

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Mannapperuma, ChanakaVan Zalen, ElenaStreet, Nathaniel R.Zhao, WeiWang, Xiao-Ru
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Frontiers in Plant Science
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