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Centromere-Specific...
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Liu, HuiNational 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
(author)
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
- Article/chapterEnglish2021
Publisher, publication year, extent ...
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2021-11-22
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Frontiers Media S.A.2021
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electronicrdacarrier
Numbers
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LIBRIS-ID:oai:DiVA.org:umu-190416
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https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-190416URI
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https://doi.org/10.3389/fpls.2021.766389DOI
Supplementary language notes
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Language:English
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Summary in:English
Part of subdatabase
Classification
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Subject category:ref swepub-contenttype
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Subject category:art swepub-publicationtype
Notes
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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.
Subject headings and genre
Added entries (persons, corporate bodies, meetings, titles ...)
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Yan, Xue-MeiNational 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
(author)
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Wang, Xin-RuiNational 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
(author)
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Zhang, Dong-XuProtected Agricultural Technology, R&D Center, Shanxi Datong University, Datong, China
(author)
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Zhou, QingyuanKey Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China
(author)
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Shi, Tian-LeNational 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
(author)
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Jia, Kai-HuaNational 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
(author)
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Tian, Xue-ChanNational 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
(author)
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Zhou, Shan-ShanNational 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
(author)
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Zhang, Ren-GangDepartment of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, China
(author)
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Yun, Quan-ZhengDepartment of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, China
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Wang, QingKey Laboratory of Forest Ecology and Environment of the National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
(author)
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Xiang, QiuhongNational 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
(author)
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Mannapperuma, Chanaka,1982-Umeå universitet,Institutionen för fysiologisk botanik,Umeå Plant Science Centre (UPSC)(Swepub:umu)mach0027
(author)
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Van Zalen, ElenaUmeå universitet,Institutionen för fysiologisk botanik,Umeå Plant Science Centre (UPSC)(Swepub:umu)elva0027
(author)
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Street, Nathaniel R.,1979-Umeå universitet,Institutionen för fysiologisk botanik,Umeå Plant Science Centre (UPSC)(Swepub:umu)rona0006
(author)
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Porth, IlgaDépartment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et de Géomatique, Université Laval Québec, Quebec City, QC, Canada
(author)
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El-Kassaby, Yousry A.Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, BC, Vancouver, Canada
(author)
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Zhao, WeiUmeå universitet,Institutionen för ekologi, miljö och geovetenskap,Umeå Plant Science Centre (UPSC),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(Swepub:umu)zhwe0002
(author)
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Wang, Xiao-RuUmeå universitet,Institutionen för ekologi, miljö och geovetenskap,Umeå Plant Science Centre (UPSC),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(Swepub:umu)xiwa0003
(author)
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Guan, WenbinNational 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
(author)
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Mao, Jian-FengNational 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
(author)
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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, ChinaProtected Agricultural Technology, R&D Center, Shanxi Datong University, Datong, China
(creator_code:org_t)
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In:Frontiers in Plant Science: Frontiers Media S.A.121664-462X
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Liu, Hui
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Yan, Xue-Mei
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Wang, Xin-Rui
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Zhang, Dong-Xu
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Shi, Tian-Le
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Jia, Kai-Hua
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Tian, Xue-Chan
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Zhou, Shan-Shan
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Zhang, Ren-Gang
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Wang, Qing
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Xiang, Qiuhong
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Mannapperuma, Ch ...
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Van Zalen, Elena
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Street, Nathanie ...
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Porth, Ilga
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El-Kassaby, Yous ...
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Zhao, Wei
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Wang, Xiao-Ru
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Guan, Wenbin
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