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

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 y...

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Autores principales:	Hui Liu, Xue-Mei Yan, Xin-rui Wang, Dong-Xu Zhang, Qingyuan Zhou, Tian-Le Shi, Kai-Hua Jia, Xue-Chan Tian, Shan-Shan Zhou, Ren-Gang Zhang, Quan-Zheng Yun, Qing Wang, Qiuhong Xiang, Chanaka Mannapperuma, Elena Van Zalen, Nathaniel R. Street, Ilga Porth, Yousry A. El-Kassaby, Wei Zhao, Xiao-Ru Wang, Wenbin Guan, Jian-Feng Mao
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	yellowhorn centromere LINE1 Gypsy very-long-chain fatty acid Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/6ca0cb9f501d4c729e444a9a80c42d7b
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spelling	oai:doaj.org-article:6ca0cb9f501d4c729e444a9a80c42d7b2021-11-30T10:09:44ZCentromere-Specific Retrotransposons and Very-Long-Chain Fatty Acid Biosynthesis in the Genome of Yellowhorn (Xanthoceras sorbifolium, Sapindaceae), an Oil-Producing Tree With Significant Drought Resistance1664-462X10.3389/fpls.2021.766389https://doaj.org/article/6ca0cb9f501d4c729e444a9a80c42d7b2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.766389/fullhttps://doaj.org/toc/1664-462XIn-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.Hui LiuXue-Mei YanXin-rui WangDong-Xu ZhangQingyuan ZhouTian-Le ShiKai-Hua JiaXue-Chan TianShan-Shan ZhouRen-Gang ZhangQuan-Zheng YunQing WangQiuhong XiangChanaka MannapperumaElena Van ZalenNathaniel R. StreetIlga PorthYousry A. El-KassabyWei ZhaoWei ZhaoXiao-Ru WangXiao-Ru WangWenbin GuanJian-Feng MaoFrontiers Media S.A.articleyellowhorncentromereLINE1Gypsyvery-long-chain fatty acidPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	yellowhorn centromere LINE1 Gypsy very-long-chain fatty acid Plant culture SB1-1110
spellingShingle	yellowhorn centromere LINE1 Gypsy very-long-chain fatty acid Plant culture SB1-1110 Hui Liu Xue-Mei Yan Xin-rui Wang Dong-Xu Zhang Qingyuan Zhou Tian-Le Shi Kai-Hua Jia Xue-Chan Tian Shan-Shan Zhou Ren-Gang Zhang Quan-Zheng Yun Qing Wang Qiuhong Xiang Chanaka Mannapperuma Elena Van Zalen Nathaniel R. Street Ilga Porth Yousry A. El-Kassaby Wei Zhao Wei Zhao Xiao-Ru Wang Xiao-Ru Wang Wenbin Guan Jian-Feng Mao 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
description	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.
format	article
author	Hui Liu Xue-Mei Yan Xin-rui Wang Dong-Xu Zhang Qingyuan Zhou Tian-Le Shi Kai-Hua Jia Xue-Chan Tian Shan-Shan Zhou Ren-Gang Zhang Quan-Zheng Yun Qing Wang Qiuhong Xiang Chanaka Mannapperuma Elena Van Zalen Nathaniel R. Street Ilga Porth Yousry A. El-Kassaby Wei Zhao Wei Zhao Xiao-Ru Wang Xiao-Ru Wang Wenbin Guan Jian-Feng Mao
author_facet	Hui Liu Xue-Mei Yan Xin-rui Wang Dong-Xu Zhang Qingyuan Zhou Tian-Le Shi Kai-Hua Jia Xue-Chan Tian Shan-Shan Zhou Ren-Gang Zhang Quan-Zheng Yun Qing Wang Qiuhong Xiang Chanaka Mannapperuma Elena Van Zalen Nathaniel R. Street Ilga Porth Yousry A. El-Kassaby Wei Zhao Wei Zhao Xiao-Ru Wang Xiao-Ru Wang Wenbin Guan Jian-Feng Mao
author_sort	Hui Liu
title	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
title_short	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
title_full	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
title_fullStr	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
title_full_unstemmed	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
title_sort	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
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/6ca0cb9f501d4c729e444a9a80c42d7b
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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

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