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. Liu, H., Yan, X., Wang, X., Zhang, D., Zhou, Q., Shi, T., Jia, K., Tian, X., Zhou, S., Zhang, R., Yun, Q., Wang, Q., Xiang, Q., Mannapperuma, C., Van Zalen, E., Street, N. R., Porth, I., El-Kassaby, Y. A., Zhao, W., Wang, X., Guan, W., & Mao, J. Frontiers in Plant Science, 12:2546, 2021. ![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 [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex 3 downloads 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.
@article{liu_centromere-specific_2021,
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}},
volume = {12},
issn = {1664-462X},
url = {https://www.frontiersin.org/article/10.3389/fpls.2021.766389},
doi = {10/gnsqvv},
abstract = {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.},
urldate = {2021-12-16},
journal = {Frontiers in Plant Science},
author = {Liu, Hui and Yan, Xue-Mei and Wang, Xin-rui and Zhang, Dong-Xu and Zhou, Qingyuan and Shi, Tian-Le and Jia, Kai-Hua and Tian, Xue-Chan and Zhou, Shan-Shan and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Qing and Xiang, Qiuhong and Mannapperuma, Chanaka and Van Zalen, Elena and Street, Nathaniel R. and Porth, Ilga and El-Kassaby, Yousry A. and Zhao, Wei and Wang, Xiao-Ru and Guan, Wenbin and Mao, Jian-Feng},
year = {2021},
pages = {2546},
}
Downloads: 3
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A.","Zhao, W.","Wang, X.","Guan, W.","Mao, J."],"bibdata":{"bibtype":"article","type":"article","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","volume":"12","issn":"1664-462X","url":"https://www.frontiersin.org/article/10.3389/fpls.2021.766389","doi":"10/gnsqvv","abstract":"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.","urldate":"2021-12-16","journal":"Frontiers in Plant Science","author":[{"propositions":[],"lastnames":["Liu"],"firstnames":["Hui"],"suffixes":[]},{"propositions":[],"lastnames":["Yan"],"firstnames":["Xue-Mei"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Xin-rui"],"suffixes":[]},{"propositions":[],"lastnames":["Zhang"],"firstnames":["Dong-Xu"],"suffixes":[]},{"propositions":[],"lastnames":["Zhou"],"firstnames":["Qingyuan"],"suffixes":[]},{"propositions":[],"lastnames":["Shi"],"firstnames":["Tian-Le"],"suffixes":[]},{"propositions":[],"lastnames":["Jia"],"firstnames":["Kai-Hua"],"suffixes":[]},{"propositions":[],"lastnames":["Tian"],"firstnames":["Xue-Chan"],"suffixes":[]},{"propositions":[],"lastnames":["Zhou"],"firstnames":["Shan-Shan"],"suffixes":[]},{"propositions":[],"lastnames":["Zhang"],"firstnames":["Ren-Gang"],"suffixes":[]},{"propositions":[],"lastnames":["Yun"],"firstnames":["Quan-Zheng"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Qing"],"suffixes":[]},{"propositions":[],"lastnames":["Xiang"],"firstnames":["Qiuhong"],"suffixes":[]},{"propositions":[],"lastnames":["Mannapperuma"],"firstnames":["Chanaka"],"suffixes":[]},{"propositions":[],"lastnames":["Van","Zalen"],"firstnames":["Elena"],"suffixes":[]},{"propositions":[],"lastnames":["Street"],"firstnames":["Nathaniel","R."],"suffixes":[]},{"propositions":[],"lastnames":["Porth"],"firstnames":["Ilga"],"suffixes":[]},{"propositions":[],"lastnames":["El-Kassaby"],"firstnames":["Yousry","A."],"suffixes":[]},{"propositions":[],"lastnames":["Zhao"],"firstnames":["Wei"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Xiao-Ru"],"suffixes":[]},{"propositions":[],"lastnames":["Guan"],"firstnames":["Wenbin"],"suffixes":[]},{"propositions":[],"lastnames":["Mao"],"firstnames":["Jian-Feng"],"suffixes":[]}],"year":"2021","pages":"2546","bibtex":"@article{liu_centromere-specific_2021,\n\ttitle = {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}},\n\tvolume = {12},\n\tissn = {1664-462X},\n\turl = {https://www.frontiersin.org/article/10.3389/fpls.2021.766389},\n\tdoi = {10/gnsqvv},\n\tabstract = {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. 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