Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata. Wang, W., He, X., Yan, X., Ma, B., Lu, C., Wu, J., Zheng, Y., Wang, W., Xue, W., Tian, X., Guo, J., El-Kassaby, Y. A., Porth, I., Leng, P., Hu, Z., & Mao, J. New Phytologist, 238(5):2016–2032, 2023. _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18814![Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.
@article{wang_chromosome-scale_2023,
title = {Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, {Quercus} dentata},
volume = {238},
issn = {1469-8137},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18814},
doi = {10.1111/nph.18814},
abstract = {Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.},
language = {en},
number = {5},
urldate = {2023-05-05},
journal = {New Phytologist},
author = {Wang, Wen-Bo and He, Xiang-Feng and Yan, Xue-Mei and Ma, Bo and Lu, Cun-Fu and Wu, Jing and Zheng, Yi and Wang, Wen-He and Xue, Wen-Bo and Tian, Xue-Chan and Guo, Jing-Fang and El-Kassaby, Yousry A. and Porth, Ilga and Leng, Ping-Sheng and Hu, Zeng-Hui and Mao, Jian-Feng},
year = {2023},
note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18814},
keywords = {Quercus, co-expression network, flavonoids, gene regulation, leaf color transition},
pages = {2016--2032},
}
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A.","Porth, I.","Leng, P.","Hu, Z.","Mao, J."],"bibdata":{"bibtype":"article","type":"article","title":"Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata","volume":"238","issn":"1469-8137","url":"https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18814","doi":"10.1111/nph.18814","abstract":"Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.","language":"en","number":"5","urldate":"2023-05-05","journal":"New Phytologist","author":[{"propositions":[],"lastnames":["Wang"],"firstnames":["Wen-Bo"],"suffixes":[]},{"propositions":[],"lastnames":["He"],"firstnames":["Xiang-Feng"],"suffixes":[]},{"propositions":[],"lastnames":["Yan"],"firstnames":["Xue-Mei"],"suffixes":[]},{"propositions":[],"lastnames":["Ma"],"firstnames":["Bo"],"suffixes":[]},{"propositions":[],"lastnames":["Lu"],"firstnames":["Cun-Fu"],"suffixes":[]},{"propositions":[],"lastnames":["Wu"],"firstnames":["Jing"],"suffixes":[]},{"propositions":[],"lastnames":["Zheng"],"firstnames":["Yi"],"suffixes":[]},{"propositions":[],"lastnames":["Wang"],"firstnames":["Wen-He"],"suffixes":[]},{"propositions":[],"lastnames":["Xue"],"firstnames":["Wen-Bo"],"suffixes":[]},{"propositions":[],"lastnames":["Tian"],"firstnames":["Xue-Chan"],"suffixes":[]},{"propositions":[],"lastnames":["Guo"],"firstnames":["Jing-Fang"],"suffixes":[]},{"propositions":[],"lastnames":["El-Kassaby"],"firstnames":["Yousry","A."],"suffixes":[]},{"propositions":[],"lastnames":["Porth"],"firstnames":["Ilga"],"suffixes":[]},{"propositions":[],"lastnames":["Leng"],"firstnames":["Ping-Sheng"],"suffixes":[]},{"propositions":[],"lastnames":["Hu"],"firstnames":["Zeng-Hui"],"suffixes":[]},{"propositions":[],"lastnames":["Mao"],"firstnames":["Jian-Feng"],"suffixes":[]}],"year":"2023","note":"_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.18814","keywords":"Quercus, co-expression network, flavonoids, gene regulation, leaf color transition","pages":"2016–2032","bibtex":"@article{wang_chromosome-scale_2023,\n\ttitle = {Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, {Quercus} dentata},\n\tvolume = {238},\n\tissn = {1469-8137},\n\turl = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18814},\n\tdoi = {10.1111/nph.18814},\n\tabstract = {Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein–protein and DNA–protein interaction assays. 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