ChengJiaLiuEtAl2021

Reference

Cheng, S.-P., Jia, K.-H., Liu, H., Zhang, R.-G., Li, Z.-C., Zhou, S.-S., Shi, T.-L., Ma, A.-C., Yu, C.-W., Gao, C., Cao, G.-L., Zhao, W., Nie, S., Guo, J.-F., Jiao, S.-Q., Tian, X.-C., Yan, X.-M., Bao, Y.-T., Yun, Q.-Z., Wang, X.-Z., Porth, I., El-Kassaby, Y.A., Wang, X.-R., Li, Z., Van de Peer, Y., Mao, J.-F. (2021) Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger. Horticulture Research, 8(1). (Scopus )

Abstract

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger. © 2021, The Author(s).

EndNote Format

You can import this reference in EndNote.

BibTeX-CSV Format

You can import this reference in BibTeX-CSV format.

BibTeX Format

You can copy the BibTeX entry of this reference below, orimport it directly in a software like JabRef .

@ARTICLE { ChengJiaLiuEtAl2021,
    AUTHOR = { Cheng, S.-P. and Jia, K.-H. and Liu, H. and Zhang, R.-G. and Li, Z.-C. and Zhou, S.-S. and Shi, T.-L. and Ma, A.-C. and Yu, C.-W. and Gao, C. and Cao, G.-L. and Zhao, W. and Nie, S. and Guo, J.-F. and Jiao, S.-Q. and Tian, X.-C. and Yan, X.-M. and Bao, Y.-T. and Yun, Q.-Z. and Wang, X.-Z. and Porth, I. and El-Kassaby, Y.A. and Wang, X.-R. and Li, Z. and Van de Peer, Y. and Mao, J.-F. },
    JOURNAL = { Horticulture Research },
    TITLE = { Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger },
    YEAR = { 2021 },
    NOTE = { cited By 0 },
    NUMBER = { 1 },
    VOLUME = { 8 },
    ABSTRACT = { Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger. © 2021, The Author(s). },
    AFFILIATION = { Pingdingshan University, Henan Province Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan, Henan 467000, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China; Ori (Shandong) Gene Science and Technology Co., Ltd, Weifang, Shandong 261000, China; Pingdingshan Academy of Agricultural Sciences, Pingdingshan, Henan 467000, China; Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden; Département des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, Québec, QC G1V 0A6, Canada; Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, 9052, Belgium; Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology Genetics, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa; College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China },
    ART_NUMBER = { 188 },
    DOCUMENT_TYPE = { Article },
    DOI = { 10.1038/s41438-021-00599-8 },
    SOURCE = { Scopus },
    URL = { https://www.scopus.com/inward/record.uri?eid=2-s2.0-85111982657&doi=10.1038%2fs41438-021-00599-8&partnerID=40&md5=83be0425683369c7e915d2603a7635d8 },
}

********************************************************** *************************** FRQNT ************************ **********************************************************

Le CEF est un
regroupement stratégique du

********************************************************** *********************** Infolettre *********************** **********************************************************

Abonnez-vous à
l'Infolettre du CEF!

********************************************************** *********************** Colloque Chaire AFD ************** **********************************************************

**********************************************************

***************** Pub - Symphonies_Boreales ****************** **********************************************************

********************************************************** ***************** Boîte à trucs *************** **********************************************************

CEF-Référence
La référence vedette !

  • Voici une liste (clairement incomplète) des packages R axés sur l'écologie! N'hésitez pas à ajouter à la liste

Voir les autres...