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Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)

BACKGROUND: Although the genome of Chinese white pear (‘Dangshansuli’) has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date. RESULTS: In this study, we identified a total of 183 NAC transcription factors (TFs) in...

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Autores principales: Gong, Xin, Zhao, Liangyi, Song, Xiaofei, Lin, Zekun, Gu, Bingjie, Yan, Jinxuan, Zhang, Shaoling, Tao, Shutian, Huang, Xiaosan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485137/
https://www.ncbi.nlm.nih.gov/pubmed/31023218
http://dx.doi.org/10.1186/s12870-019-1760-8
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author Gong, Xin
Zhao, Liangyi
Song, Xiaofei
Lin, Zekun
Gu, Bingjie
Yan, Jinxuan
Zhang, Shaoling
Tao, Shutian
Huang, Xiaosan
author_facet Gong, Xin
Zhao, Liangyi
Song, Xiaofei
Lin, Zekun
Gu, Bingjie
Yan, Jinxuan
Zhang, Shaoling
Tao, Shutian
Huang, Xiaosan
author_sort Gong, Xin
collection PubMed
description BACKGROUND: Although the genome of Chinese white pear (‘Dangshansuli’) has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date. RESULTS: In this study, we identified a total of 183 NAC transcription factors (TFs) in the pear genome, among which 146 pear NAC (PbNAC) members were mapped onto 16 chromosomes, and 37 PbNAC genes were located on scaffold contigs. No PbNAC genes were mapped to chromosome 2. Based on gene structure, protein motif analysis, and topology of the phylogenetic tree, the pear PbNAC family was classified into 33 groups. By comparing and analyzing the unique NAC subgroups in Rosaceae, we identified 19 NAC subgroups specific to pear. We also found that whole-genome duplication (WGD)/segmental duplication played critical roles in the expansion of the NAC family in pear, such as the 83 PbNAC duplicated gene pairs dated back to the two WGD events. Further, we found that purifying selection was the primary force driving the evolution of PbNAC family genes. Next, we used transcriptomic data to study responses to drought and cold stresses in pear, and we found that genes in groups C2f, C72b, and C100a were related to drought and cold stress response. CONCLUSIONS: Through the phylogenetic, evolutionary, and expression analyses of the NAC gene family in Chinese white pear, we indentified 11 PbNAC TFs associated with abiotic stress in pear. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1760-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-64851372019-05-03 Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri) Gong, Xin Zhao, Liangyi Song, Xiaofei Lin, Zekun Gu, Bingjie Yan, Jinxuan Zhang, Shaoling Tao, Shutian Huang, Xiaosan BMC Plant Biol Research Article BACKGROUND: Although the genome of Chinese white pear (‘Dangshansuli’) has been released, little is known about the functions, evolutionary history and expression patterns of NAC families in this species to date. RESULTS: In this study, we identified a total of 183 NAC transcription factors (TFs) in the pear genome, among which 146 pear NAC (PbNAC) members were mapped onto 16 chromosomes, and 37 PbNAC genes were located on scaffold contigs. No PbNAC genes were mapped to chromosome 2. Based on gene structure, protein motif analysis, and topology of the phylogenetic tree, the pear PbNAC family was classified into 33 groups. By comparing and analyzing the unique NAC subgroups in Rosaceae, we identified 19 NAC subgroups specific to pear. We also found that whole-genome duplication (WGD)/segmental duplication played critical roles in the expansion of the NAC family in pear, such as the 83 PbNAC duplicated gene pairs dated back to the two WGD events. Further, we found that purifying selection was the primary force driving the evolution of PbNAC family genes. Next, we used transcriptomic data to study responses to drought and cold stresses in pear, and we found that genes in groups C2f, C72b, and C100a were related to drought and cold stress response. CONCLUSIONS: Through the phylogenetic, evolutionary, and expression analyses of the NAC gene family in Chinese white pear, we indentified 11 PbNAC TFs associated with abiotic stress in pear. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1760-8) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-25 /pmc/articles/PMC6485137/ /pubmed/31023218 http://dx.doi.org/10.1186/s12870-019-1760-8 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Gong, Xin
Zhao, Liangyi
Song, Xiaofei
Lin, Zekun
Gu, Bingjie
Yan, Jinxuan
Zhang, Shaoling
Tao, Shutian
Huang, Xiaosan
Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)
title Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)
title_full Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)
title_fullStr Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)
title_full_unstemmed Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)
title_short Genome-wide analyses and expression patterns under abiotic stress of NAC transcription factors in white pear (Pyrus bretschneideri)
title_sort genome-wide analyses and expression patterns under abiotic stress of nac transcription factors in white pear (pyrus bretschneideri)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485137/
https://www.ncbi.nlm.nih.gov/pubmed/31023218
http://dx.doi.org/10.1186/s12870-019-1760-8
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