Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated Pathway

<i>Lycoris</i> is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsi...

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Main Authors: Fengjiao Zhang, Guanghao Cheng, Xiaochun Shu, Ning Wang, Zhong Wang
Format: Article
Language:English
Published: MDPI AG 2022-06-01
Series:Biomolecules
Subjects:
Online Access:https://www.mdpi.com/2218-273X/12/7/899
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author Fengjiao Zhang
Guanghao Cheng
Xiaochun Shu
Ning Wang
Zhong Wang
author_facet Fengjiao Zhang
Guanghao Cheng
Xiaochun Shu
Ning Wang
Zhong Wang
author_sort Fengjiao Zhang
collection DOAJ
description <i>Lycoris</i> is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsible for floral transition in bulbous flowers is lacking, and only a few genes that regulate flowering have been identified with few reports on the floral transition in <i>Lycoris</i>. In this study, we identified many differentially expressed genes (DEGs) and transcription factors (TFs) by RNA-Seq in <i>L. chinensis</i> bulbs of different ages, including one- to four-year-old nonflowering bulbs and four-year-old flowering bulbs. Some DEGs were enriched in Gene Ontology (GO) terms between the three- and four-year-old bulbs, and there most genes were enriched in terms of metabolic process and catalytic activity. In the four-year old bulbs, most of the DEGs that may be involved in flowering were classified under the GO term biological process, which was a totally different result from the vegetative bulbs. Some DEGs between flowering and nonflowering bulbs were enriched in plant hormone signal transduction, including the hormones auxin, cytokinin, abscisic acid, and ethylene, but no DEGs were enriched in the gibberellin pathway. Auxin is the main endogenous phytohormone involved in bulb growth and development, but cytokinin, abscisic acid, and ethylene were shown to increase in flowering bulbs. In addition, energy-metabolism-related genes maintain a high expression level in large bulbs, and some positive regulators (SPL, COL, and AP1) and early flowering genes were also shown to be highly expressed in the meristems of flowering bulbs. It suggested that sugar molecules may be the energy source that regulates the signal transduction of flowering by connecting with phytohormone signaling in <i>Lycoris</i>. A total of 1911 TFs were identified and classified into 89 categories, where the top six families with the largest gene numbers were C2H2, NAC, AP2/ERF-ERF, C3H, MYB-related, and WRKY. Most DEGs were in the AP2/ERF-ERF family, and most of them were downregulated in 4-year-old flowering bulbs. A number of families were reported to be involved in plant flowering, including NAC, AP2/ERF, MYB, WRKY, bZIP, MADS, and NF-Y. These results can act as a genetic resource to aid in the explanation of the genetic mechanism responsible for the flowering of <i>Lycoris</i> and other bulbous flowers.
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spelling doaj.art-9e283ea7a5eb4d20a0d5bb838e0d98db2023-12-03T14:43:16ZengMDPI AGBiomolecules2218-273X2022-06-0112789910.3390/biom12070899Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated PathwayFengjiao Zhang0Guanghao Cheng1Xiaochun Shu2Ning Wang3Zhong Wang4Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, ChinaInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China<i>Lycoris</i> is a summer bulbous flower that commonly needs to go through a long period of vegetative growth for 3 to 5 years before flowering. Plant flowering is regulated by a complex genetic network. Compared with most perennial flowers, knowledge on the molecular mechanism responsible for floral transition in bulbous flowers is lacking, and only a few genes that regulate flowering have been identified with few reports on the floral transition in <i>Lycoris</i>. In this study, we identified many differentially expressed genes (DEGs) and transcription factors (TFs) by RNA-Seq in <i>L. chinensis</i> bulbs of different ages, including one- to four-year-old nonflowering bulbs and four-year-old flowering bulbs. Some DEGs were enriched in Gene Ontology (GO) terms between the three- and four-year-old bulbs, and there most genes were enriched in terms of metabolic process and catalytic activity. In the four-year old bulbs, most of the DEGs that may be involved in flowering were classified under the GO term biological process, which was a totally different result from the vegetative bulbs. Some DEGs between flowering and nonflowering bulbs were enriched in plant hormone signal transduction, including the hormones auxin, cytokinin, abscisic acid, and ethylene, but no DEGs were enriched in the gibberellin pathway. Auxin is the main endogenous phytohormone involved in bulb growth and development, but cytokinin, abscisic acid, and ethylene were shown to increase in flowering bulbs. In addition, energy-metabolism-related genes maintain a high expression level in large bulbs, and some positive regulators (SPL, COL, and AP1) and early flowering genes were also shown to be highly expressed in the meristems of flowering bulbs. It suggested that sugar molecules may be the energy source that regulates the signal transduction of flowering by connecting with phytohormone signaling in <i>Lycoris</i>. A total of 1911 TFs were identified and classified into 89 categories, where the top six families with the largest gene numbers were C2H2, NAC, AP2/ERF-ERF, C3H, MYB-related, and WRKY. Most DEGs were in the AP2/ERF-ERF family, and most of them were downregulated in 4-year-old flowering bulbs. A number of families were reported to be involved in plant flowering, including NAC, AP2/ERF, MYB, WRKY, bZIP, MADS, and NF-Y. These results can act as a genetic resource to aid in the explanation of the genetic mechanism responsible for the flowering of <i>Lycoris</i> and other bulbous flowers.https://www.mdpi.com/2218-273X/12/7/899<i>Lycoris chinensis</i>transcriptomefloweringbulb agehormone signaling
spellingShingle Fengjiao Zhang
Guanghao Cheng
Xiaochun Shu
Ning Wang
Zhong Wang
Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated Pathway
Biomolecules
<i>Lycoris chinensis</i>
transcriptome
flowering
bulb age
hormone signaling
title Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated Pathway
title_full Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated Pathway
title_fullStr Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated Pathway
title_full_unstemmed Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated Pathway
title_short Transcriptome Analysis of <i>Lycoris chinensis</i> Bulbs Reveals Flowering in the Age-Mediated Pathway
title_sort transcriptome analysis of i lycoris chinensis i bulbs reveals flowering in the age mediated pathway
topic <i>Lycoris chinensis</i>
transcriptome
flowering
bulb age
hormone signaling
url https://www.mdpi.com/2218-273X/12/7/899
work_keys_str_mv AT fengjiaozhang transcriptomeanalysisofilycorischinensisibulbsrevealsfloweringintheagemediatedpathway
AT guanghaocheng transcriptomeanalysisofilycorischinensisibulbsrevealsfloweringintheagemediatedpathway
AT xiaochunshu transcriptomeanalysisofilycorischinensisibulbsrevealsfloweringintheagemediatedpathway
AT ningwang transcriptomeanalysisofilycorischinensisibulbsrevealsfloweringintheagemediatedpathway
AT zhongwang transcriptomeanalysisofilycorischinensisibulbsrevealsfloweringintheagemediatedpathway