Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn.
Tropical evergreen perennials undergo recurrent flush growth, and their terminal buds alternate between growth and dormancy. In sharp contrast to intensive studies on bud development in temperate deciduous trees, there is little information about bud development regulation in tropical trees. In this...
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Frontiers Media S.A.
2016-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01517/full |
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| author | Huifeng Zhang Hua Li Biao Lai Haoqiang Xia Hui-Cong Wang Xuming Huang |
| author_facet | Huifeng Zhang Hua Li Biao Lai Haoqiang Xia Hui-Cong Wang Xuming Huang |
| author_sort | Huifeng Zhang |
| collection | DOAJ |
| description | Tropical evergreen perennials undergo recurrent flush growth, and their terminal buds alternate between growth and dormancy. In sharp contrast to intensive studies on bud development in temperate deciduous trees, there is little information about bud development regulation in tropical trees. In this study, litchi (Litchi chinensis Sonn.) was used as a model tropical perennial for morphological characterization and transcriptomic analysis of bud development. Litchi buds are naked with apical meristem embraced by rudimentary leaves, which are brown at dormant stage (Stage I). They swell and turn greenish as buds break (Stage II), and as growth accelerates, the rudimentary leaves elongate and open exposing the inner leaf primodia. With the outgrowth of the needle-like leaflets, bud growth reaches a maximum (Stage III). When leaflets expand, bud growth cease with the abortion of the rudimentary leaves at upper positions (Stage IV). Then buds turn brown and reenter dormant status. Budbreak occurs again when new leaves become hard green. Buds at four stages (Stage I to IV) were collected for respiration measurements and in-depth RNA sequencing. Respiration rate was lowest at Stage I and highest at Stage II, decreasing towards growth cessation. RNA sequencing obtained over 5 Gb data from each of the bud samples and de novo assembly generated a total of 59999 unigenes, 40119 of which were annotated. Pair-wise comparison of gene expression between stages, gene profiling across stages, GO/KEGG enrichment analysis, and the expression patterns of 17 major genes highlighted by principal component (PC) analysis displayed significant changes in stress resistance, hormone signal pathways, circadian rhythm, photosynthesis, cell division, carbohydrate metabolism, programmed cell death during bud development, which might be under epigenetic control involving chromatin methylation. The qPCR results of 8 selected unigenes with high PC scores agreed with the RPKM values obtained from RNA-seq. Three Short Vegetative Phase (SVP) genes, namely LcSVP1, LcSVP2 and LcSVP3 displayed different expression patterns, suggesting their differential roles in bud development regulation. The study brought an understanding about biological processes associated with the phase transitions, molecular regulation of bud development, as well as cyclic bud growth as a strategy to survive tropical conditions. |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T15:35:19Z |
| publishDate | 2016-10-01 |
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| spelling | doaj.art-340250b20af04a2e91c4c2ddfc5c97cb2022-12-22T00:59:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-10-01710.3389/fpls.2016.01517210364Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn.Huifeng Zhang0Hua Li1Biao Lai2Haoqiang Xia3Hui-Cong Wang4Xuming Huang5South China Agricultural UniversitySouth China Agricultural UniversitySouth China Agricultural UniversitySouth China Agricultural UniversitySouth China Agricultural UniversitySouth China Agricultural UniversityTropical evergreen perennials undergo recurrent flush growth, and their terminal buds alternate between growth and dormancy. In sharp contrast to intensive studies on bud development in temperate deciduous trees, there is little information about bud development regulation in tropical trees. In this study, litchi (Litchi chinensis Sonn.) was used as a model tropical perennial for morphological characterization and transcriptomic analysis of bud development. Litchi buds are naked with apical meristem embraced by rudimentary leaves, which are brown at dormant stage (Stage I). They swell and turn greenish as buds break (Stage II), and as growth accelerates, the rudimentary leaves elongate and open exposing the inner leaf primodia. With the outgrowth of the needle-like leaflets, bud growth reaches a maximum (Stage III). When leaflets expand, bud growth cease with the abortion of the rudimentary leaves at upper positions (Stage IV). Then buds turn brown and reenter dormant status. Budbreak occurs again when new leaves become hard green. Buds at four stages (Stage I to IV) were collected for respiration measurements and in-depth RNA sequencing. Respiration rate was lowest at Stage I and highest at Stage II, decreasing towards growth cessation. RNA sequencing obtained over 5 Gb data from each of the bud samples and de novo assembly generated a total of 59999 unigenes, 40119 of which were annotated. Pair-wise comparison of gene expression between stages, gene profiling across stages, GO/KEGG enrichment analysis, and the expression patterns of 17 major genes highlighted by principal component (PC) analysis displayed significant changes in stress resistance, hormone signal pathways, circadian rhythm, photosynthesis, cell division, carbohydrate metabolism, programmed cell death during bud development, which might be under epigenetic control involving chromatin methylation. The qPCR results of 8 selected unigenes with high PC scores agreed with the RPKM values obtained from RNA-seq. Three Short Vegetative Phase (SVP) genes, namely LcSVP1, LcSVP2 and LcSVP3 displayed different expression patterns, suggesting their differential roles in bud development regulation. The study brought an understanding about biological processes associated with the phase transitions, molecular regulation of bud development, as well as cyclic bud growth as a strategy to survive tropical conditions.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01517/fulldormancyRNA-SeqTranscriptomicsGene profilingBud developmentLitchi chinensis Sonn. |
| spellingShingle | Huifeng Zhang Hua Li Biao Lai Haoqiang Xia Hui-Cong Wang Xuming Huang Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn. Frontiers in Plant Science dormancy RNA-Seq Transcriptomics Gene profiling Bud development Litchi chinensis Sonn. |
| title | Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn. |
| title_full | Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn. |
| title_fullStr | Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn. |
| title_full_unstemmed | Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn. |
| title_short | Morphological characterization and gene expression profiling during bud development in a tropical perennial, Litchi chinensis Sonn. |
| title_sort | morphological characterization and gene expression profiling during bud development in a tropical perennial litchi chinensis sonn |
| topic | dormancy RNA-Seq Transcriptomics Gene profiling Bud development Litchi chinensis Sonn. |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.01517/full |
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