Deep Sequencing and Analysis of Transcriptomes of Pinus koraiensis Sieb. &amp; Zucc.

Shi, Shaolin; Yan, Siyu; Zhao, Chao; Zhang, Peng; Yang, Ling; Wang, Chao; Shen, Hailong

doi:10.3390/f11030350

Cited by 6 publications

(5 citation statements)

References 51 publications

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“…PkDAL1 showed an increased expression pattern during Korean pine aging (Figure 4). In a previous work, a transcript (c77350.graph_c2) annotated as Picea abies DAL1 was identified as being differentially expressed between 2-and 5-, 10-, 15-, or 30-year-old Korean pine trees [31]. The age-dependent expression patterns of DAL1 homologs have also been characterized in P. abies [32], P. tabuliformis [33], and Larix kaempferi [34][35][36].…”

Section: Shading Affects the Expression Of Physiological Response-rel...mentioning

confidence: 97%

Transcriptome Analysis Provides Insights into Korean Pine Tree Aging and Response to Shading

Ye,

Liu,

Feng

et al. 2024

Forests

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Age controls a tree’s responses to environmental cues and shading influences tree growth and physiology. These are basic principles of “Afforestation under canopy”, an approach that is widely used in the regeneration of Korean pine forests. Studying the underlying mechanism helps us to understand tree adaptation and utilize it in forest management. In this study, we investigated the transcriptomic changes in the uppermost main stems of the Korean pine tree (Pinus koraiensis, Sieb. et Zucc.) at different ages (5, 7, 10, 14, and 17 years) and in different growth conditions (open-grown and shade-grown trees) using RNA-Seq. In total, 434,005,837 reads were produced and assembled into 111,786 unigenes. After pairwise comparisons, 568 differentially expressed unigenes (DEUs) were identified. The greatest number of DEUs was identified in the comparison between 5-year-old open-grown trees and 17-year-old shade-grown trees, while no DEUs were identified in 15 pairwise comparisons. Among these 568 DEUs, 45 were assigned to gene ontology (GO) terms associated with response to environmental changes, including “response to stress” (26) and “response to light and temperature” (19); 12 were assigned to GO terms associated with sexual reproduction, such as “sexual reproduction”, “specification of floral organ identity”, “pollen tube guidance”, and “fruit ripening”; 15 were heat shock protein genes and showed decreased expression patterns with age; and one, annotated as Pinus tabuliformis DEFICIENS-AGAMOUS-LIKE 1, showed an increased expression pattern with age, independent of the reproductive state or growth conditions of Korean pine trees. Altogether, these findings not only demonstrate the molecular aspects of the developmental and physiological effects of age and shading on Korean pine trees, but also improve our understanding of the basic principles of “Afforestation under canopy”.

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Section: Shading Affects the Expression Of Physiological Response-rel...mentioning

confidence: 97%

Transcriptome Analysis Provides Insights into Korean Pine Tree Aging and Response to Shading

Ye,

Liu,

Feng

et al. 2024

Forests

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“…AGL6, is controlled by age [3,4], because its transcript level is low before 5 years and then maintained at a high level after 5 years of age. This age-dependent pattern is conserved in P. abies [5], P. koraiensis [2] and P. tabuliformis [1], indicating that at ~5 years, some conserved and unknown life-cycle events occur in these trees [3]. Furthermore, over-expression of P. abies (L.) H.Karst.…”

Section: Introductionmentioning

confidence: 95%

“…& Zucc. to reveal the molecular basis of the conifer reproductive phase change [1][2][3]. Differentially expressed genes have been identified, and a regulatory network model has been proposed for L. kaempferi based on these genes [3].…”

Section: Introductionmentioning

confidence: 99%

Over-Expression of Larch DAL1 Accelerates Life-Cycle Progression in Arabidopsis

Zang

Cheng

et al. 2022

Forests

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Homologs of Larix kaempferiDEFICIENS-AGAMOUS-LIKE 1 (LaDAL1) promote flowering in Arabidopsis. However, their functional role in the whole life-cycle is limited. Here, we analyzed the phenotypes and transcriptomes of Arabidopsis plants over-expressing LaDAL1. With respect to the defined life-cycle stage of Arabidopsis based on the meristem state, the results showed that LaDAL1 promoted seed germination, bolting, flower initiation, and global proliferative arrest, indicating that LaDAL1 accelerates the meristem reactivation, the transitions of vegetative meristem to inflorescence and flower meristem, and meristem arrest. As a marker gene of meristem, TERMINAL FLOWER 1 was down-regulated after LaDAL1 over-expression. These results reveal that LaDAL1 accelerates the life-cycle progression in Arabidopsis by promoting the transition of meristem fate, providing more and novel functional information about the conifer age-related gene DAL1.

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“…Ecological and economic value may be found in the monoecious plant Pinus koraiensis , an evergreen conifer of Pinaceae with a tree height of 40 m and a breast height diameter of 1 m ( Li et al., 2022 ; Park et al., 2016 ; Ren et al., 2022 ). P. koraiensis is mostly distributed in China’s Changbai Mountains, Laoyeling Mountains, Zhangguangcailing Mountains, Xiaoxinganling Mountains and Wanda Mountains, as well as in Japan, the Far East region of Russia and the Korean Peninsula ( Aizawa et al., 2012 ; Shi et al., 2020 ; Wei et al, 2022 ; Zhang et al., 2022 ). It has state approval to be designated as a secondary wild plant for national protection ( Li et al., 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Phytohormone biosynthesis and transcriptional analyses provide insight into the main growth stage of male and female cones Pinus koraiensis

Li,

Zhao,

Cai

et al. 2023

Front. Plant Sci.

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The cone is a crucial component of the whole life cycle of gymnosperm and an organ for sexual reproduction of gymnosperms. In Pinus koraiensis, the quantity and development process of male and female cones directly influence seed production, which in turn influences the tree’s economic value. There are, however, due to the lack of genetic information and genomic data, the morphological development and molecular mechanism of female and male cones of P. koraiensis have not been analyzed. Long-term phenological observations were used in this study to document the main process of the growth of both male and female cones. Transcriptome sequencing and endogenous hormone levels at three critical developmental stages were then analyzed to identify the regulatory networks that control these stages of cones development. The most significant plant hormones influencing male and female cones growth were discovered to be gibberellin and brassinosteroids, according to measurements of endogenous hormone content. Additionally, transcriptome sequencing allowed the identification of 71,097 and 31,195 DEGs in male and female cones. The synthesis and control of plant hormones during cones growth were discovered via enrichment analysis of key enrichment pathways. FT and other flowering-related genes were discovered in the coexpression network of flower growth development, which contributed to the growth development of male and female cones of P. koraiensis. The findings of this work offer a cutting-edge foundation for understanding reproductive biology and the molecular mechanisms that control the growth development of male and female cones in P. koraiensis.

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Deep Sequencing and Analysis of Transcriptomes of Pinus koraiensis Sieb. & Zucc.

Cited by 6 publications

References 51 publications

Transcriptome Analysis Provides Insights into Korean Pine Tree Aging and Response to Shading

Transcriptome Analysis Provides Insights into Korean Pine Tree Aging and Response to Shading

Over-Expression of Larch DAL1 Accelerates Life-Cycle Progression in Arabidopsis

Phytohormone biosynthesis and transcriptional analyses provide insight into the main growth stage of male and female cones Pinus koraiensis

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