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De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development.

Jia XL, Wang GL, Xiong F, Yu XR, Xu ZS, Wang F, Xiong AS - Sci Rep (2015)

Bottom Line: Regulating lignin synthesis in celery growth development has a significant economic value.Lignin accumulation in different tissues and at different stages of celery development coincides with the anatomic characteristics and transcript levels of genes involved in lignin biosynthesis.Identifying the genes that encode lignin biosynthesis-related enzymes accompanied by lignin distribution may help elucidate the regulatory mechanisms of lignin biosynthesis in celery.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.

ABSTRACT
Celery of the family Apiaceae is a biennial herb that is cultivated and consumed worldwide. Lignin is essential for cell wall structural integrity, stem strength, water transport, mechanical support, and plant pathogen defense. This study discussed the mechanism of lignin formation at different stages of celery development. The transcriptome profile, lignin distribution, anatomical characteristics, and expression profile of leaves at three stages were analyzed. Regulating lignin synthesis in celery growth development has a significant economic value. Celery leaves at three stages were collected, and Illumina paired-end sequencing technology was used to analyze large-scale transcriptome sequences. From Stage 1 to 3, the collenchyma and vascular bundles in the petioles and leaf blades thickened and expanded, whereas the phloem and the xylem extensively developed. Spongy and palisade mesophyll tissues further developed and were tightly arranged. Lignin accumulation increased in the petioles and the mesophyll (palisade and spongy), and the xylem showed strong lignification. Lignin accumulation in different tissues and at different stages of celery development coincides with the anatomic characteristics and transcript levels of genes involved in lignin biosynthesis. Identifying the genes that encode lignin biosynthesis-related enzymes accompanied by lignin distribution may help elucidate the regulatory mechanisms of lignin biosynthesis in celery.

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Related in: MedlinePlus

Gene ontology classification of assembled unigenes.Unigenes were summarized into three main categories (biological processes, cellular components, and molecular function) and 50 subcategories. The x-axis represents the unigenes' respective categories, whereas the y-axis denotes the percentage of unigenes.
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f3: Gene ontology classification of assembled unigenes.Unigenes were summarized into three main categories (biological processes, cellular components, and molecular function) and 50 subcategories. The x-axis represents the unigenes' respective categories, whereas the y-axis denotes the percentage of unigenes.

Mentions: GO terms were assigned to assemble unigenes and provided defined ontologies to express gene product properties. GO terms are a dynamically structured control vocabulary that is applied to describe gene product in terms of their associated biological processes, cellular components, and molecular functions20. In the present study, 132,740 unigenes with known functions were assigned to one or more ontologies, and each unigene was assigned to a set of GO Slims. The GO enrichment analysis of unigenes is summarized in Figure 3. GO analysis assigned 63,809 unigenes to biological process, 50,684 to cellular component, and 18,247 to molecular function. Metabolic process (18,380 unigenes, 13.85%) and cellular process (16,165 unigenes, 12.18%) were the most highly represented groups under the biological process category. We also identified genes involved in other important biological processes, such as cellular component organization, multicellular organismal development, post-embryonic development, reproduction, response to abiotic stimulus, response to stress, and transport. For the cellular component category, cell and intracellular were the most highly represented groups, followed by cytoplasm and membrane. Regarding molecular function, binding was the most highly represented group, with numerous ligases, hydrolases, oxidoreductases, and transferases annotated. However, a few genes were assigned to the clusters of “abscission”, “fruit ripening”, “extracellular space” and “nuclear envelope” and no genes were found in the clusters of “behavior”, “translation regulator activity”, “proteinaceous extracellular matrix” or “transcription regulator activity” (Figure 3). These GO annotations demonstrate that ‘Ventura' expresses genes that encode diverse structural, regulatory, and stress proteins.


De novo assembly, transcriptome characterization, lignin accumulation, and anatomic characteristics: novel insights into lignin biosynthesis during celery leaf development.

Jia XL, Wang GL, Xiong F, Yu XR, Xu ZS, Wang F, Xiong AS - Sci Rep (2015)

Gene ontology classification of assembled unigenes.Unigenes were summarized into three main categories (biological processes, cellular components, and molecular function) and 50 subcategories. The x-axis represents the unigenes' respective categories, whereas the y-axis denotes the percentage of unigenes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4317703&req=5

f3: Gene ontology classification of assembled unigenes.Unigenes were summarized into three main categories (biological processes, cellular components, and molecular function) and 50 subcategories. The x-axis represents the unigenes' respective categories, whereas the y-axis denotes the percentage of unigenes.
Mentions: GO terms were assigned to assemble unigenes and provided defined ontologies to express gene product properties. GO terms are a dynamically structured control vocabulary that is applied to describe gene product in terms of their associated biological processes, cellular components, and molecular functions20. In the present study, 132,740 unigenes with known functions were assigned to one or more ontologies, and each unigene was assigned to a set of GO Slims. The GO enrichment analysis of unigenes is summarized in Figure 3. GO analysis assigned 63,809 unigenes to biological process, 50,684 to cellular component, and 18,247 to molecular function. Metabolic process (18,380 unigenes, 13.85%) and cellular process (16,165 unigenes, 12.18%) were the most highly represented groups under the biological process category. We also identified genes involved in other important biological processes, such as cellular component organization, multicellular organismal development, post-embryonic development, reproduction, response to abiotic stimulus, response to stress, and transport. For the cellular component category, cell and intracellular were the most highly represented groups, followed by cytoplasm and membrane. Regarding molecular function, binding was the most highly represented group, with numerous ligases, hydrolases, oxidoreductases, and transferases annotated. However, a few genes were assigned to the clusters of “abscission”, “fruit ripening”, “extracellular space” and “nuclear envelope” and no genes were found in the clusters of “behavior”, “translation regulator activity”, “proteinaceous extracellular matrix” or “transcription regulator activity” (Figure 3). These GO annotations demonstrate that ‘Ventura' expresses genes that encode diverse structural, regulatory, and stress proteins.

Bottom Line: Regulating lignin synthesis in celery growth development has a significant economic value.Lignin accumulation in different tissues and at different stages of celery development coincides with the anatomic characteristics and transcript levels of genes involved in lignin biosynthesis.Identifying the genes that encode lignin biosynthesis-related enzymes accompanied by lignin distribution may help elucidate the regulatory mechanisms of lignin biosynthesis in celery.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.

ABSTRACT
Celery of the family Apiaceae is a biennial herb that is cultivated and consumed worldwide. Lignin is essential for cell wall structural integrity, stem strength, water transport, mechanical support, and plant pathogen defense. This study discussed the mechanism of lignin formation at different stages of celery development. The transcriptome profile, lignin distribution, anatomical characteristics, and expression profile of leaves at three stages were analyzed. Regulating lignin synthesis in celery growth development has a significant economic value. Celery leaves at three stages were collected, and Illumina paired-end sequencing technology was used to analyze large-scale transcriptome sequences. From Stage 1 to 3, the collenchyma and vascular bundles in the petioles and leaf blades thickened and expanded, whereas the phloem and the xylem extensively developed. Spongy and palisade mesophyll tissues further developed and were tightly arranged. Lignin accumulation increased in the petioles and the mesophyll (palisade and spongy), and the xylem showed strong lignification. Lignin accumulation in different tissues and at different stages of celery development coincides with the anatomic characteristics and transcript levels of genes involved in lignin biosynthesis. Identifying the genes that encode lignin biosynthesis-related enzymes accompanied by lignin distribution may help elucidate the regulatory mechanisms of lignin biosynthesis in celery.

Show MeSH
Related in: MedlinePlus