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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

EggNOG classification assigned to unigenes.
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f2: EggNOG classification assigned to unigenes.

Mentions: The eggNOG database consists of protein sequences and is encoded in 21 complete genomes, including proteins of bacteria, algae, and eukaryotes. This database was built on classifications according to their evolutionary relationships19. To further evaluate the completeness of the transcriptome library and the effectiveness of the annotation process, all annotated unigene sequences were searched against the eggNOG database for functional prediction and classification. A total of 26,804 sequences were assigned to eggNOG classifications (Figure 2). Among the 26 eggNOG categories that were assigned to unigenes, the cluster for function unknown (6,606, 24.65%) was the largest group, followed by general function prediction only (5,123, 19.11%), i.e., basic physiological and metabolic functions; signal transduction mechanisms (2,226, 8.30%); and post-translational modification, protein turnover, and chaperones (1,754, 6.54%). Undetermined (1, 0.01%) represented the smallest group. The unigenes for secondary metabolite biosynthesis, transport, and catabolism accounted for 3.67% (983) of the total functional genes, which are essential for secondary metabolites that contribute to the quality and taste of celery.


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)

EggNOG classification assigned to unigenes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: EggNOG classification assigned to unigenes.
Mentions: The eggNOG database consists of protein sequences and is encoded in 21 complete genomes, including proteins of bacteria, algae, and eukaryotes. This database was built on classifications according to their evolutionary relationships19. To further evaluate the completeness of the transcriptome library and the effectiveness of the annotation process, all annotated unigene sequences were searched against the eggNOG database for functional prediction and classification. A total of 26,804 sequences were assigned to eggNOG classifications (Figure 2). Among the 26 eggNOG categories that were assigned to unigenes, the cluster for function unknown (6,606, 24.65%) was the largest group, followed by general function prediction only (5,123, 19.11%), i.e., basic physiological and metabolic functions; signal transduction mechanisms (2,226, 8.30%); and post-translational modification, protein turnover, and chaperones (1,754, 6.54%). Undetermined (1, 0.01%) represented the smallest group. The unigenes for secondary metabolite biosynthesis, transport, and catabolism accounted for 3.67% (983) of the total functional genes, which are essential for secondary metabolites that contribute to the quality and taste of celery.

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