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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.

Show MeSH
KEGG classification of assembled unigenes.The unigenes were summarized into six main categories (a: metabolism, b: genetic information processing, c: environmental information processing, d: cellular processes, e: organismal systems, and f: human diseases). The x-axis represents the unigenes' respective categories, whereas the y-axis represents the percent of unigenes.
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f4: KEGG classification of assembled unigenes.The unigenes were summarized into six main categories (a: metabolism, b: genetic information processing, c: environmental information processing, d: cellular processes, e: organismal systems, and f: human diseases). The x-axis represents the unigenes' respective categories, whereas the y-axis represents the percent of unigenes.

Mentions: KEGG analysis21 demonstrated the biological pathways in which the unigenes are involved. Assembled unigenes were compared with the KEGG database using BLASTx, and the corresponding pathways were established. Among the 10,973 unigenes assigned to KEGG pathways, 3,914 were assigned to metabolism, 2,207 to human diseases, 1,858 to genetic information processing, 1,416 to organismal systems, 962 to cellular processes, and 616 to environmental information processing (Figure 4). Among the pathways that were assigned to the unigenes, carbohydrate metabolism (1,091 unigenes) was the largest group, followed by infectious diseases (976 unigenes), translation (746 unigenes), and energy metabolism (589 unigenes). Signaling molecules and interaction (1) represented the smallest group. These annotations provide a valuable resource for investigating specific processes, structures, functions, and pathways in celery research.


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)

KEGG classification of assembled unigenes.The unigenes were summarized into six main categories (a: metabolism, b: genetic information processing, c: environmental information processing, d: cellular processes, e: organismal systems, and f: human diseases). The x-axis represents the unigenes' respective categories, whereas the y-axis represents the percent of unigenes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: KEGG classification of assembled unigenes.The unigenes were summarized into six main categories (a: metabolism, b: genetic information processing, c: environmental information processing, d: cellular processes, e: organismal systems, and f: human diseases). The x-axis represents the unigenes' respective categories, whereas the y-axis represents the percent of unigenes.
Mentions: KEGG analysis21 demonstrated the biological pathways in which the unigenes are involved. Assembled unigenes were compared with the KEGG database using BLASTx, and the corresponding pathways were established. Among the 10,973 unigenes assigned to KEGG pathways, 3,914 were assigned to metabolism, 2,207 to human diseases, 1,858 to genetic information processing, 1,416 to organismal systems, 962 to cellular processes, and 616 to environmental information processing (Figure 4). Among the pathways that were assigned to the unigenes, carbohydrate metabolism (1,091 unigenes) was the largest group, followed by infectious diseases (976 unigenes), translation (746 unigenes), and energy metabolism (589 unigenes). Signaling molecules and interaction (1) represented the smallest group. These annotations provide a valuable resource for investigating specific processes, structures, functions, and pathways in celery research.

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