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Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)

Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate th...

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Autores principales: Cui, Kai, Wang, Haiying, Liao, Shengxi, Tang, Qi, Li, Li, Cui, Yongzhong, He, Yuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909198/
https://www.ncbi.nlm.nih.gov/pubmed/27304219
http://dx.doi.org/10.1371/journal.pone.0157362
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author Cui, Kai
Wang, Haiying
Liao, Shengxi
Tang, Qi
Li, Li
Cui, Yongzhong
He, Yuan
author_facet Cui, Kai
Wang, Haiying
Liao, Shengxi
Tang, Qi
Li, Li
Cui, Yongzhong
He, Yuan
author_sort Cui, Kai
collection PubMed
description Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate the molecular processes involved in its culm elongation, Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were annotated in the NCBI non-redundant protein database and 35,262 were annotated in the Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 33,920 unigenes were assigned to 128 KEGG pathways. Meanwhile, 8,553 simple sequence repeats (SSRs) and 81,534 single-nucleotide polymorphism (SNPs) were identified, respectively. Additionally, 388 transcripts encoding lignin biosynthesis were detected, among which, 27 transcripts encoding Shikimate O-hydroxycinnamoyltransferase (HCT) specifically expressed in D. sinicus when compared to other bamboo species and rice. The phylogenetic relationship between D. sinicus and other plants was analyzed, suggesting functional diversity of HCT unigenes in D. sinicus. We conjectured that HCT might lead to the high lignin content and giant culm. Given that the leaves are not yet formed and culm is covered with sheaths during culm elongation, the existence of photosynthesis of bamboo culm is usually neglected. Surprisedly, 109 transcripts encoding photosynthesis were identified, including photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase, and 24 transcripts were characterized as antenna proteins that regarded as the main tool for capturing light of plants, implying stem photosynthesis plays a key role during culm elongation due to the unavailability of its leaf. By real-time quantitative PCR, the expression level of 6 unigenes was detected. The results showed the expression level of all genes accorded with the transcriptome data, which confirm the reliability of the transcriptome data. As we know, this is the first study underline the D. sinicus transcriptome, which will deepen the understanding of the molecular mechanisms of culm development. The results may help variety improvement and resource utilization of bamboos.
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spelling pubmed-49091982016-07-06 Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus) Cui, Kai Wang, Haiying Liao, Shengxi Tang, Qi Li, Li Cui, Yongzhong He, Yuan PLoS One Research Article Dendrocalamus sinicus is the world’s largest bamboo species with strong woody culms, and known for its fast-growing culms. As an economic bamboo species, it was popularized for multi-functional applications including furniture, construction, and industrial paper pulp. To comprehensively elucidate the molecular processes involved in its culm elongation, Illumina paired-end sequencing was conducted. About 65.08 million high-quality reads were produced, and assembled into 81,744 unigenes with an average length of 723 bp. A total of 64,338 (79%) unigenes were annotated for their functions, of which, 56,587 were annotated in the NCBI non-redundant protein database and 35,262 were annotated in the Swiss-Prot database. Also, 42,508 and 21,009 annotated unigenes were allocated to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 33,920 unigenes were assigned to 128 KEGG pathways. Meanwhile, 8,553 simple sequence repeats (SSRs) and 81,534 single-nucleotide polymorphism (SNPs) were identified, respectively. Additionally, 388 transcripts encoding lignin biosynthesis were detected, among which, 27 transcripts encoding Shikimate O-hydroxycinnamoyltransferase (HCT) specifically expressed in D. sinicus when compared to other bamboo species and rice. The phylogenetic relationship between D. sinicus and other plants was analyzed, suggesting functional diversity of HCT unigenes in D. sinicus. We conjectured that HCT might lead to the high lignin content and giant culm. Given that the leaves are not yet formed and culm is covered with sheaths during culm elongation, the existence of photosynthesis of bamboo culm is usually neglected. Surprisedly, 109 transcripts encoding photosynthesis were identified, including photosystem I and II, cytochrome b6/f complex, photosynthetic electron transport and F-type ATPase, and 24 transcripts were characterized as antenna proteins that regarded as the main tool for capturing light of plants, implying stem photosynthesis plays a key role during culm elongation due to the unavailability of its leaf. By real-time quantitative PCR, the expression level of 6 unigenes was detected. The results showed the expression level of all genes accorded with the transcriptome data, which confirm the reliability of the transcriptome data. As we know, this is the first study underline the D. sinicus transcriptome, which will deepen the understanding of the molecular mechanisms of culm development. The results may help variety improvement and resource utilization of bamboos. Public Library of Science 2016-06-15 /pmc/articles/PMC4909198/ /pubmed/27304219 http://dx.doi.org/10.1371/journal.pone.0157362 Text en © 2016 Cui et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Cui, Kai
Wang, Haiying
Liao, Shengxi
Tang, Qi
Li, Li
Cui, Yongzhong
He, Yuan
Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)
title Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)
title_full Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)
title_fullStr Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)
title_full_unstemmed Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)
title_short Transcriptome Sequencing and Analysis for Culm Elongation of the World’s Largest Bamboo (Dendrocalamus sinicus)
title_sort transcriptome sequencing and analysis for culm elongation of the world’s largest bamboo (dendrocalamus sinicus)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4909198/
https://www.ncbi.nlm.nih.gov/pubmed/27304219
http://dx.doi.org/10.1371/journal.pone.0157362
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