De novo transcriptome and small RNA analyses of two amorphophallus species.
Konjac is one of the most important glucomannan crops worldwide. The breeding and genomic researches are largely limited by the genetic basis of Amorphophallus. In this study, the transcriptomes of A. konjac and A. bulbifer were constructed using a high-throughput Illumina sequencing platform. All 1...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3997385?pdf=render |
| _version_ | 1818287407453175808 |
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| author | Ying Diao Chaozhu Yang Mi Yan Xingfei Zheng Surong Jin Youwei Wang Zhongli Hu |
| author_facet | Ying Diao Chaozhu Yang Mi Yan Xingfei Zheng Surong Jin Youwei Wang Zhongli Hu |
| author_sort | Ying Diao |
| collection | DOAJ |
| description | Konjac is one of the most important glucomannan crops worldwide. The breeding and genomic researches are largely limited by the genetic basis of Amorphophallus. In this study, the transcriptomes of A. konjac and A. bulbifer were constructed using a high-throughput Illumina sequencing platform. All 108,651 unigenes with average lengths of 430 nt in A. konjac and 119,678 unigenes with average lengths of 439 nt were generated from 54,986,020 reads and 52,334,098 reads after filtering and assembly, respectively. A total of 54,453 transcripts in A. konjac and 55,525 in A. bulbifier were annotated by comparison with Nr, Swiss-Prot, KEGG, and COG databases after removing exogenous contaminated sequences. A total of 80,332 transcripts differentially expressed between A. konjac and A. bulbifer. The majority of the genes that are associated with konjac glucomannan biosynthetic pathway were identified. Besides, the small RNAs in A. konjac leaves were also obtained by deep sequencing technology. All of 5,499,903 sequences of small RNAs were obtained with the length range between 18 and 30 nt. The potential targets for the miRNAs were also predicted according to the konjac transcripts. Our study provides a systematic overview of the konjac glucomannan biosynthesis genes that are involved in konjac leaves and should facilitate further understanding of the crucial roles of carbohydrate synthesis and other important metabolism pathways in Amorphophallus. |
| first_indexed | 2024-12-13T01:40:00Z |
| format | Article |
| id | doaj.art-738874cac6e0470e957febe6b1402367 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T01:40:00Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-738874cac6e0470e957febe6b14023672022-12-22T00:03:46ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0194e9542810.1371/journal.pone.0095428De novo transcriptome and small RNA analyses of two amorphophallus species.Ying DiaoChaozhu YangMi YanXingfei ZhengSurong JinYouwei WangZhongli HuKonjac is one of the most important glucomannan crops worldwide. The breeding and genomic researches are largely limited by the genetic basis of Amorphophallus. In this study, the transcriptomes of A. konjac and A. bulbifer were constructed using a high-throughput Illumina sequencing platform. All 108,651 unigenes with average lengths of 430 nt in A. konjac and 119,678 unigenes with average lengths of 439 nt were generated from 54,986,020 reads and 52,334,098 reads after filtering and assembly, respectively. A total of 54,453 transcripts in A. konjac and 55,525 in A. bulbifier were annotated by comparison with Nr, Swiss-Prot, KEGG, and COG databases after removing exogenous contaminated sequences. A total of 80,332 transcripts differentially expressed between A. konjac and A. bulbifer. The majority of the genes that are associated with konjac glucomannan biosynthetic pathway were identified. Besides, the small RNAs in A. konjac leaves were also obtained by deep sequencing technology. All of 5,499,903 sequences of small RNAs were obtained with the length range between 18 and 30 nt. The potential targets for the miRNAs were also predicted according to the konjac transcripts. Our study provides a systematic overview of the konjac glucomannan biosynthesis genes that are involved in konjac leaves and should facilitate further understanding of the crucial roles of carbohydrate synthesis and other important metabolism pathways in Amorphophallus.http://europepmc.org/articles/PMC3997385?pdf=render |
| spellingShingle | Ying Diao Chaozhu Yang Mi Yan Xingfei Zheng Surong Jin Youwei Wang Zhongli Hu De novo transcriptome and small RNA analyses of two amorphophallus species. PLoS ONE |
| title | De novo transcriptome and small RNA analyses of two amorphophallus species. |
| title_full | De novo transcriptome and small RNA analyses of two amorphophallus species. |
| title_fullStr | De novo transcriptome and small RNA analyses of two amorphophallus species. |
| title_full_unstemmed | De novo transcriptome and small RNA analyses of two amorphophallus species. |
| title_short | De novo transcriptome and small RNA analyses of two amorphophallus species. |
| title_sort | de novo transcriptome and small rna analyses of two amorphophallus species |
| url | http://europepmc.org/articles/PMC3997385?pdf=render |
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