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Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826)
Earthworms are useful indicator organisms of soil health and Eisenia fetida have been extensively used as test organisms in ecotoxicological studies. In order to gain insight into the gene expression profiles associated with physiological functions of earthworms, a full-length enriched cDNA library...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
D.A. Spandidos
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423580/ https://www.ncbi.nlm.nih.gov/pubmed/30720084 http://dx.doi.org/10.3892/mmr.2019.9938 |
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author | Liu, Chang Wang, Xuan Tian, Jiu-Bo Ma, Pei-Yuan Meng, Fan-Xiu Zhang, Qi Yu, Bao-Feng Guo, Rui Liu, Zhi-Zhen Wang, Hai-Long Xie, Jun Cheng, Niu-Liang Wang, Jian-Hua Niu, Bo Sun, Gong-Qin |
author_facet | Liu, Chang Wang, Xuan Tian, Jiu-Bo Ma, Pei-Yuan Meng, Fan-Xiu Zhang, Qi Yu, Bao-Feng Guo, Rui Liu, Zhi-Zhen Wang, Hai-Long Xie, Jun Cheng, Niu-Liang Wang, Jian-Hua Niu, Bo Sun, Gong-Qin |
author_sort | Liu, Chang |
collection | PubMed |
description | Earthworms are useful indicator organisms of soil health and Eisenia fetida have been extensively used as test organisms in ecotoxicological studies. In order to gain insight into the gene expression profiles associated with physiological functions of earthworms, a full-length enriched cDNA library of the Eisenia fetida genome was successfully constructed using Switching Mechanism at 5′End of RNA Template technology. Construction of a cDNA library and analysis of Expressed Sequence Tags (ESTs) are efficient approaches for collecting genomic information and identifying genes important for a given biological process. Furthermore, analysis of the expression abundance of ESTs was performed with the aim of providing genetic and transcriptomic information on the development and regenerative process of earthworms. Phrep and Crossmatch were used to process EST data and a total of 1,140 high-quality EST sequences were determined by sequencing random cDNA clones from the library. Clustering analysis of sequences revealed a total of 593 unique sequences including 225 contiguous and 368 singleton sequences. Basic Local Alignment Search Tool analysis against the Kyoto Encyclopedia of Genes and Genomes database resulted in 593 significant hits (P-value <1×10(−8)), of which 168 were annotated through Gene Ontology analysis. The STRING database was used to determine relationships among the 168 ESTs, identifying associated genes involved in protein-protein interactions and gene expression regulation. Based on nucleic acid and protein sequence homology, the mutual relationships between 287 genes could be obtained, which identified a portion of the ESTs as known genes. The present study reports on the construction of a high-quality cDNA library representative of adult earthworms, on a preliminary analysis of ESTs and on a putative functional analysis of ESTs. The present study is expected to enhance our understanding of the molecular basis underlying the biological development of earthworms. |
format | Online Article Text |
id | pubmed-6423580 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | D.A. Spandidos |
record_format | MEDLINE/PubMed |
spelling | pubmed-64235802019-03-22 Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826) Liu, Chang Wang, Xuan Tian, Jiu-Bo Ma, Pei-Yuan Meng, Fan-Xiu Zhang, Qi Yu, Bao-Feng Guo, Rui Liu, Zhi-Zhen Wang, Hai-Long Xie, Jun Cheng, Niu-Liang Wang, Jian-Hua Niu, Bo Sun, Gong-Qin Mol Med Rep Articles Earthworms are useful indicator organisms of soil health and Eisenia fetida have been extensively used as test organisms in ecotoxicological studies. In order to gain insight into the gene expression profiles associated with physiological functions of earthworms, a full-length enriched cDNA library of the Eisenia fetida genome was successfully constructed using Switching Mechanism at 5′End of RNA Template technology. Construction of a cDNA library and analysis of Expressed Sequence Tags (ESTs) are efficient approaches for collecting genomic information and identifying genes important for a given biological process. Furthermore, analysis of the expression abundance of ESTs was performed with the aim of providing genetic and transcriptomic information on the development and regenerative process of earthworms. Phrep and Crossmatch were used to process EST data and a total of 1,140 high-quality EST sequences were determined by sequencing random cDNA clones from the library. Clustering analysis of sequences revealed a total of 593 unique sequences including 225 contiguous and 368 singleton sequences. Basic Local Alignment Search Tool analysis against the Kyoto Encyclopedia of Genes and Genomes database resulted in 593 significant hits (P-value <1×10(−8)), of which 168 were annotated through Gene Ontology analysis. The STRING database was used to determine relationships among the 168 ESTs, identifying associated genes involved in protein-protein interactions and gene expression regulation. Based on nucleic acid and protein sequence homology, the mutual relationships between 287 genes could be obtained, which identified a portion of the ESTs as known genes. The present study reports on the construction of a high-quality cDNA library representative of adult earthworms, on a preliminary analysis of ESTs and on a putative functional analysis of ESTs. The present study is expected to enhance our understanding of the molecular basis underlying the biological development of earthworms. D.A. Spandidos 2019-04 2019-02-05 /pmc/articles/PMC6423580/ /pubmed/30720084 http://dx.doi.org/10.3892/mmr.2019.9938 Text en Copyright: © Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. |
spellingShingle | Articles Liu, Chang Wang, Xuan Tian, Jiu-Bo Ma, Pei-Yuan Meng, Fan-Xiu Zhang, Qi Yu, Bao-Feng Guo, Rui Liu, Zhi-Zhen Wang, Hai-Long Xie, Jun Cheng, Niu-Liang Wang, Jian-Hua Niu, Bo Sun, Gong-Qin Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826) |
title | Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826) |
title_full | Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826) |
title_fullStr | Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826) |
title_full_unstemmed | Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826) |
title_short | Construction of a cDNA library and preliminary analysis of the expressed sequence tags of the earthworm Eisenia fetida (Savigny, 1826) |
title_sort | construction of a cdna library and preliminary analysis of the expressed sequence tags of the earthworm eisenia fetida (savigny, 1826) |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423580/ https://www.ncbi.nlm.nih.gov/pubmed/30720084 http://dx.doi.org/10.3892/mmr.2019.9938 |
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