Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China.
Department of Biotechnology, Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, P.R. China.
Mol Med Rep. 2019 Apr;19(4):2537-2550. doi: 10.3892/mmr.2019.9938. Epub 2019 Feb 5.
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 <1x10‑8), 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.
蚯蚓是土壤健康的有用指示生物，赤子爱胜蚓已被广泛用作生态毒理学研究中的测试生物。为了深入了解与蚯蚓生理功能相关的基因表达谱，我们成功地利用 RNA 模板 5'端转换机制技术构建了赤子爱胜蚓全基因组 cDNA 文库。构建 cDNA 文库和分析表达序列标签 (ESTs) 是收集基因组信息和鉴定特定生物学过程中重要基因的有效方法。此外，还对 ESTs 的表达丰度进行了分析，旨在为蚯蚓的发育和再生过程提供遗传和转录组信息。Phrep 和 Crossmatch 用于处理 EST 数据，通过对文库中的随机 cDNA 克隆进行测序，共确定了 1140 条高质量的 EST 序列。对序列进行聚类分析，共得到 593 条独特序列，包括 225 条连续序列和 368 条单序列。对数据库进行基本局部比对搜索分析，共得到 593 个显著匹配（P 值<1x10-8），其中 168 个通过基因本体论分析进行了注释。STRING 数据库用于确定 168 个 EST 之间的关系，确定了参与蛋白质-蛋白质相互作用和基因表达调控的相关基因。根据核酸和蛋白质序列的同源性，可以获得 287 个基因之间的相互关系，其中一部分 EST 被鉴定为已知基因。本研究报告了构建一个代表成年蚯蚓的高质量 cDNA 文库的情况，对 ESTs 进行了初步分析，并对 ESTs 的假定功能进行了分析。本研究有望加深我们对蚯蚓生物学发育的分子基础的理解。
