Korean Journal of Agricultural Science (농업과학연구)

Institute of Agricultural Science, CNU (충남대학교 농업과학연구소)
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Construction of a full-length cDNA library from Typha laxmanni Lepech. and T. angustifolia L. from an EST dataset

  • Received : 2018.03.12
  • Accepted : 2018.07.03
  • Published : 2018.12.31
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Abstract

Genus Typha L. (Typhaceae; Cattail in common) is one of the hydrophytic plants found in semi-aquatic regions. About nine to 18 species of the genus exist all over the world. In Korea, the most commonly found cattail species are T. laxmanni and T. angustifolia. The aim of this study was to prepare a cDNA library and sequences and analyze expressed sequence tags (ESTs) from these species, T. laxmanni and T. angustifolia. In the case of T. laxmanni, we observed that 715 out of 742 ESTs had high quality sequences, whereas the remaining 27 ESTs were low quality sequences. In this study, we identified 77 contigs, 393 unassembled clones and 65.7% singletons. Furthermore, in the case of T. angustifolia, we recorded 992 high quality EST sequences, and by excluding 28 low quality sequences from among them, we retrieved 120 contigs, 348 unassembled clones and 48.9% singletons. The basic local alignment search tool (BLAST) and Kyoto encyclopedia of genes and genomes (KEGG) database results enabled us to identify the functional categories, i.e., molecular function (16.5%), biological process (22.2%) and cellular components (61.3%). In addition, between these two species, the no hits and anonymous genes were 4.2% and 11.7% and 6.2% and 11.2% in T. laxmanni and T. angustifolia, respectively, based on the BLAST results. The study concluded that they have certain species-specific genes. Hence, the results of this study on these two species could be a valuable resource for further studies.

Keywords

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Fig. 1. Identification of cDNA library inserts size. (A) T. angustifolia Lepech; M-size marker; lane 1to 24-PCR products from different clones. (B) T. laxmanni; M-size marker; lane 1 to 24-PCR products from different clones.

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Fig. 2. Graphical representation of Typha angustifolia sequence similarity with top-hits plant species using BLASTX.

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Fig. 3. Classifcation of ESTs functions in Typha angustifolia with diferent databases (A) BLAST2GO and (B)Kyoto encyclopedia of genes and genomes (KEGG).

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Fig. 4. Graphical representation of Typha laxmanni sequence similarity with top-hits plant species usingBLASTX.

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Fig. 5. Classification of ESTs functions in Typha laxmanni with different databases (A) BLAST2GO and (B)Kyoto encyclopedia of genes and genomes (KEGG).

Table 1. Summary of cDNA library construction in Typha angustifolia and Typha laxmanni.

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Table 2. Classifcation of functional annotations of all ESTs based on BLASTX analysis.

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