Insights from the cDNA and EST analysis of Antrodia cinnamomea.

Zhanxi Lin

doi:10.6026/97320630017109

Zhanxi Lin

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https://doi.org/10.6026/97320630017109

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Journal: Bioinformation	Publication Date: Jan 31, 2021
License type: cc-by

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It is of interest to document the insights gleaned from the cDNA and EST analysis of Antrodia cinnamomea (a fungal species). Hence a library of sequences was constructed and analysed using standard procedures to gain new insights. Therefore, 65 ESTs, with size ranging from 300-2000 bp, were constructed. This included 46 ESTs with definite annotation, 18 ESTs were hypothetical and 1 new protein derived from BLAST analysis. We assigned 227 Gene Ontology terms linked to cell composition, transport, catalytic activity, and regulation functions in these sequences. Moreover, 56 matching genes were found in 8 Kyoto Encyclopedia of Genes and Genomes pathways. Data also showed 271 SSRs from Antrodia cinnamomea ESTs with an occurrence frequency of 96.82%. The STRING data analysis showed 29 genes encoded enzymes highly involved in protein-to-protein interactions linked to expression of regulation function. Thus, we documented some insights from the cDNA and EST analysis of Antrodia cinnamomea for further data mining.

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It is of interest to document the insights gleaned from the Complementary DNA (cDNA) and expressed sequence tags (ESTs) analysis of Antrodia cinnamomea
Results & Discussion: Total RNA assessment: The total RNA extracted from the mycelium of A. cinnamomea was detected to be 963 ng/μL, the total amount was 481 μg, and the OD260/OD280 was 2.14, which indicated that the total RNA was integrated and stable enough for cDNA library construction
EST analysis: Several clones were randomly picked from the cDNA library for sequencing, and a total of 65 valid single sequences were obtained after removing the vector sequence and low-quality sequences (

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Introduction

It is of interest to document the insights gleaned from the cDNA and EST analysis of Antrodia cinnamomea (a fungal species). The NCBI BLAST program was used to compare the spliced single copy sequence with the nucleic acid library (NT) and protein (NR) databases (www.ncbi.nlm.nih.gov/) to complete the homology alignment of BLASTX. The GO analysis included functional classification of Molecular Function, Cellular Component, and Biological Process for EST sequence data by BLAST2GO software.

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