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Bedtime Stories - Tales from Our Commmunity

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Thomas Sanchez
Thomas Sanchez

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The de novo assembled sequences of A. spathulifolius were used to identify the most significant match against the National Centre for Biotechnology Information (NCBI) database like the non-redundant protein (nr) and nucleotide using BLASTX tool with an E-value (1E-05). The BLASTP tool used against the Uniprot database ( ) was downloaded for uniprotein identification with E-vaue of 1E-05. Pfam related unigene was retained using HMMER. The nr, Pfam and Uniprot database results are further used to retrieve Gene Ontology (GO) terms. The retrieved GO terms were classified into three categories: Cellular Component, Molecular Function and Biological process. Further, KEGG Automated Annotation Server (KAAS) was used for pathway mapping of species specified data with 1E-05 parameter.

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To determine the Aster group phylogenetic relationship with other known Asteraceae species (S1 Table), 50-plastid protein-coding region was chosen from the entire plastid genome. The plastid genomes of these species were retrieved from NCBI database. MAFFT was used to align the 50-plastid protein-coding region and then aligned sequences were loaded to the fast tree to construct the phylogeny tree among nine species. For the plastid-based phylogeny and visualization, the GeneiousR11 version was used. Transcriptome data for orthologs genes were used to draw the phylogenetic relationship between the eight species from Asteraceae as in-groups and one out-group from Goodeniaceae family. The SRA raw database from NCBI was downloaded using the SRA tool kit and fastq-dumb tool to extract the leaf and right raw reads, de novo assembly done by Trinity with Trimmomatic tool and Transdecoder to find ORF (S2 Table). The longest ORF coding region was extracted from all contig to minimize the layoff. Then, the cdhit tool [20] was used to reduce the redundancy of amino acids. Orthofinder [21] tool were finally ran to analyze the single-copy orthologs genes (auto selection of out-group) to construct phylogeny tree.


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