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Assembly and Annotation of Red Spruce () Chloroplast Genome, Identification of Simple Sequence Repeats, and Phylogenetic Analysis in

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Journal Int J Mol Sci
Publisher MDPI
Date 2022 Dec 11
PMID 36499570
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Abstract

We have sequenced the chloroplast genome of red spruce () for the first time using the single-end, short-reads (44 bp) Illumina sequences, assembled and functionally annotated it, and identified simple sequence repeats (SSRs). The contigs were assembled using SOAPdenovo2 following the retrieval of chloroplast genome sequences using the black spruce () chloroplast genome as the reference. The assembled genome length was 122,115 bp (gaps included). Comparatively, the chloroplast genome reported here may be considered a near-complete draft. Global genome alignment and phylogenetic analysis based on the whole chloroplast genome sequences of and 10 other species revealed high sequence synteny and conservation among 11 species and phylogenetic relationships consistent with their known classical interrelationships and published molecular phylogeny. The chloroplast genome sequence showed the highest similarity with that of and the lowest with that of . We have annotated 107 genes including 69 protein-coding genes, 28 tRNAs, 4 rRNAs, few pseudogenes, identified 42 SSRs, and successfully designed primers for 26 SSRs. Mononucleotide A/T repeats were the most common followed by dinucleotide AT repeats. A similar pattern of microsatellite repeats occurrence was found in the chloroplast genomes of 11 species.

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