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

Abstract

We have sequenced the chloroplast genome of red spruce (Picea rubens) 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 (Picea mariana) chloroplast genome as the reference. The assembled genome length was 122,115 bp (gaps included). Comparatively, the P. rubens 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 Picea rubens and 10 other Picea species revealed high sequence synteny and conservation among 11 Picea species and phylogenetic relationships consistent with their known classical interrelationships and published molecular phylogeny. The P. rubens chloroplast genome sequence showed the highest similarity with that of P. mariana and the lowest with that of P. sitchensis. 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 Picea species.

Complete chloroplast genome sequences of the ornamental plant Prunus cistena and comparative and phylogenetic analyses with its closely related species

“…The overall GC content of the genome is approximately 36.72%, with the IR regions exhibiting a higher GC content of 42.53% compared to the GC content of LSC (34.59%) and SSC (30.22%). This GC content distribution pattern is consistent with that observed in other plants [ 19 – 21 ].

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Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

“…The overall GC content was about 36.72%, while IR regions displayed a higher GC content (42.53%) than the GC content of LSC (34.59%) and SSC (30.22%). The GC content distribution pattern was similar to that of other plants [18][19][20].…”

The complete chloroplast genome of Keteleeria evelyniana Mast var. pendula Hsüeh (Pinaceae), a species with extremely small populations in China

“… 2008 ), Pinus taeda NC021440, P. thunbergii NC001631, P. massoniana NC021439 Picea abies HF937082, P. glauca KT634228 (Parmar et al. 2022 ), P. sitchensis NC011152 (Cronn et al. 2008 ), Cathaya argyophylla AB547400 (Lin et al.…”