Complete Chloroplast Genome Sequence of a Black Spruce (Picea mariana) from Eastern Canada

Abstract

Here, we present the chloroplast genome sequence of black spruce (Picea mariana), a conifer widely distributed throughout North American boreal forests. This complete and annotated chloroplast sequence is 123,961 bp long and will contribute to future studies on the genetic basis of evolutionary change in spruce and adaptation in conifers.

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

“…The number of genes (107) annotated in the P. rubens chloroplast genome was the same as in P. jezoensis (107), lower than that annotated in the chloroplast genomes of P. sitchensis (114), P. mariana (114), P. glauca (114), P. engelmannii (114), P. neoveitchii (116), P. asperata (108), P. crassifolia (108), and P. abies (108), and higher than that annotated in P. chihuahuana (89). The protein-coding genes annotated were lower, 69 vs. 73 each in P. mariana , P. glauca, and P. engelmanii , and 72 in P. abies , P. asperata , P. crassifolia [ 17 , 18 , 19 , 20 , 21 ] ( Supplementary Table S1 ). Thus, a somewhat lower number of genes annotated is more likely due to an incomplete genome owing to the very short single-end sequence reads used in our study and less likely due to inherent differences in the chloroplast genome structure between P. rubens and 10 other Picea species, although the existence of some inherent differences cannot be ruled out.…”

“…Thus, a somewhat lower number of genes annotated is more likely due to an incomplete genome owing to the very short single-end sequence reads used in our study and less likely due to inherent differences in the chloroplast genome structure between P. rubens and 10 other Picea species, although the existence of some inherent differences cannot be ruled out. Longer, paired-end sequences (150 bp) were used for the assembly and annotation of the chloroplast genomes of all other Picea species [ 18 , 19 , 20 , 21 , 22 ]. It is worth noting that with single-end Illumina sequence reads, a near-complete draft chloroplast genome of P. rubens could be assembled and annotated.…”

“…Indeed, chloroplast DNA markers and genes have been used for examining phylogeny and phylogeography in the genus Picea [ 15 , 16 , 17 ]. Until now, the complete chloroplast genomes of a few Picea species are available, including more recent chloroplast genomes of North American P. mariana (123,961 bp) [ 18 ], P. glauca (123,421 bp) [ 19 ], P. sitchensis (124,049 bp) [ 20 ], P. engelmannii (123,542 bp) [ 21 ], and European P. abies (124,084 bp) [ 22 ]. The chloroplast genome sequence and annotation of P. rubens have not yet been reported.…”

Plastaumatic: Automating plastome assembly and annotation

“…The following versions of software were used in all the runs, Trimmomatic v0.39 , NOVOPlasty v4.3.1 , SAMtools v1.13 and BLAST+ v2.12.0, fastp v0.23.2 . The pipeline was also tested with more complex gymnosperms and angiosperms such as Cryptocoryne elliptica ( Talkah et al., 2022 ), Cyperus rotundus ( Wu et al, 2021b ), and Picea mariana ( Lo et al., 2020 ).…”

Wood Formation under Changing Environment: Omics Approaches to Elucidate the Mechanisms Driving the Early-to-Latewood Transition in Conifers

“…Complete chloroplast and mitochondrial genome sequences are also represented, with 185 plastomes [84][85][86], but only a few mitogenomes [87][88][89][90], including those coming from whole genome sequencing projects. Genome sequences must be deposited in publicly accessible databases, in addition to well-known molecular biology portals, including GenBank, EMBL-EBI, CNGBdb, Phytozome.…”