Complete Chloroplast Genome Sequence of a White Spruce (Picea glauca, Genotype WS77111) from Eastern Canada

Piece and parcel of gymnosperm organellar genomes

MAIN CONCLUSION

Significant past, present, and potential future research into the organellar (plastid and mitochondrial) genomes of gymnosperms that can provide insight into the unknown origin and evolution of plants is highlighted. Gymnosperms are vascular seed plants that predominated the ancient world before their sister clade, angiosperms, took over during the Late Cretaceous. The divergence of gymnosperms and angiosperms took place around 300 Mya, with the latter evolving into the diverse group of flowering plants that dominate the plant kingdom today. Although gymnosperms have reportedly made some evolutionary innovations, the literature on their genome advances, particularly their organellar (plastid and mitochondrial) genomes, is relatively scattered and fragmented. While organellar genomes can shed light on plant origin and evolution, they are frequently overlooked, due in part to their limited contribution to gene expression and lack of evolutionary dynamics when compared to nuclear genomes. A better understanding of gymnosperm organellar genomes is critical because they reveal genetic changes that have contributed to their unique adaptations and ecological success, potentially aiding in plant survival, enhancement, and biodiversity conservation in the face of climate change. This review reveals significant information and gaps in the existing knowledge base of organellar genomes in gymnosperms, as well as the challenges and research needed to unravel their complexity.

Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response

Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.

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

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.

The genome of the forest insect pest Pissodes strobi reveals genome expansion and evidence of a Wolbachia endosymbiont

The highly diverse insect family of true weevils, Curculionidae, includes many agricultural and forest pests. Pissodes strobi, commonly known as the spruce weevil or white pine weevil, is a major pest of spruce and pine forests in North America. Pissodes strobi larvae feed on the apical shoots of young trees, causing stunted growth and can destroy regenerating spruce or pine forests. Here, we describe the nuclear and mitochondrial Pissodes strobi genomes and their annotations, as well as the genome of an apparent Wolbachia endosymbiont. We report a substantial expansion of the weevil nuclear genome, relative to other Curculionidae species, possibly driven by an abundance of class II DNA transposons. The endosymbiont observed belongs to a group (supergroup A) of Wolbachia species that generally form parasitic relationships with their arthropod host.

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

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.

Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements

Microbiology Resource Announcements (MRA) provides peer-reviewed announcements of scientific resources for the microbial research community. We describe the best practices for writing an announcement that ensures that these publications are truly useful resources. Adhering to these best practices can lead to successful publication without the need for extensive revisions.

Microbiology Resource Announcements (MRA) provides peer-reviewed announcements of scientific resources for the microbial research community. We describe the best practices for writing an announcement that ensures that these publications are truly useful resources. Adhering to these best practices can lead to successful publication without the need for extensive revisions.