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The sister species, lodgepole pine (Pinus contorta var. latifolia Engelm.) and jack pine (Pinus bariksiana Lamb), face pressures from a multitude of biotic agents, including mountain pine beetle (Dendroctonus ponderosae Hopkins, 1902) and their pathogenic fungal associates (e.g., Grosmannia clavigera (Rob.-Jeffr. & R.W. Davidson) Zipfel, Z.W. de Beer & M.J. Wingf.), mistletoe (Arceuthobium americanum Nutt. ex A.Gray), and the pathogen causing western gall rust (Cronartium harknessii E. Meinecke). Here, we report new stem tissue transcriptome resources developed for lodgepole and jack pines subjected to these biotic stresses. The annotated transcriptomes were compared to determine species-specific responses to the necrotrophic G. clavigera and the biotrophic Cronartium harknessii. We focused on chitinases, a family that includes members with well-documented roles in defense. Putative chitinase family members were identified via annotation, sequence similarity to reference chitinase genes, phylogenetic analyses, and in silico motif characterization. RNA-Seq revealed marked differences in the responses of lodgepole and jack pine chitinases to G. clavigera and Cronartium harknessii. The potential for adaptive variation in chitinases was investigated by assessing the level of genetic differentiation between and within lodgepole and jack pines using single nucleotide polymorphisms within chitinases. These analyses illustrate the potential of combining transcriptomic and genotyping resources to investigate genotype-phenotype correlations for non-model species. Key words: defense genes, western gall rust, Grosmannia clavigera, necrotroph, biotroph, conifer. Les especes saeurs du pin lodgepole (Pinus contorta var. latifolia Engelm.) et du pin gris (Pinus banksiana Lamb) subissent les pressions d'une multitude d'agents biotiques, dont le dendroctone du pin (Dendroctonus ponderosae Hopkins, 1902) et leurs champignons pathogenes associes (p. ex. Grosmannia clavigera (Rob.-Jeffr. & R.W. Davidson) Zipfel, Z.W. de Beer & M.J. Wingf.), le gui (Arceuthobium americanum Nutt. ex A.Gray) et l'agent pathogene responsable de la rouille-tumeur autonome (Cronartium harknessii E. Meinecke). Les chercheuses presentent ici de nouvelles ressources transcriptomiques du tissu de la tige developpees pour le pin lodgepole et le pin gris soumis a ces stress biotiques. Les transcriptomes annotes ont ete compares pour determiner les reponses au necrotrophe G. clavigera et au biotrophe Cronartium harknessii specifiques a l'espece. Elles se sont concentrees sur les chitinases, une famille qui comprend des membres ayant des roles bien documentes dans la defense. Les membres presumes de la famille des chitinases ont ete identifies par l'annotation, la similarite des sequences avec les genes de reference de chitinases, des analyses phylogenetiques et la caracterisation de motifs in silico. Le sequencage d'ARN a revele des differences marquees dans les reponses des chitinases du pin lodgepole et du pin gris a G. clavigera et Cronartium harknessii. Le potentiel de variation adaptative des chitinases a ete etudie en evaluant le niveau de differenciation genetique entre et au sein des pins lodgepole et pins gris en utilisant des polymorphismes de nucleotides uniques au sein des chitinases. Ces analyses illustrent le potentiel de la combinaison des ressources de la transcriptomique et du genotypage pour etudier les correlations genotype-phenotype pour les especes non modeles. [Traduit par la Redaction] Mots-cles: genes de defense, rouille-tumeur autonome, Grosmannia clavigera, necrotrophe, biotrophe, conifere., Introduction Conifers are generally long-living, dominant species within the environs that they inhabit. Conifer taxa are targeted by a plethora of pests and pathogens, which has led to the evolution [...]

Abstract Background Sacred lotus is a basal eudicot with agricultural, medicinal, cultural and religious importance. It was domesticated in Asia about 7,000 years ago, and cultivated for its rhizomes and seeds as a food crop. It is particularly noted for its 1,300-year seed longevity and exceptional water repellency, known as the lotus effect. The latter property is due to the nanoscopic closely packed protuberances of its self-cleaning leaf surface, which have been adapted for the manufacture of a self-cleaning industrial paint, Lotusan. Results The genome of the China Antique variety of the sacred lotus was sequenced with Illumina and 454 technologies, at respective depths of 101× and 5.2×. The final assembly has a contig N50 of 38.8 kbp and a scaffold N50 of 3.4 Mbp, and covers 86.5% of the estimated 929 Mbp total genome size. The genome notably lacks the paleo-triplication observed in other eudicots, but reveals a lineage-specific duplication. The genome has evidence of slow evolution, with a 30% slower nucleotide mutation rate than observed in grape. Comparisons of the available sequenced genomes suggest a minimum gene set for vascular plants of 4,223 genes. Strikingly, the sacred lotus has 16 COG2132 multi-copper oxidase family proteins with root-specific expression; these are involved in root meristem phosphate starvation, reflecting adaptation to limited nutrient availability in an aquatic environment. Conclusions The slow nucleotide substitution rate makes the sacred lotus a better resource than the current standard, grape, for reconstructing the pan-eudicot genome, and should therefore accelerate comparative analysis between eudicots and monocots.

Identification of population structure is a common goal for a variety of applications, including conservation, wildlife management, and medical genetics. The outcome of these analyses can have far reaching implications; therefore, it is important to ensure an understanding of the strengths and weaknesses of the methodologies used. Increasing in popularity, the discriminant analysis of principal components (DAPC) method incorporates combinations of genetic variables (alleles) into a model that differentiates individuals into genetic clusters. However, users may not have a full understanding of how to best parameterize the model. In this issue of Thia (Molecular Ecology Resources, 2022) looks under the hood of the DAPC. Using simulated data, he demonstrates the importance of careful parameter selection in developing a DAPC model, what the implications are for over‐fitting the model, and finally, how best to evaluate the results of DAPC models. This work highlights the issues that can arise when over‐parameterizing the DAPC model when gene flow is high among clusters and provides important guidelines to ensure researchers are making conclusions that are biologically relevant. [ABSTRACT FROM AUTHOR]

Abstract Background The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition. Results The Nuphar [GenBank:NC_008788] and Ranunculus [GenBank:NC_008796] plastid genomes share characteristics of gene content and organization with many other chloroplast genomes. Like other plastid genomes, these genomes are A+T-rich, except for rRNA and tRNA genes. Detailed comparisons of Nuphar with Nymphaea, another Nymphaeaceae, show that more than two-thirds of these genomes exhibit at least 95% sequence identity and that most SSRs are shared. In broader comparisons, SSRs vary among genomes in terms of abundance and length and most contain repeat motifs based on A and T nucleotides. Conclusion SSR and SDR abundance varies by genome and, for SSRs, is proportional to genome size. Long SDRs are rare in the genomes assessed. SSRs occur less frequently than predicted and, although the majority of the repeat motifs do include A and T nucleotides, the A+T bias in SSRs is less than that predicted from the underlying genomic nucleotide composition. In codon usage third positions show an A+T bias, however variation in codon usage does not correlate with differences in A+T-richness. Thus, although plastome nucleotide composition shows "A+T richness", an A+T bias is not apparent upon more in-depth analysis, at least in these aspects. The pattern of evolution in the sequences identified as ycf15 and ycf68 is not consistent with them being protein-coding genes. In fact, these regions show no evidence of sequence conservation beyond what is normal for non-coding regions of the IR.

During the past decade, there has been a rapid increase in our understanding of plastid genome organization and evolution due to the availability of many new completely sequenced genomes. There are 45 complete genomes published and ongoing projects are likely to increase this sampling to nearly 200 genomes during the next 5 years. Several groups of researchers including ours have been developing new techniques for gathering and analyzing entire plastid genome sequences and details of these developments are summarized in this chapter. The most important developments that enhance our ability to generate whole chloroplast genome sequences involve the generation of pure fractions of chloroplast genomes by whole genome amplification using rolling circle amplification, cloning genomes into Fosmid or bacterial artificial chromosome (BAC) vectors, and the development of an organellar annotation program (Dual Organellar GenoMe Annotator [DOGMA]). In addition to providing details of these methods, we provide an overview of methods for analyzing complete plastid genome sequences for repeats and gene content, as well as approaches for using gene order and sequence data for phylogeny reconstruction. This explosive increase in the number of sequenced plastid genomes and improved computational tools will provide many insights into the evolution of these genomes and much new data for assessing relationships at deep nodes in plants and other photosynthetic organisms.