Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae

Stochastic processes and changes in evolutionary rate are associated with diversification in a lineage of tropical hard pines (Pinus)

The study of the patterns of polymorphism and molecular evolution among closely related species is key to understanding the evolutionary forces involved in the diversification of lineages. This point is a big challenge in species with slow evolutionary rates, long life cycles, and ancient, shared polymorphisms such as conifers. Under the premise of divergence in a stepwise migration process, we expect clinal geographical patterns of purifying selection efficiency, and genetic structure related to latitude or longitude. If migration is accompanied by changes in the environment, we could further expect a role of positive selection in driving species divergence. Here, we infer patterns of polymorphism, efficiency of purifying selection, and molecular evolution using a dataset of 161 nuclear genes (∼71 Kb) in a lineage of hard pines from North America, the Caribbean, Mexico, and Central America presumed to have migrated from North America toward lower latitudes with tropical conditions. Under the premise of differences in selective pressures, we also look for possible signals of positive selection. To test our hypothesis, first we estimated different indices to infer patterns of polymorphism and efficiency of purifying selection (Ka, Ks, Ka/Ks, dN, dS, dN/dS, and dxy) and compared these metrics across five clades. Also, we investigated possible clinal patterns in these indices and morphological traits (needle length and cone length). Then we inferred genetic structure and environmental differences among species to test for possible signals of positive selection using phylogenetic methods in specific clades. We found differences among clades using Ka, Ks, and Ka/Ks with a relaxation of purifying selection, especially in the Elliotti and Patula clades. We also found environmental differences related to geographic distance, and among clades suggesting differences in selective pressures. The indices Ks, dxy, and needle length had relationships with geography but not ovulate cone length. Finally, we found that most analyzed genes are under purifying selection, but there was an exception of faster evolutionary rate in some pine species, suggesting the possible action of positive selection in divergence. Our study indicated that stochastic processes have played a key role in the diversification of the group, with a possible input of positive selection in pines from Mexico and Central America.

Real-Time PCR Assays to Detect and Distinguish the Rapid 'Ōhi'a Death Pathogens Ceratocystis lukuohia and C. huliohia

Ceratocystis lukuohia and C. huliohia are recently described fungal species that cause rapid 'ōhi'a death (ROD) of Metrosideros polymorpha, Hawaii's most abundant and ecologically important native species. Although the pathogens are now widespread on Hawai'i Island, a major effort is underway to study and manage affected forests, and particularly to prevent the disease from spreading to other islands in the State or throughout the Pacific. Rapid and accurate detection is critical. Molecular diagnostic real-time PCR protocols were developed to detect and distinguish the two pathogens, suitable for detection of fungal DNA from extracts of wood, soil, and insect frass. The assays detect as few as 2 to 4 or 16 spores of C. huliohia or C. lukuohia, respectively. These assays are valuable tools for monitoring disease spread and offer a significant advantage over culture-based methods for diagnostics, requiring <1 day to arrive at definitive results.

MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes

PREMISE OF THE STUDY

Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited.

METHODS AND RESULTS

We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales.

CONCLUSIONS

MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.