Adding resolution and dimensionality to comparative genomics: moving from reference genomes to clade genomics

A phylogeny for the Drosophila montium species group: A model clade for comparative analyses

The Drosophila montium species group is a clade of 94 named species, closely related to the model species D. melanogaster. The montium species group is distributed over a broad geographic range throughout Asia, Africa, and Australasia. Species of this group possess a wide range of morphologies, mating behaviors, and endosymbiont associations, making this clade useful for comparative analyses. We use genomic data from 42 available species to estimate the phylogeny and relative divergence times within the montium species group, and its relative divergence time from D. melanogaster. To assess the robustness of our phylogenetic inferences, we use 3 non-overlapping sets of 20 single-copy coding sequences and analyze all 60 genes with both Bayesian and maximum likelihood methods. Our analyses support monophyly of the group. Apart from the uncertain placement of a single species, D. baimaii, our analyses also support the monophyly of all seven subgroups proposed within the montium group. Our phylograms and relative chronograms provide a highly resolved species tree, with discordance restricted to estimates of relatively short branches deep in the tree. In contrast, age estimates for the montium crown group, relative to its divergence from D. melanogaster, depend critically on prior assumptions concerning variation in rates of molecular evolution across branches, and hence have not been reliably determined. We discuss methodological issues that limit phylogenetic resolution - even when complete genome sequences are available - as well as the utility of the current phylogeny for understanding the evolutionary and biogeographic history of this clade.

Comparative genomics can provide new insights into the evolutionary mechanisms and gene function in CAM plants

Crassulacean acid metabolism (CAM) photosynthesis is an important biological innovation enabling plant adaptation to hot and dry environments. CAM plants feature high water-use efficiency, with potential for sustainable crop production under water-limited conditions. A deep understanding of CAM-related gene function and molecular evolution of CAM plants is critical for exploiting the potential of engineering CAM into C3 crops to enhance crop production on semi-arid or marginal agricultural lands. With the newly emerging genomics resources for multiple CAM species, progress has been made in comparative genomics studies on the molecular basis and subsequently on the evolution of CAM. Here, recent advances in CAM comparative genomics research in constitutive and facultative CAM plants are reviewed, with a focus on the analyses of DNA/protein sequences and gene expression to provide new insights into the path and driving force of CAM evolution and to identify candidate genes involved in CAM-related biological processes. Potential applications of new computational and experimental technologies (e.g. CRISPR/Cas-mediated genome-editing technology) to the comparative and evolutionary genomics research on CAM plants are offered.

De Novo, Divergence, and Mixed Origin Contribute to the Emergence of Orphan Genes in Pristionchus Nematodes

Homology is a fundamental concept in comparative biology. It is extensively used at the sequence level to make phylogenetic hypotheses and functional inferences. Nonetheless, the majority of eukaryotic genomes contain large numbers of orphan genes lacking homologs in other taxa. Generally, the fraction of orphan genes is higher in genomically undersampled clades, and in the absence of closely related genomes any hypothesis about their origin and evolution remains untestable. Previously, we sequenced ten genomes with an underlying ladder-like phylogeny to establish a phylogenomic framework for studying genome evolution in diplogastrid nematodes. Here, we use this deeply sampled data set to understand the processes that generate orphan genes in our focal species Pristionchus pacificus Based on phylostratigraphic analysis and additional bioinformatic filters, we obtained 29 high-confidence candidate genes for which mechanisms of orphan origin were proposed based on manual inspection. This revealed diverse mechanisms including annotation artifacts, chimeric origin, alternative reading frame usage, and gene splitting with subsequent gain of de novo exons. In addition, we present two cases of complete de novo origination from non-coding regions, which represents one of the first reports of de novo genes in nematodes. Thus, we conclude that de novo emergence, divergence, and mixed mechanisms contribute to novel gene formation in Pristionchus nematodes.