Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

Premise of the study: The stability of the bimodal karyotype found in Agave and closely related species has long interested botanists. The origin of the bimodal karyotype has been attributed to allopolyploidy, but this hypothesis has not been tested. Next-generation transcriptome sequence data were used to test whether a paleopolyploid event occurred on the same branch of the Agavoideae phylogenetic tree as the origin of the Yucca-Agave bimodal karyotype. Methods: Illumina RNA-seq data were generated for phylogenetically strategic species in Agavoideae. Paleopolyploidy was inferred in analyses of frequency plots for synonymous substitutions per synonymous site (K-s) between Hosta, Agave, and Chlorophytum paralogous and orthologous gene pairs. Phylogenies of gene families including paralogous genes for these species and outgroup species were estimated to place inferred paleopolyploid events on a species tree. Key results: K-s frequency plots suggested paleopolyploid events in the history of the genera Agave, Hosta, and Chlorophytum. Phylogenetic analyses of gene families estimated from transcriptome data revealed two polyploid events: one predating the last common ancestor of Agave and Hosta and one within the lineage leading to Chlorophytum. Conclusions: We found that polyploidy and the origin of the Yucca-Agave bimodal karyotype co-occur on the same lineage consistent with the hypothesis that the bimodal karyotype is a consequence of allopolyploidy. We discuss this and alternative mechanisms for the formation of the Yucca-Agave bimodal karyotype. More generally, we illustrate how the use of next-generation sequencing technology is a cost-efficient means for assessing genome evolution in nonmodel species

Dissecting the contributions of dispersal and host properties to the local abundance of a tropical mistletoe

The interplay between dispersal and adaptation to local environments ultimately determines the distribution of plant species, but their relative contribution remains little understood. Tropical mistletoes provide the opportunity to dissect these contributions of dispersal and adaptation, because as hemiparasitic plants, they are typically adapted to grow on a handful of species within diverse tropical communities and are non-randomly dispersed by mutualistic frugivorous birds. Here we hypothesized that the primary determinant of the abundance of a tropical mistletoe (Dendropemon caribaeus, Loranthaceae) in Puerto Rico will be the compatibility between the mistletoe and plant species in a community. Alternatively, the mistletoe's abundance could be primarily shaped by other factors such as the availability of potential host plants, or factors that determine how mistletoe seeds are dispersed by avian frugivores. We conducted surveys and experiments to assess the capacity of this mistletoe to grow on trees available in the local community, and measured the monthly phenology and seed dispersal patterns of the mistletoe and other bird-dispersed plants in the community over a period of 4 years. A path model was used to evaluate how the abundance of the mistletoe was shaped by host abundance, fruiting phenology, bird dispersal and compatibilities with host plants. Our analyses show that the compatibility between mistletoe and host tree species, measured by mistletoe survival and growth rate, was the most important factor for mistletoe abundance. The next most important factor was the phenological characteristics of the hosts; this outcome likely arose because frugivory and seed dispersal services for mistletoes and hosts are performed by the same birds. Synthesis. Mistletoes often parasitize only a subset of the suitable plant species that are available in a given community. Our results indicate that such patterns are not only determined by host quality and abundance but also by the phenological patterns of trees that influence the probabilities of mistletoe seeds being deposited on them by shared avian seed dispersers.This research was supported by NSF grants DEB‐1028174 and DEB‐1145994 to T.A.C., the Alfred P. Sloan Foundation to M.A.C.O. and the Biology Department at the Pennsylvania State University.Peer Reviewe

PlantTribes: a gene and gene family resource for comparative genomics in plants

The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm MCL [Van Dongen (Technical Report INS-R0010 2000) and Enright et al. (Nucleic Acids Res. 2002; 30: 1575–1584)] to classify all of these species’ protein-coding genes into putative gene families, called tribes, using three clustering stringencies (low, medium and high). For all tribes, we have generated protein and DNA alignments and maximum-likelihood phylogenetic trees. A parallel database of microarray experimental results is linked to the genes, which lets researchers identify groups of related genes and their expression patterns. Unified nomenclatures were developed, and tribes can be related to traditional gene families and conserved domain identifiers. SuperTribes, constructed through a second iteration of MCL clustering, connect distant, but potentially related gene clusters. The global classification of nearly 200 000 plant proteins was used as a scaffold for sorting 4 million additional cDNA sequences from over 200 plant species. All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -3

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -5

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>ficantly higher /are marked with one (p < 0.01), two, (p < 0.001), or three asterisks (p < 0.0001). Values of and /on relevant branches are given in Table 3

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -2

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>ns at the LSC/IRjunction and increases numerically counterclockwise around the genome. Genes are denoted as in Figure 1

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -10

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>s at the LSC/IRjunction and increases numerically counterclockwise around the genome. Genes are denoted as in Figure 1

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus -6

<p><b>Copyright information:</b></p><p>Taken from "Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus "</p><p>http://www.biomedcentral.com/1471-2229/7/57</p><p>BMC Plant Biology 2007;7():57-57.</p><p>Published online 24 Oct 2007</p><p>PMCID:PMC2216012.</p><p></p>(and ) are particularly divergent in