Point mutations result from errors made during DNA replication or repair, so they are usually expected to be homogeneous across all regions of a genome. However, we have found a region of chloroplast DNA in plants related to sweetpea (Lathyrus) whose local point mutation rate is at least 20 times higher than elsewhere in the same molecule. There are very few precedents for such heterogeneity in any genome, and we suspect that the hypermutable region may be subject to an unusual process such as repeated DNA breakage and repair. The region is 1.5 kb long and coincides with a gene, ycf4, whose rate of evolution has increased dramatically. The product of ycf4, a photosystem I assembly protein, is more divergent within the single genus Lathyrus than between cyanobacteria and other angiosperms. Moreover, ycf4 has been lost from the chloroplast genome in Lathyrus odoratus and separately in three other groups of legumes. Each of the four consecutive genes ycf4-psaI-accD-rps16 has been lost in at least one member of the legume ''inverted repeat loss'' clade, despite the rarity of chloroplast gene losses in angiosperms. We established that accD has relocated to the nucleus in Trifolium species, but were unable to find nuclear copies of ycf4 or psaI in Lathyrus. Our results suggest that, as well as accelerating sequence evolution, localized hypermutation has contributed to the phenomenon of gene loss or relocation to the nucleus.

Subgenus Grammica, the largest and most diverse group in the parasitic genus Cuscuta, includes 130 species distributed primarily throughout the New World, with Mexico as its center of diversity. To circumscribe the subgenus and assess the relationships among its major lineages, we conducted the first phylogenetic study of Grammica using plastid trnL-F and nrITS sequences from a wide taxonomic sampling covering its morphological, physiological, and geographical diversity. With the exception of one species belonging elsewhere, the subgenus was found to be monophyletic. The results further indicate the presence of 15 well-supported major clades within Grammica. Some of those lineages correspond partially to earlier taxonomic treatments, but the majority of groups are identified in this study for the first time. The backbone relationships among major clades, however, remain weakly supported or unresolved in some cases. The phylogenetic results indicate that the fruit dehiscence character is homoplastic, thus compromising its value as a major taxonomic and evolutionary feature. While several striking cases of long-distance dispersal are inferred, vicariance emerges as the most dominant biogeographical pattern for Cuscuta. Species placed within one of the clades with a predominantly South American distribution are hypothesized to have substantially altered plastid genomes.

Convolvulaceae, a large family of worldwide distribution, exhibit a rich diversity of morphological characteristics and ecological habitats. Previous efforts to systematize this diversity without a cladistic phylogenetic framework have disagreed on the circumscription of the family as well as tribal composition and relationship. In order to circumscribe the family and assess the relationships among its major lineages, a broad data set was constructed containing representatives of all ten recognized tribes of Convolvulaceae plus representatives of putatively related families within Asteridae. This is done by using four chloroplast regions: rbcL, atpB, psbE-J operon, and trnL-trnF intron/spacer. The results indicate that Convolvulaceae are monophyletic and sister to Solanaceae. Two of the three groups that have been proposed previously as separate families, Cuscuta and Dichondreae, are nested within the Convolvulaceae in this analysis, and the third, Humbertia, is the sister to all other members of the family. The exact position of Cuscuta could not be ascertained, but some alternatives were rejected with confidence. The study identified several distinct monophyletic groups, some of which correspond to earlier taxonomic treatments. Close relationships of tribes Hildebrandtieae with Cresseae and Ipomoeeae with Argyreieae (forming Echinoconieae) were confirmed. The polyphyly of Merremieae, Convolvuleae, Poraneae, and Erycibeae is first identified in this study.

Plant mitochondrial genes are transmitted horizontally across mating barriers with surprising frequency, but the mechanism of transfer is unclear. Here we describe two new cases of horizontal gene transfer, from parasitic flowering plants to their host flowering plants, and present phylogenetic and biogeographic evidence that this occurred as a result of direct physical contact between the two. Our findings complement the discovery that genes can be transferred in the opposite direction, from host to parasite plant.

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Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.

The exact phylogenetic position of Gnetales, a small, highly modified group of gymnosperms with an accelerated rate of molecular evolution, is one of the most challenging issues for seed plant systematics. Recent results from entire plastid genome (ptDNA) sequencing revealed the absence of the entire suite of plastid ndh genes in several species of Gnetales and the pine family (Pinaceae) potentially highlighting a major structural feature linking these two groups-concerted loss of all plastid genes for the NADH dehydrogenase complex. However, the precise extent of ndh gene loss in gymnosperms has not been surveyed. Using a slot-blot hybridization method, we probed all 11 ndh genes in 162 species from 70 of 85 gymnosperm genera. We find that all ndh genes are absent across Gnetales and Pinaceae, but not in any other group of gymnosperms. This feature represents either a major synapomorphy for a clade consisting of these two lineages or, less likely, a convergent loss. Our survey substantially extends previous inferences based on more limited sampling and, if the former evolutionary interpretation is correct, it provides additional support for the contentious "gnepine" hypothesis, which places Gnetales as sister to Pinaceae.

BackgroundHorizontal gene transfer (HGT) is relatively common in plant mitochondrial genomes but the mechanisms, extent and consequences of transfer remain largely unknown. Previous results indicate that parasitic plants are often involved as either transfer donors or recipients, suggesting that direct contact between parasite and host facilitates genetic transfer among plants.ResultsIn order to uncover the mechanistic details of plant-to-plant HGT, the extent and evolutionary fate of transfer was investigated between two groups: the parasitic genus Cuscuta and a small clade of Plantago species. A broad polymerase chain reaction (PCR) survey of mitochondrial genes revealed that at least three genes (atp1, atp6 and matR) were recently transferred from Cuscuta to Plantago. Quantitative PCR assays show that these three genes have a mitochondrial location in the one species line of Plantago examined. Patterns of sequence evolution suggest that these foreign genes degraded into pseudogenes shortly after transfer and reverse transcription (RT)-PCR analyses demonstrate that none are detectably transcribed. Three cases of gene conversion were detected between native and foreign copies of the atp1 gene. The identical phylogenetic distribution of the three foreign genes within Plantago and the retention of cytidines at ancestral positions of RNA editing indicate that these genes were probably acquired via a single, DNA-mediated transfer event. However, samplings of multiple individuals from two of the three species in the recipient Plantago clade revealed complex and perplexing phylogenetic discrepancies and patterns of sequence divergence for all three of the foreign genes.ConclusionsThis study reports the best evidence to date that multiple mitochondrial genes can be transferred via a single HGT event and that transfer occurred via a strictly DNA-level intermediate. The discovery of gene conversion between co-resident foreign and native mitochondrial copies suggests that transferred genes may be evolutionarily important in generating mitochondrial genetic diversity. Finally, the complex relationships within each lineage of transferred genes imply a surprisingly complicated history of these genes in Plantago subsequent to their acquisition via HGT and this history probably involves some combination of additional transfers (including intracellular transfer), gene duplication, differential loss and mutation-rate variation. Unravelling this history will probably require sequencing multiple mitochondrial and nuclear genomes from Plantago.See Commentary: http://www.biomedcentral.com/1741-7007/8/147.