The plastid genome of mycoheterotrophic monocot Petrosavia stellaris exhibits both gene losses and multiple rearrangements.

Plastid genomes of nonphotosynthetic plants represent a perfect model for studying evolution under relaxed selection pressure. However, the information on their sequences is still limited. We sequenced and assembled plastid genome of Petrosavia stellaris, a rare mycoheterotrophic monocot plant. After orchids, Petrosavia represents only the second family of nonphotosynthetic monocots to have its plastid genome examined. Several unusual features were found: retention of the ATP synthase genes and rbcL gene; extensive gene order rearrangement despite a relative lack of repeat sequences; an unusually short inverted repeat region that excludes most of the rDNA operon; and a lack of evidence for accelerated sequence evolution. Plastome of photosynthetic relative of P. stellaris, Japonolirion osense, has standard gene order and does not have the predisposition to inversions. Thus, the rearrangements in the P. stellaris plastome are the most likely associated with transition to heterotrophic way of life.

De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum).

BACKGROUND: Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, Fagopyrum esculentum and F. tataricum, belong to the order Caryophyllales--a large group of flowering plants with uncertain evolutionary relationships. F. esculentum (common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations Fagopyrum species have not been the subject of large-scale sequencing projects. RESULTS: Normalized cDNA corresponding to genes expressed in flowers and inflorescences of F. esculentum and F. tataricum was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for F. esculentum) and 229 (F. tataricum) thousands of reads with average length of 341-349 nucleotides. De novo assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences. CONCLUSIONS: 454 transcriptome sequencing and de novo assembly was performed for two congeneric flowering plant species, F. esculentum and F. tataricum. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.

A comparison of nrDNA ITS and ETS loci for phylogenetic inference in the Umbelliferae: an example from tribe Tordylieae.

The Umbelliferae is a large and taxonomically complex family of flowering plants whose phylogenetic relationships, particularly at low taxonomic levels, are generally obscure based on current and widely used molecular markers. Thus, information on the phylogenetic utility of additional molecular markers at these levels is highly favorable. We investigate the utility of nuclear ribosomal DNA (nrDNA) external transcribed spacer (ETS) sequences for phylogenetic inference in Umbelliferae tribe Tordylieae, a group whose relationships have been previously difficult to resolve owing to low sequence variability, and compare the results to those obtained from the nrDNA internal transcribed spacer (ITS) region. We report that the ETS region evolves at a slightly faster rate and has a higher percentage of parsimony informative characters than that of ITS and all chloroplast DNA loci examined to date. The ETS region is a valuable phylogenetic marker in Umbelliferae for low level analysis, especially when used in combination with ITS.