The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative “parasitism genes.” Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria.

Highlights d The Striga genome reflects a three-phase model of parasitic plant genome evolution d A family of strigolactone receptors has undergone a striking expansion in Striga d Genes in lateral root development are coordinately induced in a parasitic organ d Host genes and retrotransposons are horizontally transferred into Striga

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs, and a few nonbioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only approximately 1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein-coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole-genome shotgun read depth is 1,400× coverage for the plastome, whereas the mitochondrial genome is covered at 40× and the nuclear genome at 2×. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally active open-reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in H. visseri. A four-stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.

The Parasitic Plant Genome Project has sequenced transcripts from three parasitic species and a nonparasitic relative in the Orobanchaceae with the goal of understanding genetic changes associated with parasitism. The species studied span the trophic spectrum from free-living nonparasite to obligate holoparasite. Parasitic species used wereTriphysaria versicolor, a photosynthetically competent species that opportunistically parasitizes roots of neighboring plants;Striga hermonthica, a hemiparasite that has an obligate need for a host; andOrobanche aegyptiaca, a holoparasite with absolute nutritional dependence on a host.Lindenbergia philippensisrepresents the closest nonparasite sister group to the parasitic Orobanchaceae and was included for comparative purposes. Tissues for transcriptome sequencing from each plant were gathered to identify expressed genes for key life stages from seed conditioning through anthesis. Two of the species studied,S. hermonthicaandO. aegyptiaca, are economically important weeds and the data generated by this project are expected to aid in research and control of these species and their relatives. The sequences generated through this project will provide an abundant resource of molecular markers for understanding population dynamics, as well as provide insight into the biology of parasitism and advance progress toward understanding parasite virulence and host resistance mechanisms. In addition, the sequences provide important information on target sites for herbicide action or other novel control strategies such as trans-specific gene silencing.

SummaryAmino acids represent the major form of reduced nitrogen that is transported in plants. Amino acid transporters in plants often show tissue-specific expression patterns and are used by plants to transport these metabolites from source to sink during development and under changing environmental conditions. We identified one amino acid transporter, AtCAT6, which is expressed in sink tissues such as lateral root primordia, flowers and seeds. Additionally AtCAT6 was induced during infestation of roots by the plantparasitic root-knot nematode, Meloidogyne incognita. Quantitative reverse-transcriptase PCR revealed nematode inducibility throughout the duration of nematode infestation and in nematode-induced feeding sites. Promoter analyses confirmed expression in endogenous sink tissues and nematode-induced feeding sites. In Xenopus oocytes, AtCAT6 mediated electrogenic transport of proteinogenic as well as nonproteinogenic amino acids with moderate affinity. AtCAT6 transported large, neutral and cationic amino acids in preference to other amino acids. Knockout mutants of this transporter failed to grow on medium containing L-glutamine as the sole nitrogen source. Our data suggest that AtCAT6 plays a role in supplying amino acids to sink tissues of plants and nematode-induced feeding structures.