Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae)

Abstract

Background: The genus Cuscuta L. (Convolvulaceae), commonly known as dodders, are epiphytic vines that invade the stems of their host with haustorial feeding structures at the points of contact. Although they lack expanded leaves, some species are noticeably chlorophyllous, especially as seedlings and in maturing fruits. Some species are reported as crop pests of worldwide distribution, whereas others are extremely rare and have local distributions and apparent niche specificity. A strong phylogenetic framework for this large genus is essential to understand the interesting ecological, morphological and molecular phenomena that occur within these parasites in an evolutionary context.

Results: Here we present a well-supported phylogeny of Cuscuta using sequences of the nuclear ribosomal internal transcribed spacer and plastid rps2, rbcL and matK from representatives across most of the taxonomic diversity of the genus. We use the phylogeny to interpret morphological and plastid genome evolution within the genus. At least three currently recognized taxonomic sections are not monophyletic and subgenus Cuscuta is unequivocally paraphyletic. Plastid genes are extremely variable with regards to evolutionary constraint, with rbcL exhibiting even higher levels of purifying selection in Cuscuta than photosynthetic relatives. Nuclear genome size is highly variable within Cuscuta, particularly within subgenus Grammica, and in some cases may indicate the existence of cryptic species in this large clade of morphologically similar species.

Conclusion: Some morphological characters traditionally used to define major taxonomic splits within Cuscuta are homoplastic and are of limited use in defining true evolutionary groups. Chloroplast genome evolution seems to have evolved in a punctuated fashion, with episodes of loss involving suites of genes or tRNAs followed by stabilization of gene content in major clades. Nearly all species of Cuscuta retain some photosynthetic ability, most likely for nutrient apportionment to their seeds, while complete loss of photosynthesis and possible loss of the entire chloroplast genome is limited to a single small clade of outcrossing species found primarily in western South America.

Figure 1

Gynoecia and ovules of species across the taxonomic diversity of Cuscuta. Species in subgenus Monogyna have fused styles, species in subgenus Cuscuta have linear stigmas and species in subgenus Grammica have globose stigmas. All species examined had chlorophyllous ovules and gynoecia except C. chilensis, for which two different flower morphs with gynoecia of various shapes, sizes and colors were examined.

Figure 2

Maximum parsimony bootstrap consensus trees. Consensus trees of 500 bootstrap replicates for plastid rbcL, plastid rps2, nuclear ITS and all three genes combined with plastid matK. Parsimony bootstrap values are shown above the branches at nodes above 50% support, while Bayesian posterior probabilities are given below the branches.

Figure 3

Maximum-likelihood phylograms. Phylograms of individual genes produced by maximum likelihood with bootstrap values shown at the nodes.

Figure 4

Cladogram mapping taxonomic classifications and plastid genome changes onto recovered phylogeny. Parsimony bootstrap consensus tree (500 replicates) with taxonomic classifications according to Yuncker [1] to the right of taxon names. Changes to the plastid genome inferred via parsimony mapping are shown on the nodes.

Figure 5

Results of long PCR tests to detect differences in intergenic spacer regions. Here trnfM-CAU to psbD (top), psbD to trnC-GCA (middle) and atpB to rps4 (bottom) are shown. Lengths are calculated from complete plastid genome sequences of Ipomoea purpurea, Cuscuta exaltata and C. obtusiflora are shown beneath genes contained within each region.

Figure 6

Unconstrained maximum-likelihood tree estimates for atpE, rbcL, rps2 and rpoA. Non-synonymous to synonymous rate ratio values calculated in HyPhy are shown above and synonymous rate values are shown below all branches with overallrate values greater than 0.02.

Figure 7

Floral diversity within the genus Cuscuta. Ruler marks to the left are millimeters. Cuscuta chilensis and C. rostrata were unable to produce selfed seed when hand-pollinated, whereas all other species readily produced selfed seed with no assistance. C. coryli flower is rehydrated from an herbarium specimen; all other flowers were collected fresh from the Pennsylvania State University greenhouse.

Figure 8

Approximation of phylogenetic inferences suggested by Yunker. A rough phylogeny by Yunker was provided in the most recent monograph of the entire Cuscuta genus on page116 of [1]. In cases where one or more subsection was shown by Yunker to arise from another, the given node in the tree was converted to a polytomy between the presumed progenitor subsection and its 'offspring' subsections. Taxa included in this study are shown to the right of subsection classifications to which they belong.