The Plastomes of Two Species in the Endoparasite Genus Pilostyles (Apodanthaceae) Each Retain Just Five or Six Possibly Functional Genes

Abstract

The 23 species of mycoheterotrophic or exoparasitic land plants (from 15 genera and 6 families) studied so far all retain a minimal set of 17 of the normally 116 plastome genes. Only Rafflesia lagascae, an endoparasite concealed in its host except when flowering, has been reported as perhaps lacking a plastome, although it still possesses plastid-like compartments. We analyzed two other endoparasites, the African Apodanthaceae Pilostyles aethiopica and the Australian Pilostyles hamiltonii, both living inside Fabaceae. Illumina and 454 data and Sanger resequencing yielded circularized plastomes of 11,348 and 15,167 bp length, with both species containing five possibly functional genes (accD, rps3, rps4, rrn16, rrn23) and two/three pseudogenes (rpoC2 in P. aethiopica and rpl2 and rps12 in both species; rps12 may be functional in P. hamiltonii). Previously known smallest land plant plastomes contain 27-29 genes, making these Apodanthaceae plastomes the most reduced in size and gene content. A similar extent of divergence might have caused the plastome of Rafflesia to escape detection. The higher plastome degeneration in both these families of endoparasites, Rafflesiaceae and Apodanthaceae, of similar high age, compared with exoparasites points to a difference of plastome function between those two modes of parasitic life.

Keywords: chloroplast genome; endoparasite; gene loss; minimal plastome; photosynthesis.

Fig. 1.—

Flowers of Pilostyles aethiopica emerging from the host Julbernardia globiflora (Fabaceae) in Harare, Zimbabwe. Scale bar is 5 mm. Photo S. Bellot.

Fig. 2.—

Read depth of Pilostyles contigs with plastome-like regions. Unclear: Contigs with plastome-like regions whose flanking regions were too short to infer their genomic location. Arrows indicate contigs that are part of plastomes (Results). The means for P. aethiopica are based on 34 contigs located in the chondriome, 670 located in the nuclear genome, 38 inferred to be in the chondriome from their flanks, and 19 of unclear location. The means for P. hamiltonii are based on 32 contigs located in the chondriome, 369 located in the nuclear genome, 31 inferred to be in the chondriome from their flanks, and 37 of unclear location.

Fig. 3.—

Map of the plastid genomes of P. aethiopica and P. hamiltonii. The skyline graphs represent the GC% with the minimum, mean, and maximum values indicated on the right. The blue and red bands indicate identity greater than 70% for bitscores greater than 100, red bands show a match in the same orientation whereas blue bands symbolize reversed-complement matches. The three bars above the gene labels refer to the reading frames; stop codons are represented by vertical black bars, and start codons (methionine) by purple vertical bars. Ψ means the gene is pseudogenized. Visualization obtained with the Artemis Comparison Tool (Carver et al. 2005).

Fig. 4.—

The plastome genes retained in parasitic and mycoheterotrophic land plants, based on Li et al. (2013), Barrett et al. (2014), Schelkunov et al. (2015), and Lam et al. (2015). White/grey fields indicate that a gene is lost/pseudogenized in at least one lineage of a given type of parasitism. Black fields indicate that a gene is functional in all lineages of the respective parasitism category. For Pilostyles, we did not take pseudogenized tRNAs into account, and the functioning of the genes remains to be confirmed (question marks).