Comparative Analysis of Plastid Genomes in the Non-photosynthetic Genus Thismia Reveals Ongoing Gene Set Reduction

Abstract

Heterotrophic plants provide intriguing examples of reductive evolution. This is especially evident in the reduction of their plastid genomes, which can potentially proceed toward complete genome loss. Several milestones at the beginning of this path of degradation have been described; however, little is known about the latest stages of plastome reduction. Here we analyze a diversity of plastid genomes in a set of closely related non-photosynthetic plants. We demonstrate how a gradual loss of genes shapes the miniaturized plastomes of these plants. The subject of our study, the genus Thismia, represents the mycoheterotrophic monocot family Thismiaceae, a group that may have experienced a very ancient (60-80 mya) transition to heterotrophy. In all 18 species examined, the plastome is reduced to 14-18 kb and is highly AT-biased. The most complete observed gene set includes accD, seven ribosomal protein genes, three rRNA, and two tRNA genes. Different clades of Thismia have undergone further gene loss (complete absence or pseudogenization) compared to this set: in particular, we report two independent losses of rps2 and rps18.

Keywords: Thismia; genome reductive evolution; mycoheterotrophy; non-photosynthetic plants; plastid genome.

FIGURE 1

Plastid genome of Thismia puberula, its GC-content, gene expression and coverage by genomic DNA sequencing reads. This species has the largest gene set and was available as a living plant allowing to analyze the transcriptome. Dark gray dashes denote GC content; thick black lines denote IR and thinner lines denote single copy regions. Genes shown outside of the circle are transcribed counterclockwise and those inside are transcribed clockwise. Green and blue lines show coverage by transcriptome reads and genomic DNA reads. Gray circles correspond to a 1000x coverage for transcriptome and 2000x for DNA.

FIGURE 2

Amino acid content of plastid genes in Thismia and photosynthetic Dioscoreales. Values for Thismia are depicted by orange bars, values for photosynthetic species by green bars. The species, from left to right: Thismia thaithongiana, Thismia hawkesii, Thismia lanternata, Thismia filiformis, Thismia mucronata, Thismia puberula, Thismia gardneriana, Thismia tentaculata, Burmannia coelestis, Burmannia disticha, Tacca chantrieri, Tacca leontopetaloides. Asterisk indicates statistically significant difference between Thismia species and photosynthetic species (q-value < 0.05).

FIGURE 3

Phylogenetic tree based on Thismia plastid genes. (A) Phylogenetic tree inferred from ML analysis of 13 plastid genes by IQ-Tree with branch lengths and bootstrap values (only values < 100 are shown). (B) The same tree showing gene losses and IR borders changes.