Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS)

Abstract

Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respectively. The chloroplast genome of A. indica shows massive plastid genes and the loss of one IR (inverted repeat). A comparison of the A. indica chloroplast genome sequence with that of a previous study demonstrated that the two chloroplast genomes encode a similar number of proteins (except atpH) but differ greatly in length. The A. indica mitochondrial genome has 53 genes, including 35 protein-coding genes (34 native mitochondrial genes and one chloroplast gene), 15 tRNA (11 native mitochondrial genes and four chloroplast genes) genes, and three rRNA genes. Evidence for intracellular gene transfer (IGT) and horizontal gene transfer (HGT) was obtained for plastid and mitochondrial genomes. ψndhB and ψcemA in the A. indica mitogenome were transferred from the plastid genome of A. indica. The atpH gene in the plastid of A. indica was transferred from another plastid angiosperm plastid and the atpI gene in mitogenome A. indica was transferred from a host plant like Miscanthus siensis. Cox2 (orf43) encodes proteins containing a membrane domain, making ORF (Open Reading Frame) the most likely candidate gene for CMS development in A. indica.

Keywords: Aeginetia indica; Orobanchaceae; cytoplasmic male sterility (CMS); horizontal gene transfer (HGT); intracellular gene transfer (IGT); mitogenome; plastid.

Figure 1

(A) Chloroplast genome of Aeginetia indica. (B) Mitochondrial genome of A. indica. Top and bottom genes are transcribed in forward and reverse directions, respectively.

Figure 2

Cladogram of species included in the study. Topology was based on the ML tree generated concatenated MT genes listed in Table S6. Genome size, amount of plastid-like and repetitive DNA in seven Limiales species. Blue branches and red branches indicate Lamiales and Orobanchaceae species, respectively.

Figure 3

Phylogenetic evidence for intercellular gene transfer (IGT) and horizontal gene transfer (HGT). Maximum-likelihood trees based on chloroplast genes (A–D). Bootstrap values of > 60% are shown on branches. (A) IGT of fragment of the cemA gene in the A. indica mitogenome (B) IGT of fragments of the ndhB gene in the A. indica mitogenome (C) HGT of atpH in the A. indica plastid genome (D) HGT of atpI in the A. indica mitochondrial genome. Colors indicate A. indica (red) and Miscanthus sinensis (blue).

Figure 4

Comparison of cox2 and orf43 encoded proteins and prediction of transmembrane helices. (A) Comparison of the amino acids coded by cox2 and orf43. (B) Prediction of transmembrane helices coded by cox2. (C) Prediction of transmembrane helices coded by orf43. (D) Location of the cox2 gene in the A. indica mitogenome. (E) Location of the orf43 gene in the A. indica mitogenome. Small repeats that generate chimeric portions in the cox2 xon1 and orf 43 are shown in green (D,E). The arrow indicates each length.