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

Kyoung-Su Choi,Seonjoo Park

doi:10.3390/ijms22116143

Kyoung-Su Choi, Seonjoo Park

Open Access

https://doi.org/10.3390/ijms22116143

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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.

Highlights

The structure and gene contents of plastid genomes are highly conserved in most flowering plants and range from 110 to 160 kb in length and contain 110 genes (~79 protein coding, 29 tRNA, and 4 rRNA genes) [1]
Plant mitochondria contain mitochondrial-encoded cytoplasmic male sterility (CMS) genes, which are related to the production of functional pollen or functional male reproductive organs [12]
(32.9%) was higher than in the previous study (34.4%), and 18 tRNAs was smaller in the present study

Summary

Introduction

The structure and gene contents of plastid genomes are highly conserved in most flowering plants and range from 110 to 160 kb in length and contain 110 genes (~79 protein coding, 29 tRNA, and 4 rRNA genes) [1]. Orobanchaceae is a family of mostly parasitic plants of the order Lamiales and contains about more than 2000 species in 90–115 genera. Members of this family include all types of parasitic plants such as hemiparasites and holoparasites [17,18,19]. The plastomes of Orobanchaceae (parasite species) are remarkably variable with respect to genome size, genome structure, and gene contents. A. indica and to compare these with previously reported results [31], especially with respect to mitogenome size, gene, and intron contents and repeats, and to analyze the HGT, IGT, and CMS genes in the A. indica mitogenome

Results and Discussion

Phylogenetic

Plant Samplingand DNA Sequencing

Organellar Genome Assembly and Annotation

Plastome and Mitogenome Analyses

Phylogenetic Analysis of Plastid and Mitochondrial Genes