Walther, D. | Search bioRxiv

bioRxiv2018

Biparental inheritance of chloroplasts is controlled by lipid biosynthesis

In most eukaryotes, organellar genomes are transmitted preferentially by the mother, but molecular mechanisms and evolutionary forces underlying this fundamental biological principle are far from understood. It is believed that biparental inheritance promotes competition between the cytoplasmic organelles and allows the spread of so-called selfish cytoplasmic elements. Those can be, for example, fast replicating or aggressive chloroplasts (plastids) that are incompatible with the hybrid nuclear genome and therefore maladaptive.\n\nHere we show that the ability of plastids to compete against each other is a metabolic phenotype determined by extremely rapidly evolving genes in the plastid genome of the evening primrose Oenothera. Repeats in the regulatory region of accD (the plastid-encoded subunit of the acetyl-CoA carboxylase, which catalyzes the first and rate limiting step of lipid biosynthesis), as well as in ycf2 (a giant reading frame of still unknown function), are responsible for the differences in competitive behavior of plastid genotypes. Polymorphisms in these genes influence lipid synthesis and most likely profiles of the plastid envelope membrane. These in turn determine plastid division and/or turn-over rates and hence competitiveness. This work uncovers cytoplasmic drive loci controlling the outcome of biparental chloroplast transmission. Here, they define the mode of chloroplast inheritance, since plastid competitiveness can result in uniparental inheritance (through elimination of the \"weak\" plastid) or biparental inheritance (when two similarly \"strong\" plastids are transmitted).\n\nSignificance statementPlastids and mitochondria are usually uniparentally inherited, typically maternally. When the DNA-containing organelles are transmitted to the progeny by both parents, evolutionary theory predicts that the maternal and paternal organelles will compete in the hybrid. As their genomes do not undergo sexual recombination, one organelle will \"try\" to outcompete the other, thus favoring the evolution and spread of aggressive cytoplasms. The investigations described here in the evening primrose, a model species for biparental plastid transmission, have discovered that chloroplast competition is a metabolic phenotype. It is conferred by rapidly evolving genes that are encoded on the chloroplast genome and control lipid biosynthesis. Due to their high mutation rate these loci can evolve and become fixed in a population very quickly.

genetics↗

bioRxiv2018

A genome-wide scan for correlated mutations detects macromolecular and chromatin loop interactions in Arabidopsis thaliana.

The concept of exploiting correlated mutations has been introduced and applied successfully to identify interactions within and between biological macromolecules. Its rationale lies in the preservation of physical interactions via compensatory mutations. With the massive increase of available sequence information, approaches based on correlated mutations have regained considerable attention.\n\nWe analyzed a set of 10,707,430 single nucleotide polymorphisms detected in 1,135 accessions of the plant Arabidopsis thaliana. To measure their covariance and to reveal the global genome-wide sequence correlation structure of the Arabidopsis genome, the adjusted mutual information has been estimated for each possible pair of polymorphic sites. We developed a series of filtering steps to account for genetic linkage and lineage relations between Arabidopsis accessions, as well as transitive covariance as possible confounding factors. We show that upon appropriate filtering, correlated mutations prove indeed informative with regard to molecular interactions, and furthermore, appear to reflect on chromosomal interactions.\n\nOur study demonstrates that the concept of correlated mutations can also be applied successfully to within-species sequence variation and establishes a promising approach to help unravel the complex molecular interactions in A. thaliana and other species with broad sequence information.

genomics↗