Analyses of foreign plastid sequences in plant mitochondria

GANDINI, CL; SANCHEZ PUERTA, MV

Bahia Blanca

Congreso; VI Argentinian Conference on Bioinformatics and Computational Biology; 2015

Asociacion Argentina de Bioinformatica y Biologia Computacional

BackgroundHorizontal gene transfer (HGT) is defined as the exchange of genetic material between species, and is now believed to have a significant role in land plant evolution. In contrast to plastids, plant mitochondrial genomes (mtDNA) present exceptionally high rates of HGT [1-3]. A ?fusion-compatibility model?, in which entire mitochondria are transferred and fused with the native ones, has been recently postulated to explain the mechanisms underlying the HGT process between plants. In recent years, the number of HGT events between mitochondria of unrelated angiosperms has increased considerably [1,2,4]. Most cases involve foreign mitochondrial sequences, although a few fragments of plastid origin were reported [4]. We hypothesize that foreign plastid sequences were initially acquired by the native mtDNA via intracellular gene transfer (IGT) and then horizontally transferred to a distantly related plant following the fusion-compatibility model, rather than directly from a foreign plastid to the mitochondrial genome (Figure 1). Figure 1(1) Plastid sequences are transferred by intracellular gene transfer (IGT) from the plastid (pt) to the mitochondria (mt) within a single plant cell; (2) plant-to-plant interactions (direct contact or via vector intermediates direct contact or interspecies vectors) enable the transfer of entire foreign mitochondria into the recipient species and; (3) both mitochondria (donor and recipient) fuse and their genomes recombine. Thus, the recipient species acquires the plastid sequence from the donor species.Materials and methodsMitochondrial genomes containing foreign plastid sequences were obtained from GenBank. We searched for homologous sequences using BLASTN and aligned them with MUSCLE v3.7. To identify the donor lineages, phlylogenetic analyses under Maximum Likelihood with the GTR+G substitution model were performed with RAxML v.8.0. BLAST and evolutionary analyses of regions flanking the aforementioned plastid sequences were done to identify their origin. ResultsWe explored public databases and the literature for foreign plastid regions within angiosperm mitochondrial genomes [1,5-8]. Out of ~60 sequenced angiosperm mitochondrial genomes we identified less than 20 cases of foreign plastid sequences. Phylogenetic analyses confirmed their acquisition by HGT. Analyses of flanking regions revealed the presence of foreign mitochondrial sequences surrounding eight of the foreign plastid sequences. These results suggested that those sequences were first transferred to the mtDNA within the donor cell and then horizontally transferred to the mitochondria of the recipient plant. The rest of the cases could not be fairly tested because there was no mitochondrial data available of the putative donor lineages. ConclusionsPhylogenetic trees are helpful to recognize events of HGT and infer the donor lineage. However, identifying the genomic compartment within the donor species involved in the transfer is more complex. In particular, analysis of regions flanking foreign plastid sequences in plant mitochondria contributes to distinguish between plastid-to-mitochondria or mitochondria-to-mitochondria transfers. To date, there is no unambiguous evidence for plastid to mitochondria HGT among angiosperms. Detecting the source of the transfer is relevant to understanding the mechanism of HGT among plants.References1.Rice DW, Alverson AJ, Richardson AO, Young GJ, Sanchez-Puerta MV, Munzinger J, Barry K, Boore JL, Zhang Y, dePamphilis CW et al.: Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 2014, 342:1468?1473.2.Bergthorsson U, Adams K, Thomason B, Palmer JD: Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 2003, 424:197?201.3.Cho Y, Qiu YL, Kuhlman P, Palmer JD: Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci U S A 1998, 95:14244?14249.4.Sanchez-Puerta MV: Involvement of plastid, mitochondrial and nuclear genomes in plant-to-plant horizontal gene transfer. Acta Soc Bot Pol 2014, 83: 317?323.5.Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Rest JS, Davis CC: Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet 2013, 9:e1003265.6.Sloan DB, Wu Z: History of plastid DNA insertions reveals weak deletion and AT mutation biases in angiosperm mitochondrial genomes. Genome Biol Evol 2014, 6:3210?3221.7.Woloszynska M, Bocer T, Mackiewicz P, Janska H: A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus. Plant Mol Biol 2005, 56:811?820.8.Sanchez-Puerta MV, Abbona CC: The chloroplast genome of Hyoscyamus niger and a phylogenetic study of the tribe Hyoscyameae (Solanaceae). PLoS One 2014, 9:e98353.