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Mitochondrial Genome Evolution (Advances in Botanical Research)
Alzohairy A M. Guo W, Mower JP. Alzohairy A. Downie S. Park S. Ruhlman T. Weng, M. Zhang J. Springer, Bock R and Knoop V eds. Springer, Dordrecht".
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Mower Lab Publications
One pathway Fig 5A involves recombination between a circular moss genome arbitrarily chosen to represent the Hookeriales donor and a Ptychomniales-like genome that has integrated into the Amborella genome via a breakpoint arbitrarily selected to lie within the cob intron see Fig 1 , top, and next section. The other pathway Fig 5B involves recombination between circular genomes derived strictly from the two donor mosses.
In the first step in each pathway, the two moss genomes recombine at a homologous site located somewhere within either of the two regions corresponding to Amborella DNA of uncertain moss origin Fig 5 arbitrarily shows this recombination as occurring between loci G and M; see Fig 1 , top. This produces a chimeric head-to-tail dimer moss genome that is either integrated in the Amborella genome Fig 5A or not Fig 5B. In the second step, recombination occurs somewhere within the other region corresponding to Amborella DNA of uncertain moss origin the A-J region; see Fig 1 , top. The left output genome in each panel possesses the same, ca.
We hypothesize that a full-length moss mitochondrial genome, either already chimeric or not, was inserted into the Amborella mitochondrial genome. This insertion could have occurred at any one of several recombination breakpoints depicted in Fig 6 , which shows a model for the rearrangement of the moss DNA in Amborella subsequent to its integration.
For the sake of diagrammatic simplicity, we arbitrarily chose an insertion breakpoint between the 80 th and th bases of the cob intron, thus positioning the resulting portions of the cob gene at the termini of the horizontally acquired genome Fig 1 , top, and Fig 6 , In1. Eight recombination events r1-r8 in Fig 6 are sufficient to derive the current organization of the moss DNA in Amborella Fig 1 , bottom from an intact, chimeric moss genome represented by the Hookeriales and Ptychomniales-like tracts mapped onto the Anomodon reference genome in Fig 1 , top after its integration into the Amborella mitochondrial genome.
The order of the eight rearrangement events as presented here is largely arbitrary and was chosen because it enables a convenient and straightforward model of rearrangement intermediates and recombination steps. Shown are a set of eight recombination events sufficient to produce the current organization and sequence content of the moss mtDNA present in the Amborella mitochondrial genome subsequent to its integration under the hypothesis of whole-moss-genome transfer.
Note also that the order of r1-r8 as presented here is largely arbitrary see Results.
Intermediate stages of rearrangement are labeled In1-In5, while the final four products of rearrangement i. The top map In1 shows as in Fig 1 , top the mitochondrial genome of the reference moss Anomodon [ 13 ] arbitrarily linearized see Results within the cob intron to correspond to a donor moss genome immediately after its integration in Amborella mtDNA.
Colored boxes and arrows indicate the position and relative orientation, respectively, of the seven blocks of synteny between the Anomodon genome and the four moss-derived regions in Amborella , with black arrows marking regions of Ptychomniales-like origin and open arrows marking regions of Hookeriales origin. The 16 loci used for phylogenetic analysis are marked in In1 and in MoAm1-MoAm4 with rectangles or lines labeled A-P see Fig 2 and S1 Fig and Table 1 ; a filled rectangle indicates a Ptychomniales-like origin, an open rectangle a Hookeriales origin, and a thin line an unresolved origin.
Five of the eight rearrangements invoked under this model can be rationalized based on identified repeats Fig 7 and below. Three of these putatively repeat-mediated rearrangements occurred at very short repeats 10—13 bp in length.
Studies of plant mtDNA recombination suggest that recombination at such short repeats takes place via a microhomology-mediated break-induced replication MMBIR mechanism [ 27 , 28 ] that leads to a duplicative, non-reciprocal cross-over event, i. For example, if such recombination occurred across very short direct repeats, then either the circularized DNA between the repeats, or the union of the sequences flanking them, would be produced, but not both, and in either case the recombination substrate would be preserved.
The other two inferred repeat-mediated rearrangements occurred non-duplicatively via reciprocal recombination across longer repeats 84 and bp in length. For recombination events r1, r2, and 4, the very short repeats 10—13 bp in sizes inferred to have mediated non-reciprocal recombination via the MMBIR pathway are in blue, while the left and right flanking sequences that are shared by two of the three extant examples of those repeats shown here are in green or red, respectively. Events r3 and r6 are reciprocal recombination events mediated by longer repeats, of either 84 bp trnS or bp a portion of rrnL , respectively.
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The first recombination event in this model Fig 6 , r1 occurred non-reciprocally between bp direct repeats Fig 7 located within moss genes rpl2 and rpl10 to form the circular product shown in Fig 6 , In2. This nonreciprocal event, instead of circularizing the intervening stretch of DNA as with r1, formed a linear recombination product, i.
This event formed one of the four extant moss-derived regions in Amborella Fig 6 , MoAm1. Subsequent to r1 and r2, the original chimeric moss integrate was lost, leaving Amborella mtDNA with the two rearrangement products shown in Fig 6 , In2. This loss required no further recombination and presumably occurred by random sorting out. This is because, as initially produced, MoAm1 was functionally redundant to the original chimeric moss integrate, i. The kb circular molecule from r1 was reintegrated via reciprocal recombination r3 between its rrnL gene and an rrnL sequence probably of angiosperm origin located within the Amborella mitochondrial genome Fig 6 , In2.
Recombination r4 occurred non-reciprocally between bp repeats Fig 7 located within the moss rps3 gene and an angiosperm nad2 intron to create the extant region MoAm2 Fig 6. Following this event, recombination r5, of unknown nature, separated the 6 2 3 4 5 substrate used for r4 into two regions, 3 4 5 Fig 6 , In4 and 6 2 not shown.
The 6 2 region was eventually lost, presumably by random sorting out.
Table of Contents
The trnS spanning the boundary of segments 4 and 5 recombined reciprocally r6 with an angiosperm trnS elsewhere in the genome to create both intermediates shown in Fig 6 , In5 products A and B of r6. Amborella mtDNA contains a horizontally transferred region that includes this angiosperm trnS context and which is identical to the Hevea sequence shown in Fig 7.
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