Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

<p>Abstract</p> <p>Background</p> <p>The mitochondrial genome of higher plants is unusually dynamic, with recombination and nonhomologous end-joining (NHEJ) activities producing variability in size and organization. Plant mitochondrial DNA also generally displays much lower nucleotide substitution rates than mammalian or yeast systems. Arabidopsis displays these features and expedites characterization of the mitochondrial recombination surveillance gene <it>MSH1 </it>(MutS 1 homolog), lending itself to detailed study of <it>de novo </it>mitochondrial genome activity. In the present study, we investigated the underlying basis for unusual plant features as they contribute to rapid mitochondrial genome evolution.</p> <p>Results</p> <p>We obtained evidence of double-strand break (DSB) repair, including NHEJ, sequence deletions and mitochondrial asymmetric recombination activity in Arabidopsis wild-type and <it>msh1 </it>mutants on the basis of data generated by Illumina deep sequencing and confirmed by DNA gel blot analysis. On a larger scale, with mitochondrial comparisons across 72 Arabidopsis ecotypes, similar evidence of DSB repair activity differentiated ecotypes. Forty-seven repeat pairs were active in DNA exchange in the <it>msh1 </it>mutant. Recombination sites showed asymmetrical DNA exchange within lengths of 50- to 556-bp sharing sequence identity as low as 85%. <it>De novo </it>asymmetrical recombination involved heteroduplex formation, gene conversion and mismatch repair activities. Substoichiometric shifting by asymmetrical exchange created the appearance of rapid sequence gain and loss in association with particular repeat classes.</p> <p>Conclusions</p> <p>Extensive mitochondrial genomic variation within a single plant species derives largely from DSB activity and its repair. Observed gene conversion and mismatch repair activity contribute to the low nucleotide substitution rates seen in these genomes. On a phenotypic level, these patterns of rearrangement likely contribute to the reproductive versatility of higher plants.</p

壊疽性安魏那ニ就テ

SNP calls for chromosome 5 from bulked segregant analysis. F1s were generated from crosses between a self-incompatible and a self-compatible parent of Arabidopsis lyrata, sampled from the Great Lakes region of Eastern North America, which were then crossed amongst themselves to create F2s. Pools were created from: 1) 10 individuals that were phenotypically self-incompatible; and 2) 10 individuals that were phenotypically self-compatible. Three lanes of separate runs (two 150 bp and one 100 bp paired-end read run) were sequenced on an Illumina GAII instrument for each pool. The Illumina quality-filtered reads were mapped against the A. lyrata reference genome sequence MN47 (Hu et al. 2011) using GenomeMapper (Schneeberger et al. 2009), allowing for up to 10% mismatches/gaps relative to the read length. All alternative alleles relative to the reference base with a minimum frequency within each pool of 10% and a score of at least 25 were called by SHORE, as described (Ossowski et al. 2008). SNP calls (in genes only) were made using SHORE and compared for the two pools against the MN47 reference and for a reference genome constructed from two self-compatible individuals (AL4). These individuals were created by hybridisation between individuals sampled from the same population used for the self-compatible parent of the pools with the MN47 reference strain. The genomic sequence thus was determined by subtraction from the MN47 reference. The data file shows the SNP calls, % of reads with the variant and read coverage for that position. See readme file for complete details. References Hu TT, Pattyn P, Bakker EG, et al. (2011) The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nature Genetics 43, 476-481. doi: 10.1038/ng.807 Ossowski S, Schneeberger K, Clark RM, et al. (2008) Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Research 18, 2024-2033. 10.1101/gr.080200.108 Schneeberger K, Hagmann J, Ossowski S, et al. (2009) Simultaneous alignment of short reads against multiple genomes. Genome Biology 10, 1-12. 10.1186/gb-2009-10-9-r9

Positive end-expiratory pressure titrated according to respiratory system mechanics or to ARDSNetwork table did not guarantee positive end-expiratory transpulmonary pressure in acute respiratory distress syndrome

Purpose: Pulmonary recruitment and positive end-expiratory pressure (PEEP) titrated according to minimal static elastance of the respiratory system (PEEP Estat,RS ) compared to PEEP set according to the ARDSNetwork table (PEEP ARDSNetwork ) as a strategy to prevent ventilator-associated lung injury (VALI) in patients with acute respiratory distress syndrome (ARDS) increases mortality. Alternatively, avoiding negative end-expiratory transpulmonary pressure has been discussed as superior PEEP titration strategy. Therefore, we tested whether PEEP Estat,RS or PEEP ARDSNetwork prevent negative end-expiratory transpulmonary pressure in ARDS patients. Material and methods: Thirteen patients with moderate to severe ARDS were studied at PEEP ARDSNetwork versus PEEP Estat,RS . Patients were then grouped post hoc according to the end-expiratory transpulmonary pressure (positive or negative). Results: 7 out of 13 patients showed negative end-expiratory transpulmonary pressures (Ptp 12) with both strategies (PEEP ARDSNetwork : - 5.4 \ub1 3.5 vs. 2.2 \ub1 3.7 cm H 2 O, p =.005; PEEP Estat,RS : - 3.6 \ub1 1.5 vs. 3.5 \ub1 3.3 cm H 2 O, p <.001). Ptp 12 was associated with higher intra-abdominal pressure and lower end-expiratory lung volume with both PEEP strategies. Conclusions: In patients with moderate-to-severe ARDS, PEEP titrated according to the minimal static elastance of the respiratory system or according to the ARDSNetwork table did not prevent negative end-expiratory transpulmonary pressure

B70haplotypes

Alignment of haplotypes from the gene B70 (Ethylene-responsive protein related; At4g21340). Individual sequences have also been uploaded to Genbank

Data from: What causes mating system shifts in plants? Arabidopsis lyrata as a case study

The genetic breakdown of self-incompatibility (SI) and subsequent mating system shifts to inbreeding has intrigued evolutionary geneticists for decades. Most of our knowledge is derived from interspecific comparisons between inbreeding species and their outcrossing relatives, where inferences may be confounded by secondary mutations that arose after the initial loss of SI. Here, we study an intraspecific breakdown of SI and its consequences in North American Arabidopsis lyrata to test whether: (1) particular S-locus haplotypes are associated with the loss of SI and/or the shift to inbreeding; (2) a population bottleneck may have played a role in driving the transition to inbreeding; and (3) the mutation(s) underlying the loss of SI are likely to have occurred at the S-locus. Combining multiple approaches for genotyping, we found that outcrossing populations on average harbour 5 to 9 S-locus receptor kinase (SRK) alleles, but only two, S1 and S19, are shared by most inbreeding populations. Self-compatibility (SC) behaved genetically as a recessive trait, as expected from a loss-of-function mutation. Bulked segregant analysis in SC × SI F2 individuals using deep sequencing confirmed that all SC plants were S1 homozygotes but not all S1 homozygotes were SC. This was also revealed in population surveys, where only a few S1 homozygotes were SC. Together with crossing data, this suggests that there is a recessive factor that causes SC that is physically unlinked to the S-locus. Overall, our results emphasise the value of combining classical genetics with advanced sequencing approaches to resolve long outstanding questions in evolutionary biology

b160haplotypes

Alignment of haplotypes at B160 (transcription factor; At4g21430). Sequences were deposited to Genbank for a previous project (Popset accession: 374282986)

On the Origin of De Novo Genes in Arabidopsis thaliana Populations

De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications ( DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process

b120haplotypes

Alignment of haplotypes found at B120 (S-locus lectin kinase 9; At4g21390). Individual sequences have been deposited to Genbank

b80haplotypes

Alignment of haplotypes found at B80 (U-box domain protein; At4g21350). Sequences had been uploaded to Genbank for a previous paper (Popset accession 374282218)