Non-self- and self-recognition models in plant self-incompatibility

Nature Plants, Journal Year: 2016, Volume and Issue: 2(9)

Published: Sept. 6, 2016

Language: Английский

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Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

Nature Genetics, Journal Year: 2016, Volume and Issue: 48(9), P. 1077 - 1082

Published: July 18, 2016

Magnus Nordborg and colleagues report a genomic analysis of all 27 known species in the genus Arabidopsis. They find evidence for complex speciation history that is not accurately reflected by traditional bifurcating tree identify widespread shared polymorphisms between species. The notion as reproductively isolated units related through implies gene trees should generally agree with sister taxa share unless they diverged recently be equally closely to outgroups. It now possible evaluate this model systematically. We sequenced multiple individuals from described representing entire Arabidopsis genus. Cluster identified seven groups, corresponding capture structure However, at level trees, only separation thaliana remaining was universally supported, and, overall, amount polymorphism demonstrated reproductive isolation considerably more recent than estimated divergence times. uncovered cases past flow contradict tree. Finally, we showed pattern differs ontologies, suggesting role selection.

Language: Английский

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African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana

Proceedings of the National Academy of Sciences, Journal Year: 2017, Volume and Issue: 114(20), P. 5213 - 5218

Published: May 4, 2017

Over the past 20 y, many studies have examined history of plant ecological and molecular model, Arabidopsis thaliana, in Europe North America. Although these informed us about recent species, early has remained elusive. In a large-scale genomic analysis African A. we sequenced genomes 78 modern herbarium samples from Africa analyzed together with over 1,000 previously Eurasian samples. striking contrast to expectations, find that all individuals sampled are native this continent, including those sub-Saharan Africa. Moreover, show harbors greatest variation represents deepest thaliana lineage. Our results also reveal evidence selfing, major defining characteristic evolved single geographic region, best represented today within Demographic inference supports model which ancestral population began split by 120-90 kya, during last interglacial Abbassia pluvial, populations subsequently separated one another at around 40 kya. This bears similarities patterns observed for diverse humans, implying key role climatic events pluvial periods shaping histories current distributions wide range species.

Language: Английский

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Reference-guided de novo assembly approach improves genome reconstruction for related species

BMC Bioinformatics, Journal Year: 2017, Volume and Issue: 18(1)

Published: Nov. 10, 2017

The development of next-generation sequencing has made it possible to sequence whole genomes at a relatively low cost. However, de novo genome assemblies remain challenging due short read length, missing data, repetitive regions, polymorphisms and errors. As more are sequenced, reference-guided assembly approaches can be used assist the process. previous methods mostly focused on other genotypes within same species. We adapted extended approach, which enables usage related reference guide assembly. In order compare evaluate our approaches, we simulated data set heterozygotic plant genome. approach almost always outperforms corresponding program even when different species is used. Similar improvements observed in high coverage situations. addition, show that single evaluation metric, like widely N50 not enough properly rate as points best evaluated with criteria. Therefore, summed z-scores 36 statistics assemblies. combination mapping provides powerful tool improve reconstruction by integrating information Our extension application this strategy only but also between Finally, often straight forward, truth known. Thus one should use metrics, try assess continuity accuracy an

Language: Английский

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Genome assembly and annotation ofArabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology

Molecular Ecology Resources, Journal Year: 2016, Volume and Issue: 17(5), P. 1025 - 1036

Published: Sept. 27, 2016

The self-incompatible species Arabidopsis halleri is a close relative of the self-compatible model plant thaliana. broad European and Asian distribution heavy metal hyperaccumulation ability make A. useful for ecological genomics studies. We used long-insert mate-pair libraries to improve genome assembly ssp. gemmifera Tada mine genotype (W302) collected from site with high contamination by metals in Japan. After five rounds forced selfing, heterozygosity was reduced 0.04%, which facilitated subsequent assembly. Our now covers 196 Mb or 78% estimated size achieved scaffold N50 length 712 kb. To validate annotation, we synteny previously published high-quality reference closely related species, lyrata. Further validation quality comes phylogenetic analysis HEAVY METAL ATPASE4 (HMA4) TOLERANCE PROTEIN1 (MTP1) regions using sequences comparison. Three tandemly duplicated copies HMA4, key gene involved cadmium zinc hyperaccumulation, were assembled on single scaffold. will enhance genomewide studies as well allopolyploid kamchatica derived lyrata halleri.

Language: Английский

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Reproductive transitions in plants and animals: selfing syndrome, sexual selection and speciation

New Phytologist, Journal Year: 2019, Volume and Issue: 224(3), P. 1080 - 1094

Published: July 23, 2019

The evolution of predominant self-fertilisation frequently coincides with the a collection phenotypes that comprise 'selfing syndrome', in both plants and animals. Genomic features also display selfing syndrome. Selfing syndrome traits often involve changes to male female reproductive characters were subject sexual selection conflict obligatorily outcrossing ancestor, including gametic phase for Rapid traits, due relaxed directional under new status selfing, lays genetic groundwork isolation. Consequently, shifts pressures coupled transitions provide powerful paradigm investigating speciation process. Plant animal studies, however, emphasise distinct selective forces influencing reproductive-mode transitions: transmission advantage or assurance outweighing costs inbreeding depression vs males meiosis. Here, I synthesise links between selection, speciation, particular focus on identifying commonalities differences plant systems pointing areas warranting further synergy.

Language: Английский

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The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Nature Plants, Journal Year: 2016, Volume and Issue: 2(11)

Published: Oct. 31, 2016

Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled high-quality reference genome Cardamine hirsuta , close relative the model Arabidopsis thaliana . We combined comparative transcriptome analyses with experimental tools available in C. to investigate gene function diversification. Our findings highlight prevalent role transcription factors tandem duplications morphological evolution. identified specific for transcriptional regulators PLETHORA5 / 7 shaping leaf diversity link duplication differential expression explosive seed pod hirsuta. work highlights value approaches genetically tractable species understand genetic basis change.

Language: Английский

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Plant adaptive radiation mediated by polyploid plasticity in transcriptomes

Molecular Ecology, Journal Year: 2016, Volume and Issue: 26(1), P. 193 - 207

Published: June 29, 2016

The habitats of polyploid species are generally distinct from their parental species. Stebbins described polyploids as 'general purpose genotypes', which can tolerate a wide range environmental conditions. However, little is known about its molecular basis because the complexity genomes. We hypothesized that allopolyploid might utilize expression patterns both parents depending on environments (polyploid plasticity hypothesis). focused hydrological niche segregation along fine-scale soil moisture and waterlogging gradients. Two diploid species, Cardamine amara hirsuta, grew best in submerged unsubmerged conditions, respectively, consistent with natural habitats. Interestingly, allotetraploid flexuosa derived them similarly fluctuating well tolerance. A similar pattern was found another trio: scutata parents. Using close relatedness Arabidopsis, we quantified genomewide following dry wet treatments using an Arabidopsis microarray. Hierarchical clustering analysis revealed C. clustered hirsuta condition condition, supporting our hypothesis. Furthermore, induction levels most genes were lower than specialist This reflects disadvantage being arising fixed heterozygosity. propose recurrent speciation gradients confers differentiation reproductive isolation simultaneously serves model for studying ecological adaptive radiation.

Language: Английский

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A nonS-locus F-box gene breaks self-incompatibility in diploid potatoes

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: July 6, 2021

Potato is the third most important staple food crop. To address challenges associated with global security, a hybrid potato breeding system, aimed at converting from tuber-propagated tetraploid crop into seed-propagated diploid through crossing inbred lines, under development. However, given that potatoes are self-incompatible, this represents major obstacle which needs to be addressed in order develop lines. Here, we report on self-compatible potato, RH89-039-16 (RH), can efficiently induce mating transition self-incompatibility self-compatibility, when crossed self-incompatible We identify S-locusinhibitor (Sli) gene RH, capable of interacting multiple allelic variants pistil-specific S-ribonucleases (S-RNases). Further, Sli functions like general S-RNase inhibitor, impart SC RH and other potatoes. Discovery now offers path forward for program.

Language: Английский

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Parallel evolution of morphological and genomic selfing syndromes accompany the breakdown of heterostyly

New Phytologist, Journal Year: 2024, Volume and Issue: 242(1), P. 302 - 316

Published: Jan. 12, 2024

Summary Evolutionary transitions from outcrossing to selfing in flowering plants have convergent morphological and genomic signatures can involve parallel evolution within related lineages. Adaptive of traits is often assumed evolve faster than nonadaptive features the syndrome. We investigated phenotypic changes associated with distyly homostyly Primula oreodoxa complex. determined whether transition occurred more once stages syndromes using 22 floral both nuclear plastid data 25 populations. Two independent were detected representing an earlier a recently derived lineage. The older lineage exhibited classic Although less developed younger lineage, they development This finding contrasts prediction that some should lag behind adaptive traits. Our findings highlight value comparative studies on timing extent between lineages for investigating tempo molecular evolution.

Language: Английский

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