Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants

Genome biology, Journal Year: 2019, Volume and Issue: 20(1)

Published: Feb. 21, 2019

Abstract Background The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences gene duplication in a range taxa, unravel common principles underlying duplicate retention. Results We survey 141 sequenced genomes elucidate duplication, processes central the evolution biodiversity. develop pipeline named DupGen_finder identify different modes plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed differ abundance, selection pressure, expression divergence, conversion rate among genomes. number WGD-derived genes decreases exponentially with increasing age events—transposed duplication- duplication-derived declined parallel. In contrast, frequency tandem proximal duplications showed no significant decrease over time, providing continuous supply variants available for adaptation continuously changing environments. Moreover, duplicates experienced stronger selective pressure than formed by other evolved toward biased functional roles involved self-defense. pairs peaking shortly after polyploidization. To platform accessing duplicated plants, we constructed Plant Duplicate Gene Database. Conclusions comprehensive landscape across kingdom comparing genomes, which provides solid foundation further investigation dynamic genes.

Language: Английский

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The Sol Genomics Network (SGN)—from genotype to phenotype to breeding

Nucleic Acids Research, Journal Year: 2014, Volume and Issue: 43(D1), P. D1036 - D1041

Published: Nov. 26, 2014

The Sol Genomics Network (SGN, http://solgenomics.net) is a web portal with genomic and phenotypic data, analysis tools for the Solanaceae family close relatives. SGN hosts whole genome data an increasing number of members including tomato, potato, pepper, eggplant, tobacco Nicotiana benthamiana. database also stores loci phenotype which researchers can upload edit user-friendly interfaces. Tools such as BLAST, GBrowse JBrowse browsing genomes, expression map viewers, locus community annotation system QTL are available. A new tool was recently implemented to improve Virus-Induced Gene Silencing (VIGS) constructs called VIGS tool. With growing in database, now advancing develop web-based breeding implement code structure other species or clade-specific databases.

Language: Английский

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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution

Nature Genetics, Journal Year: 2016, Volume and Issue: 48(6), P. 657 - 666

Published: May 9, 2016

Philipp Simon, Massimo Iorizzo, Allen Van Deynze and colleagues report the high-quality assembly of carrot genome, providing an important resource for crop improvement. They find a candidate gene that regulates carotenoid accumulation gain further insights into asterid genome evolution, including characterization two new polyploidization events. We chromosome-scale analysis (Daucus carota) first sequenced to include comparative evolutionary among members euasterid II clade. characterized events, both occurring after divergence from Asterales order, clarifying scenario before radiation main clades. Large- small-scale lineage-specific duplications have contributed expansion families, those with roles in flowering time, defense response, flavor, pigment accumulation. identified gene, DCAR_032551, conditions (Y) taproot is coexpressed several isoprenoid biosynthetic genes. The primary mechanism regulating not at level. hypothesize DCAR_032551 upstream photosystem development functional processes, photomorphogenesis root de-etiolation.

Language: Английский

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The Epigenome and Transcriptional Dynamics of Fruit Ripening

Annual Review of Plant Biology, Journal Year: 2017, Volume and Issue: 68(1), P. 61 - 84

Published: Feb. 22, 2017

Fruit has evolved myriad forms that facilitate seed dispersal in varied environmental and ecological contexts. Because fleshy fruits become attractive nutritious to seed-dispersing animals, the transition from unripe ripe fruit represents a dramatic shift survival strategy-from protecting against damaging animals making it appealing those same once ripened. For optimal fitness, ripening therefore must be tightly controlled coordinated with development. Fruits, like many vegetative tissues of plants contribute human diets, are also subject decay, which is enhanced as consequence transition. As such, control enormous relevance for both plant biology food security. Here, we review complex interactions hormones transcription factors during fleshy-fruit ripening, an emphasis on recent discovery epigenome dynamics critical early regulator cascade molecular events ultimately maturation ripening.

Language: Английский

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Evolution of plant genome architecture

Genome biology, Journal Year: 2016, Volume and Issue: 17(1)

Published: Feb. 29, 2016

We have witnessed an explosion in our understanding of the evolution and structure plant genomes recent years. Here, we highlight three important emergent realizations: (1) that evolutionary history all contains multiple, cyclical episodes whole-genome doubling were followed by myriad fractionation processes; (2) vast majority variation genome size reflects dynamics proliferation loss lineage-specific transposable elements; (3) various classes small RNAs help shape genomic architecture function. illustrate ways which these organism-level molecular genetic processes can be used for crop improvement.

Language: Английский

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Advances in the understanding of cuticular waxes in Arabidopsis thaliana and crop species

Plant Cell Reports, Journal Year: 2015, Volume and Issue: 34(4), P. 557 - 572

Published: Feb. 18, 2015

Language: Английский

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Transcriptional control of fleshy fruit development and ripening

Journal of Experimental Botany, Journal Year: 2014, Volume and Issue: 65(16), P. 4527 - 4541

Published: July 28, 2014

Fleshy fruits have evolved to be attractive frugivores in order enhance seed dispersal, and become an indispensable part of the human diet. Here we review recent advances understanding transcriptional regulation fleshy fruit development ripening with a focus on tomato. While aspects are probably conserved throughout angiosperms, including model plant Arabidopsis thaliana, it is shown that likely orthologues genes distinct functions fruits. The for study tomato, because availability single gene mutants transgenic knock-down lines. In other species, our knowledge often incomplete or absent. Tomato size shape co-determined by transcription factors acting during formation ovary. Other play role chloroplast formation, upon impact quality such as secondary metabolite content. NON-RIPENING (NOR), COLORLESS (CNR), RIPENING INHIBITOR (MADS-RIN) concert ethylene signalling regulate ripening, possibly response developmental switch. Additional components include TOMATO AGAMOUS-LIKE1 (TAGL1), APETALA2a (AP2a), FRUITFULL (FUL1 FUL2). links between this highly connected regulatory network downstream effectors modulating colour, texture, flavour still relatively poorly understood. Intertwined post-transcriptional fruit-expressed microRNAs targeting several these factors. This important process also governed changes DNA methylation levels chromatin remodelling.

Language: Английский

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Plant Glandular Trichomes: Natural Cell Factories of High Biotechnological Interest

PLANT PHYSIOLOGY, Journal Year: 2017, Volume and Issue: 175(1), P. 6 - 22

Published: July 19, 2017

Multicellular glandular trichomes are epidermal outgrowths characterized by the presence of a head made cells that have ability to secrete or store large quantities specialized metabolites. Our understanding transcriptional control trichome initiation and development is still in its infancy. This review points some central questions need be addressed better understand how such cell structures arise from plant protodermis. A key unique feature their synthesize amounts, relative size, limited number As such, they qualify as true factories, making them interesting targets for metabolic engineering. In this review, recent advances regarding terpene engineering highlighted, with special focus on tobacco (Nicotiana tabacum). particular, choice promoters drive transgene expression best ways sink existing pools precursors discussed. The bioavailability natural precursor molecules parameter controlled so-called cross talk between different biosynthetic pathways. highlighted exact nature extent only partially understood at present. future, awareness of, detailed knowledge on, biology metabolism will generate new leads tap largely unexploited potential resistance pests lead improved production metabolites high industrial pharmacological value.

Language: Английский

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New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

Genome biology, Journal Year: 2017, Volume and Issue: 18(1)

Published: Oct. 31, 2017

Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable in the expansion nucleotide-binding leucine-rich-repeat proteins (NLRs), disease-resistance gene families, has been unexplored plants.We report two high-quality de novo genomes (Capsicum baccatum C. chinense) an improved reference (C. annuum) for peppers. Dynamic rearrangements involving translocations among chromosomes 3, 5, 9 were detected comparison between other amplification athila LTR-retrotransposons, members gypsy superfamily, led to baccatum. In-depth genome-wide genes repeats unveiled that copy numbers NLRs greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated abundant across angiosperms and, most cases, lineage-specific.Our study reveals retroduplication played key roles massive emergence NLR including functional pepper plants.

Language: Английский

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Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

PLANT PHYSIOLOGY, Journal Year: 2016, Volume and Issue: 170(4), P. 2095 - 2109

Published: Feb. 2, 2016

Abstract Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, expansion history NBS-LRR during evolution is largely unknown. By identifying more than 6,000 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework angiosperm. Three anciently diverged classes (TNLs, CNLs, RNLs) were distinguished unique exon-intron structures DNA motif sequences. A total seven ancient TNL, 14 CNL, two RNL lineages discovered ancestral angiosperm, from which all current repertoires evolved. pattern gradual first 100 million years clade was observed for CNLs. TNL numbers remained stable this period but eventually deleted three divergent lineages. We inferred that an intense both CNL started Cretaceous-Paleogene boundary. Because dramatic environmental changes explosion fungal diversity occurred period, expansions R probably reflect convergent adaptive responses various families. An whole-genome duplication event ancestor resulted lineages, conservatively evolved acted as scaffold proteins defense signal transduction. Overall, reconstructed study may serve fundamental reference better understanding genes.

Language: Английский

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