The tomato genome sequence provides insights into fleshy fruit evolution

Nature, Journal Year: 2012, Volume and Issue: 485(7400), P. 635 - 641

Published: May 1, 2012

This paper reports the genome sequence of domesticated tomato, a major crop plant, and draft for its closest wild relative; comparative genomics reveal very little divergence between two genomes but some important differences with potato genome, another food in genus Solanum. Tomato (Solanum lycopersicum) is plant model system fruit development. Solanum one largest angiosperm genera1 includes annual perennial plants from diverse habitats. Here we present high-quality relative, pimpinellifolium2, compare them to each other tuberosum). The tomato show only 0.6% nucleotide signs recent admixture, more than 8% potato, nine large several smaller inversions. In contrast Arabidopsis, similar soybean, small RNAs map predominantly gene-rich chromosomal regions, including gene promoters. lineage has experienced consecutive triplications: that ancient shared rosids, one. These triplications set stage neofunctionalization genes controlling characteristics, such as colour fleshiness.

Language: Английский

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The oyster genome reveals stress adaptation and complexity of shell formation

Nature, Journal Year: 2012, Volume and Issue: 490(7418), P. 49 - 54

Published: Sept. 19, 2012

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, Mollusca. Here we report sequencing and assembly genome using short reads a fosmid-pooling strategy, along with transcriptomes development stress response proteome shell. is highly polymorphic rich in repetitive sequences, some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set genes responding environmental stress. expansion coding for heat shock protein 70 inhibitors apoptosis probably central oyster's adaptation sessile life stressful intertidal zone. Our analyses also show that shell formation molluscs more complex than currently understood involves participation cells their exosomes. sequence fills void our understanding Lophotrochozoa. through combination fosmid pooling, complemented transcriptome analysis shell, provides new insight into biology changeable environment. Oysters are keystone species estuarine ecology among important aquaculture worldwide. oyster, gigas, now reported. Comparisons other genomes defence as zone, surprisingly pathway dramatic evolution related larval development, highlighting adaptive significance marine invertebrates.

Language: Английский

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Repetitive DNA and next-generation sequencing: computational challenges and solutions

Nature Reviews Genetics, Journal Year: 2011, Volume and Issue: 13(1), P. 36 - 46

Published: Nov. 29, 2011

Language: Английский

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Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Nature Genetics, Journal Year: 2014, Volume and Issue: 46(3), P. 270 - 278

Published: Jan. 19, 2014

Doil Choi and colleagues report the genome sequence of hot pepper, Capsicum annuum, as well resequencing two cultivated peppers a wild species, chinense. Comparative genomic analysis across Solanaceae provides insights into expansion, pungency, ripening disease resistance in peppers. Hot pepper (Capsicum annuum), one oldest domesticated crops Americas, is most widely grown spice crop world. We whole-genome sequencing assembly (Mexican landrace annuum cv. CM334) at 186.6× coverage. also de novo species The size was approximately fourfold larger than that its close relative tomato, showed an accumulation Gypsy Caulimoviridae family elements. Integrative transcriptomic analyses suggested change gene expression neofunctionalization capsaicin synthase have shaped capsaicinoid biosynthesis. found differential molecular patterns regulators ethylene synthesis tomato. reference will serve platform for improving nutritional medicinal values species.

Language: Английский

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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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A heterozygous moth genome provides insights into herbivory and detoxification

Nature Genetics, Journal Year: 2013, Volume and Issue: 45(2), P. 220 - 225

Published: Jan. 13, 2013

Minsheng You and colleagues report the whole-genome sequence of diamondback moth, Plutella xylostella. Their transcriptome analysis from different life stages, together with comparative genomic phylogenetic analysis, provides insights into herbivore evolution insect adaptation to plant feeding detoxification. How an evolves become a successful is profound biological practical importance. Herbivores are often adapted feed on specific group evolutionarily biochemically related host plants1, but genetic molecular bases for defense compounds remain poorly understood2. We first basal lepidopteran species, xylostella, which contains 18,071 protein-coding 1,412 unique genes expansion gene families associated perception detoxification compounds. A recent retrotransposons near detoxification-related wider system used in metabolism shown also be involved development insecticide resistance. This work shows evolutionary success this worldwide offers feeding, as well opening avenues more sustainable pest management.

Language: Английский

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Crop genomics: advances and applications

Nature Reviews Genetics, Journal Year: 2011, Volume and Issue: 13(2), P. 85 - 96

Published: Dec. 29, 2011

Language: Английский

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A Review of Dromaeosaurid Systematics and Paravian Phylogeny

Bulletin of the American Museum of Natural History, Journal Year: 2012, Volume and Issue: 371, P. 1 - 206

Published: Aug. 17, 2012

Coelurosauria is the most diverse clade of theropod dinosaurs. Much this diversity present in Paraves—the dinosaurs containing dromaeosaurids, troodontids, and avialans. Paraves has over 160 million years evolutionary history that continues to day. The represents living tetrapod group (there are 9000 extant species Aves—a word used here as synonomous with "bird"), it at root paravian radiation, when avialans were diverging from one another, we find morphology soft tissue changes associated origin modern avian flight. Within first 15 known members exhibited a difference nearly four orders magnitude body size, value similar extreme size disparity today mammalian carnivorans, avians, varanoid squamates. In respect, an important case study characterizing patterns, processes, dynamics change. This last point particular interest because historical significance placed on role reduction powered flight.Our reviews revises membership Dromaeosauridae provides apomorphy-based diagnosis for all valid taxa. Of currently 31 named dromaeosaurid species, found 26 be valid. We provide detailed comprehensive phylogenetic analysis paravians date order explore general pattern relationships explored within broader context emphasis sampling basal avialans, their importance character optimizations base Paraves.A large dataset was constructed by merging two datasets, examining coelurosaur broadly (based previous TWiG datasets) other avialan specifically (Clarke et al., 2006). merged then significantly revised supplemented novel focusing During analysis, attention given Dromaeosauridae, enigmatic such Jinfengopteryx elegans Anchiornis huxleyi, incorporation new morphological information undescribed troodontid Late Cretaceous Mongolia. A final 474 characters scored 111 taxa address evolution. bridges gap had persisted between studies birds coelurosaurs. Most scorings matrix based direct observation specimens.All parsimonious trees recovered cladistic support monophyly Paraves, Troodontidae, Deinonychosauria. troodontids discovered including Mongolian elegans. Xiaotingia form Troodontidae. Recently proposed further supported succession clades Gondwana Asia sister Laurasian dromaeosaurids. Avialan strongly Archaeopteryx, Sapeornis, Jeholornis, Jixiangornis forming successive Confuciusornis node. topology supports more position Sapeornis than analyses indicates progressive acquisition fully "avian" shoulder morphology.

Language: Английский

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An integrative approach to understanding bird origins

Science, Journal Year: 2014, Volume and Issue: 346(6215)

Published: Dec. 11, 2014

Recent discoveries of spectacular dinosaur fossils overwhelmingly support the hypothesis that birds are descended from maniraptoran theropod dinosaurs, and furthermore, demonstrate distinctive bird characteristics such as feathers, flight, endothermic physiology, unique strategies for reproduction growth, a novel pulmonary system originated among Mesozoic terrestrial dinosaurs. The transition ground-living to flight-capable dinosaurs now probably represents one best-documented major evolutionary transitions in life history. studies developmental biology other disciplines provide additional insights into how evolved. iconic features extant most part evolved gradual stepwise fashion throughout archosaur evolution. However, new data also highlight occasional bursts morphological novelty at certain stages particularly close origin an unavoidable complex, mosaic distribution on tree. Research origins provides premier example paleontological neontological can interact reveal complexity innovations, answer key questions, lead research directions. A better understanding requires multifaceted integrative approaches, yet necessarily final test any model.

Language: Английский

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Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition

Current Biology, Journal Year: 2014, Volume and Issue: 24(20), P. 2386 - 2392

Published: Sept. 25, 2014

Language: Английский

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