agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

Nucleic Acids Research, Journal Year: 2017, Volume and Issue: 45(W1), P. W122 - W129

Published: April 25, 2017

The agriGO platform, which has been serving the scientific community for >10 years, specifically focuses on gene ontology (GO) enrichment analyses of plant and agricultural species. We continuously maintain update databases accommodate various requests our global users. Here, we present updated that a largely expanded number supporting species (394) datatypes (865). In addition, larger have classified into groups covering crops, vegetables, fish, birds insects closely related to community. further improved computational efficiency, including batch analysis P-value distribution (PVD), user-friendliness web pages. More visualization features were added SEACOMPARE (cross comparison singular analysis), direct acyclic graph (DAG) Scatter Plots, can be merged by choosing any significant GO term. platform v2.0 is now publicly accessible at http://systemsbiology.cau.edu.cn/agriGOv2/.

Language: Английский

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The evolutionary significance of polyploidy

Nature Reviews Genetics, Journal Year: 2017, Volume and Issue: 18(7), P. 411 - 424

Published: May 15, 2017

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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Carotenoid Metabolism in Plants: The Role of Plastids

Molecular Plant, Journal Year: 2017, Volume and Issue: 11(1), P. 58 - 74

Published: Sept. 25, 2017

Language: Английский

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Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce

Nature Communications, Journal Year: 2017, Volume and Issue: 8(1)

Published: April 12, 2017

Abstract Lettuce ( Lactuca sativa ) is a major crop and member of the large, highly successful Compositae family flowering plants. Here we present reference assembly for species family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it validated genetically superscaffolds were oriented genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed success family, including genes encoding Cycloidea -like transcription factors, kinases, enzymes involved rubber biosynthesis disease resistance proteins are expanded genome. characterize 21 novel microRNAs, one which trigger phasiRNAs from numerous kinase transcripts. provide evidence triplication event specific but basal Compositae. detect 26% genome triplicated regions containing 30% all enriched regulatory sequences depleted defence.

Language: Английский

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Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

Molecular Plant, Journal Year: 2018, Volume and Issue: 11(3), P. 414 - 428

Published: Jan. 6, 2018

Language: Английский

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The alternative reality of plant mitochondrial DNA: One ring does not rule them all

PLoS Genetics, Journal Year: 2019, Volume and Issue: 15(8), P. e1008373 - e1008373

Published: Aug. 30, 2019

Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held view across broad community of life scientists that genome-sized molecules primary form plant DNA, despite understanding by researchers this is an inaccurate outdated concept. Many have one or more pairs large repeats can act sites for inter- intramolecular recombination, leading to multiple alternative arrangements (isoforms). Most been using methods unable capture complete spectrum isoforms within a species, incomplete inference their structure recombinational activity. To document investigate underlying reasons structural diversity in we used long-read (PacBio) short-read (Illumina) sequencing data assemble compare domesticated (Lactuca sativa) wild (L. saligna L. serriola) lettuce species. We characterized comprehensive, complex set each species compared genome structures between Physical analysis sativa mtDNA fluorescence microscopy revealed variety linear, branched, structures. The serriola were identical sequence arrangement differed substantially from saligna, indicating did not change during domestication. From our data, infer recombination occurs at all sizes variable frequencies. differences two other Lactuca be largely explained rare events rearranged structure. Our demonstrate representations simple, accurate descriptions true nature reality DNA complex, dynamic mixture forms.

Language: Английский

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Twenty years of plant genome sequencing: achievements and challenges

Trends in Plant Science, Journal Year: 2021, Volume and Issue: 27(4), P. 391 - 401

Published: Nov. 12, 2021

Language: Английский

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Advances in research on the carrot, an important root vegetable in the Apiaceae family

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: June 1, 2019

Carrots (Daucus carota L.), among the most important root vegetables in Apiaceae family, are cultivated worldwide. The storage is widely utilized due to its richness carotenoids, anthocyanins, dietary fiber, vitamins and other nutrients. Carrot extracts, which serve as sources of antioxidants, have functions preventing many diseases. biosynthesis, metabolism, medicinal properties carotenoids carrots been studied. Research on hormone regulation growth development has also performed. Recently, with high-throughput sequencing technology, efficient tools adopted carrot research. A large amount sequence data produced applied improve breeding. genome editing system based CRISPR/Cas9 was constructed for In this review, we will briefly summarize origins, genetic breeding, resistance editing, omics research, regulation, nutritional composition carrots. Perspectives about future research work provided.

Language: Английский

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Structural, Functional, and Genomic Diversity of Plant NLR Proteins: An Evolved Resource for Rational Engineering of Plant Immunity

Annual Review of Phytopathology, Journal Year: 2018, Volume and Issue: 56(1), P. 243 - 267

Published: June 27, 2018

Plants employ a diverse intracellular system of NLR (nucleotide binding–leucine-rich repeat) innate immune receptors to detect pathogens all types. These represent valuable agronomic traits that plant breeders rely on maximize yield in the face devastating pathogens. Despite their importance, mechanistic underpinnings NLR-based disease resistance remain obscure. The rapidly increasing numbers genomes are revealing array NLR-type receptors. In parallel, studies describing functions for this review, we intend broadly describe how structural, functional, and genomic diversity can provide resource rational engineering immunity.

Language: Английский

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