(Q41276536)

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Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean

scientific article published on 6 March 2015

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Europe PubMed Central

PubMed publication ID

29 September 2017

Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean (English)

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Europe PubMed Central

PubMed publication ID

29 September 2017

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5 June 2020

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5 June 2020

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5 June 2020

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5 June 2020

author name string

Chunmei Cai

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5 June 2020

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6 March 2015

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29 September 2017

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5 June 2020

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5 June 2020

3

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5 June 2020

546-562

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5 June 2020

Preservation of duplicate genes by complementary, degenerative mutations

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https://pubmed.ncbi.nlm.nih.gov/25747880

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CENTROIDFOLD: a web server for RNA secondary structure prediction

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https://pubmed.ncbi.nlm.nih.gov/25747880

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The gene balance hypothesis: from classical genetics to modern genomics

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https://pubmed.ncbi.nlm.nih.gov/25747880

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Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily

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https://pubmed.ncbi.nlm.nih.gov/25747880

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MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana

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https://pubmed.ncbi.nlm.nih.gov/25747880

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Role of microRNAs in plant and animal development

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https://pubmed.ncbi.nlm.nih.gov/25747880

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Duplicated fie genes in maize: expression pattern and imprinting suggest distinct functions.

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https://pubmed.ncbi.nlm.nih.gov/25747880

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On the possibility of constructive neutral evolution

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Do genetic recombination and gene density shape the pattern of DNA elimination in rice long terminal repeat retrotransposons?

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis

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Duplicated genes evolve slower than singletons despite the initial rate increase

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Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence.

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Pack-MULE transposable elements mediate gene evolution in plants

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Origin, biogenesis, and activity of plant microRNAs

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Circos: an information aesthetic for comparative genomics

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https://pubmed.ncbi.nlm.nih.gov/25747880

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MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs.

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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TopHat: discovering splice junctions with RNA-Seq

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https://pubmed.ncbi.nlm.nih.gov/25747880

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The evolutionary position of subfunctionalization, downgraded

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the paleopolyploid soybean

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Changes in twelve homoeologous genomic regions in soybean following three rounds of polyploidy

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Conservation and divergence of plant microRNA genes.

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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The B73 Maize Genome: Complexity, Diversity, and Dynamics

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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PAML 4: phylogenetic analysis by maximum likelihood

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs.

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Polyploidy: recurrent formation and genome evolution

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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The plant immune system

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Analyses of a Glycine max degradome library identify microRNA targets and microRNAs that trigger secondary siRNA biogenesis

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Plant pathogens and integrated defence responses to infection

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Factors that contribute to variation in evolutionary rate among Arabidopsis genes

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Gene movement by Helitron transposons contributes to the haplotype variability of maize

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Illegitimate recombination is a major evolutionary mechanism for initiating size variation in plant resistance genes

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Molecular mapping of two genes conferring resistance to Phytophthora sojae in a soybean landrace PI 567139B

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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DNA rearrangement in orthologous orp regions of the maize, rice and sorghum genomes

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Evolution and functional diversification of MIRNA genes

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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The fate of duplicated genes in a polyploid plant genome

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

based on heuristic

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A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

MicroRNAs: genomics, biogenesis, mechanism, and function

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Redundancy and rewiring of genetic networks following genome-wide duplication events

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Genome sequence of the palaeopolyploid soybean

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Consequences of Whole-Genome Triplication as Revealed by Comparative Genomic Analyses of the Wild Radish Raphanus raphanistrum and Three Other Brassicaceae Species

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Plant secondary siRNA production determined by microRNA-duplex structure

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Cellular reactions to gene dosage imbalance: genomic, transcriptomic and proteomic effects

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes.

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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microRNA-directed phasing during trans-acting siRNA biogenesis in plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Comprehensive analyses of microRNA gene evolution in paleopolyploid soybean genome.

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Recombination: an underappreciated factor in the evolution of plant genomes

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https://pubmed.ncbi.nlm.nih.gov/25747880

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High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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SoyTEdb: a comprehensive database of transposable elements in the soybean genome

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Synteny mapping between common bean and soybean reveals extensive blocks of shared loci

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https://pubmed.ncbi.nlm.nih.gov/25747880

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Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae

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https://pubmed.ncbi.nlm.nih.gov/25747880

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Transposon domestication versus mutualism in ciliate genome rearrangements

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https://pubmed.ncbi.nlm.nih.gov/25747880

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Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis.

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Preferential duplication of conserved proteins in eukaryotic genomes

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Criteria for annotation of plant MicroRNAs

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https://pubmed.ncbi.nlm.nih.gov/25747880

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MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Gene complexity and gene duplicability

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Genomic duplication, fractionation and the origin of regulatory novelty

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Neofunctionalization of young duplicate genes in Drosophila

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Polyploid Incidence and Evolution

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Striking similarities in the genomic distribution of tandemly arrayed genes in Arabidopsis and rice

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Origins and Mechanisms of miRNAs and siRNAs

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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MicroRNA regulation of plant innate immune receptors.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Transcriptional control of gene expression by microRNAs

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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miRBase: integrating microRNA annotation and deep-sequencing data

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

based on heuristic

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Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Recurrent tandem gene duplication gave rise to functionally divergent genes in Drosophila

1 reference

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12 December 2020

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Novel and nodulation-regulated microRNAs in soybean roots.

1 reference

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12 December 2020

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A reference genome for common bean and genome-wide analysis of dual domestications

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Global dissection of alternative splicing in paleopolyploid soybean

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis

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https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes.

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs.

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12 December 2020

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Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting

1 reference

https://pubmed.ncbi.nlm.nih.gov/25747880

12 December 2020

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