Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome

Nature Genetics, Journal Year: 2019, Volume and Issue: 51(5), P. 896 - 904

Published: May 1, 2019

Language: Английский

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PHI-base: the pathogen–host interactions database

Nucleic Acids Research, Journal Year: 2019, Volume and Issue: unknown

Published: Nov. 14, 2019

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of reported in peer reviewed research articles. also curates literature describing specific gene alterations that did not disease interaction phenotype, order provide complete datasets for comparative purposes. Viruses are included, due their extensive coverage other databases. In this article, we describe increased data content PHI-base, plus new features further integration with complementary release version 4.8 (September 2019) 3454 manually references, provides 6780 from 268 pathogens, tested 210 hosts 13,801 interactions. Prokaryotic eukaryotic pathogens represented almost equal numbers. Host species consist approximately 60% plants (split 50:50 between cereal non-cereal plants), 40% medical and/or environmental importance. pathogen effectors has risen by more than a third, entries infect crop global importance dramatically release. We briefly future direction project, some existing problems curation process.

Language: Английский

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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Science, Journal Year: 2022, Volume and Issue: 376(6588)

Published: March 31, 2022

Mobile elements and repetitive genomic regions are sources of lineage-specific innovation uniquely fingerprint individual genomes. Comprehensive analyses such repeat elements, including those found in more complex the genome, require a complete, linear genome assembly. We present de novo discovery annotation T2T-CHM13 human reference genome. identified previously unknown satellite arrays, expanded catalog variants families for repeats mobile characterized classes composite repeats, located retroelement transduction events. detected nascent transcription delineated CpG methylation profiles to define structure transcriptionally active retroelements humans, centromeres. These data expand our insight into diversity, distribution, evolution that have shaped

Language: Английский

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Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

Genome biology, Journal Year: 2018, Volume and Issue: 19(1)

Published: Aug. 14, 2018

The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access bread wheat reference genome sequence produced by International Wheat Genome Sequencing Consortium. browsers, BLAST, InterMine tools have established for in-depth exploration together additional linked datasets including physical maps, variations, gene expression, genetic phenomic data from other collaborative projects already stored in GnpIS information system. provides enhanced search browser features that will facilitate deployment latest genomics resources improvement.

Language: Английский

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Genome‐wide analysis of MIKC‐type MADS‐box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization

New Phytologist, Journal Year: 2019, Volume and Issue: 225(1), P. 511 - 529

Published: Aug. 16, 2019

Wheat (Triticum aestivum) is one of the most important crops worldwide. Given a growing global population coupled with increasingly challenging cultivation conditions, facilitating wheat breeding by fine-tuning traits great importance. MADS-box genes are prime candidates for this, as they involved in virtually all aspects plant development. Here, we present detailed overview phylogeny and expression 201 MIKC-type genes. Homoeolog retention significantly above average genome-wide rate genes, indicating that many homoeologs functionally not redundant. Gene generally agreement expected subfamily-specific pattern, broad conservation function during evolution. We also found extensive expansion some subfamilies, especially those potentially adaptation to different environmental conditions like flowering time Duplications prominent distal telomeric regions. A number show novel patterns respond, example, biotic stress, pointing towards neofunctionalization. speculate conserved, duplicated neofunctionalized may have played an role diversity hence contributing importance staple food.

Language: Английский

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