![]() LTR-REs that are missing one or more domains use enzymes produced by other LTR-REs to replicate and move. This portion encodes Pol, a polyprotein which includes four enzyme domains, protease, reverse transcriptase (RT), RNaseH and integrase, involved in the mechanism of replication and integration in the chromosomes of the host and Gag, a protein resembling that of virus-like particles. The most frequent REs in plants show two direct long terminal repeats (LTRs) flanking a coding portion. In particular, class I elements (retrotransposons or retroelements, REs) represent the main fraction of the repetitive component of eukaryotic genomes because they transpose by producing RNA intermediates which are copied to cDNA and inserted into different chromosomal sites, leading to their accumulation in the genome. Transposable elements (TEs) are DNA sequences, widespread in the nuclear genome of all eukaryotes and potentially moving across the genome. In contrast, the influence of AM symbiosis on the activity of transposable elements (TEs) is not known. It is known that besides affecting gene expression, pathogenic fungi and their elicitors, as well as compounds related to plant defence, can activate the expression of transposons, especially retrotransposons (e.g Nicotiana tabacum and Solanum lycopersicum). Moreover, AMF may protect host plants by directly inhibiting deleterious microbe propagation or through induced systemic resistance as observed in of Solanum lycopersicum, Nicotiana tabacum and Phaseolus vulgaris. Ĭompared with pathogenic fungi, many similarities occur in the molecular interaction of plant roots with beneficial microorganisms, including the activation of pathogen-related genes, radical oxygen species burst and callose deposition, as part of the AMF transiently induced early defence responses. In roots, where AM symbiosis is established, such changes in both plant and fungal transcriptomes were related to mycorrhizal establishment and development, involving post-translational regulation, signalling, transport, hormone metabolism, and biotic and abiotic stresses. These physiological modifications are, in turn, linked to the activation/repression of several genes, as observed using mRNA sequencing (RNA-Seq) analyses, in a few plant species such as Medicago truncatula, Solanum lycopersicum, Solanum tuberosum, Glycine max, Oryza sativa, Lotus japonicus and Helianthus annuus. The symbiosis induces physiological changes in the colonised plants, affecting the fundamental metabolism of the host cells, and modulates their secondary metabolism, for example, enhances the activity of the antioxidant enzymatic systems and the biosynthesis of diverse phytochemicals with health-promoting activities. AMF also provide some ecosystem services, improving plant tolerance to biotic and abiotic stresses, thereby reducing the need for chemical fertiliser and pesticide inputs in agriculture. These fungi facilitate mineral nutrient uptake, particularly phosphorus and nitrogen from soil, producing large networks of fungal hyphae, which spread from colonised roots into the soil, receiving plant carbon compounds, in exchange. AM fungi (AMF) are beneficial obligate biotrophic microorganisms, represent essential elements of soil fertility, and are involved in plant nutrition and productivity. Therefore, we expect these data to be useful for revealing novel information about the human genome and improving sequencing technologies, SNP, indel, and structural variant calling, and de novo assembly.Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of roots of most plant species, including many cultivated plants. Cell lines, DNA, and data from these individuals are publicly available. The data come from 12 technologies: BioNano Genomics, Complete Genomics paired-end and LFR, Ion Proton exome, Oxford Nanopore, Pacific Biosciences, SOLiD, 10X Genomics GemCode WGS, and Illumina exome and WGS paired-end, mate-pair, and synthetic long reads. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry. The pilot genome, NA12878, has been released as NIST RM 8398. Here, we describe a large, diverse set of sequencing data for seven human genomes five are current or candidate NIST Reference Materials. The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. ![]()
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