Rfam 12.0: updates to the RNA families database

Nawrocki, Eric P.; Burge, Sarah; Bateman, Alex; Daub, Jennifer; Eberhardt, Ruth Y; Eddy, Sean R.; Floden, Evan; Gardner, Paul P.; Jones, Thomas A.; Tate, John; Finn, Robert D.

doi:10.1093/nar/gku1063

Cited by 942 publications

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“…Noncoding RNAs were predicted by the Infernal program using default parameters 54 . Through comparing the similarity of secondary structure between the B. juncea sequence and Rfam (v12.0) database 55 , the noncoding RNAs were classified into different families (Supplementary Table 21).…”

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The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

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2 2 5The Brassica genus contains a diverse range of oilseed and vegetable crops important for human nutrition 1 . Crops of particular agricultural importance include three diploid species, Brassica rapa (AA), Brassica nigra (BB) and Brassica oleracea (CC), and three allopolyploid species, B. napus (AACC), B. juncea (AABB) and Brassica carinata (BBCC). The evolutionary relationships among these Brassica species are described by what is called the 'triangle of U' model 2 , which proposes how the genomes of the three ancestral Brassica species, B. rapa, B. nigra and Brassica oleracae, combined to give rise to the allopolyploid species of this genus. B. juncea formed by hybridization between the diploid ancestors of B. rapa and B. nigra, followed by spontaneous chromosome doubling. Subsequent diversifying selection then gave rise to the vegetable-and oil-use subvarieties of B. juncea. These subvarieties include vegetable and oilseed mustard in China, oilseed crops in India, canola crops in Canada and Australia, and condiment crops in Europe and other regions 3 . Cultivation of B. juncea began in China about 6,000 to 7,000 years ago 4 , and flourished in India from 2,300 BC onward 5 .The genomes of B. rapa, B. oleracea and their allopolyploid offspring B. napus have been published recently [6][7][8] , and are often used to explain genome evolution in angiosperms [6][7][8] . The genomes of all Brassica species underwent a lineage-specific whole-genome triplication 6,7,9 , followed by diploidization that involved substantial genome reshuffling and gene losses 6,10-13 . In general, plant genomes are typically repetitive, polyploid and heterozygous, which complicates genome assembly 14 . The short read lengths of next-generation sequencing hinder assembly through complex regions, and fragmented draft and reference genomes usually lack skewed (G+C)-content sequences and repetitive intergenic sequences. Furthermore, in allopolyploid species, homoeolog expression dominance or bias, and specifically differential homoelog gene expression, has often been detected, for instance in Gossypium [15][16][17] Triticum 18,19 and Arabidopsis 20,21 , but the role of this phenomenon in selection for phenotypic traits remains mechanistically mysterious 22 .We reported here the draft genomes of an allopolyploid, B. juncea var. tumida, constructed by de novo assembly using shotgun reads, single-molecule long reads (PacBio sequencing), genomic (optical) mapping (BioNano sequencing) and genetic mapping, serving to resolve complicated allopolyploid genomes. The multiuse allopolyploid B. juncea genome offers a distinctive model to study the underlying genomic basis for selection in breeding improvement. These findings place this work into the broader context of plant breeding, highlighting The Brassica genus encompasses three diploid and three allopolyploid genomes, but a clear understanding of the evolution of agriculturally important traits via polyploidy is lacking. We assembled an allopolyploid Brassica juncea genome by shotgun and single-m...

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Section: Competing Financial Interestsmentioning

confidence: 99%

The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection

et al. 2016

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“…6mA was specifically tied to regulation of protein coding genes, as it was rarely found on predicted microRNAs 15 (Supplementary Fig. 6b) and almost never directly on tRNAs (Supplementary Fig.…”

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Widespread adenine N6-methylation of active genes in fungi

et al. 2017

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N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes 1-4 , but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in early-diverging fungal lineages 5 . Using single-molecule long-read sequencing of 16 diverse fungal genomes, we observed that up to 2.8% of all adenines were methylated in early-diverging fungi, far exceeding levels observed in other eukaryotes and more derived fungi. 6mA occurred symmetrically at ApT dinucleotides and was concentrated in dense methylated adenine clusters surrounding the transcriptional start sites of expressed genes; its distribution was inversely correlated with that of 5-methylcytosine. Our results show a striking contrast in the genomic distributions of 6mA and 5-methylcytosine and reinforce a distinct role for 6mA as a gene-expressionassociated epigenomic mark in eukaryotes.

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“…Consensus sequences for 11 individuals were also called separately, which assembled 82.5-99.1% of the genome. Gene annotation was done using DOGMA (Wyman et al 2004) and MITOS (Bernt et al 2013), with additional verification of transfer RNA (tRNA) by tRNAscan-SE (Schattner et al 2005) and RFam (Nawrocki et al 2015). The leftover specimens are stored at Kewalo Marine Laboratory (sample ID: C6, C16, K2, M2, M7, M12, N1 and N3) and at HIMB (sample ID: PLob1, PLob2 and PLob3).…”

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confidence: 99%