NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

Pruitt, Kim D.; Tatusova, Tatiana; Brown, Garth; Maglott, Donna

doi:10.1093/nar/gkr1079

Cited by 1,042 publications

(991 citation statements)

References 14 publications

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“…The N-terminal sequence (~ 240 aa) of E. coli MnmC (Uniprot id P77182) was used as a bait to recover bacterial homologous from RefSeq database [28]. A multiple sequence alignment of the MnmC(m) domain with 70 non-redundant sequences was constructed using iterative refinement methods [29].…”

Section: Methodsmentioning

confidence: 99%

Bacillus subtilis exhibits MnmC-like tRNA modification activities

et al. 2018

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The MnmE-MnmG complex of Escherichia coli uses either ammonium or glycine as a substrate to incorporate the 5-aminomethyl or 5-carboxymethylaminomethyl group into the wobble uridine of certain tRNAs. Both modifications can be converted into a 5-methylaminomethyl group by the independent oxidoreductase and methyltransferase activities of MnmC, which respectively reside in the MnmC(o) and MnmC(m) domains of this bifunctional enzyme. MnmE and MnmG, but not MnmC, are evolutionarily conserved. Bacillus subtilis lacks genes encoding MnmC(o) and/or MnmC(m) homologs. The glycine pathway has been considered predominant in this typical gram-positive species because only the 5-carboxymethylaminomethyl group has been detected in tRNALysUUU and bulk tRNA to date. Here, we show that the 5-methylaminomethyl modification is prevalent in B. subtilis tRNAGlnUUG and tRNAGluUUC. Our data indicate that B. subtilis has evolved MnmC(o)- and MnmC(m)-like activities that reside in non MnmC homologous protein(s), which suggests that both activities provide some sort of biological advantage.

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Section: Methodsmentioning

confidence: 99%

Bacillus subtilis exhibits MnmC-like tRNA modification activities

et al. 2018

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“…http://dx.doi.org/10.1101/022384 doi: bioRxiv preprint first posted online Jul. 12, 2015; (Pruitt et al 2012), a minimum E-value of 1e-6 was used and only best hits were considered. BLAST XML result file was imported in Blast2go.…”

Section: Cc-by-nc-ndmentioning

confidence: 99%

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

Jin

Liu

et al. 2015

Preprint

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Variation in gene expression contributes to the diversity of phenotype. The construction of the pan-transcriptome is especially necessary for species with complex genomes, such as maize. However, knowledge of the regulation mechanisms and functional consequences of the pan-transcriptome is limited. In this study, we identified 13,382 nuclear expression presence and absence variation candidates (ePAVs, expressed in 5%~95% lines; based on the reference genome) by re-analyzing the RNA sequencing data from the kernels (15 days after pollination) of 368 maize diverse inbreds. It was estimated that only ~1% of the ePAVs are explained by DNA sequence presence and absence variations (PAV). The ePAV genes tend to be regulated by distant eQTLs when compared with non-ePAV genes (called here core expression genes, expressed in more than 95% lines). When the expression presence/absence status was used as the "genotype" to perform genome-wide association study, 56 (0.42%) ePAVs were significantly associated with 15 agronomic traits and 1,967 (14.74%) with 526 metabolic traits, measured from the mature kernels. While the above was majorly based on the reference genome, by using a modified 'assemble-then-align' strategy, 2,355 high confidence novel sequences with a total length of 1.9Mb were found absent in the current B73 reference genome (v2). Ten randomly selected novel sequences were validated with genomic PCR. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes. Two novel validated sequences annotated as NBS_LRR like genes were found to associate with flavonoid content and their homologs in rice were also found to affect flavonoids and disease-resistance. Novel sequences absent in the present reference genome might be functionally important and deserve more attentions. This study provides novel perspectives and resources to discover maize quantitative trait variations and help us to better understand the kernel regulation networks, thus enhancing maize breeding.

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“…BLASTp alignments against the non-redundant RefSeq protein database (22 January 2014) (Ye et al 2006; Pruitt et al 2012), UniProt (22 January 2014) (Consortium 2014) (including Swiss-Prot, fungal taxonomic division and uniref90) and KEGG (Release 69.0, 1 January 2014) (Kanehisa et al 2002) were performed to assign general protein function profiles. Protein domains were assigned using InterProScan 5.2-45.0 (Quevillon et al 2005) (including Pfam 27.0 (Punta et al 2012), SUPERFAMILY 1.75 (Wilson et al 2009), SMART 7 (Letunic et al 2012), TIGRFAMs 13.0 (Haft et al 2013), TMHMM 2.0c (Krogh et al 2001), PROSITE 20.99 (Sigrist et al 2013) and PANTHER 8.1 (Mi et al 2013) databases).…”

Section: Methodsmentioning

confidence: 99%

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

et al. 2018

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The high lignocellulolytic activity displayed by the soft-rot fungus Penicillium purpurogenum has made it a target for the study of novel lignocellulolytic enzymes. We have obtained a reference genome of 36.2 Mb of non-redundant sequence (11,057 protein-coding genes). The 49 largest scaffolds cover 90% of the assembly, and Core Eukaryotic Genes Mapping Approach (CEGMA) analysis reveals that our assembly captures almost all protein-coding genes. RNA-seq was performed and 93.1% of the reads aligned to the assembled genome. These data, plus the independent sequencing of a set of genes of lignocellulose-degrading enzymes, validate the quality of the genome sequence. P. purpurogenum shows a higher number of proteins with CAZy motifs, transcription factors and transporters as compared to other sequenced Penicillia. These results demonstrate the great potential for lignocellulolytic activity of this fungus and the possible use of its enzymes in related industrial applications.

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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

Cited by 1,042 publications

References 14 publications

Bacillus subtilis exhibits MnmC-like tRNA modification activities

Bacillus subtilis exhibits MnmC-like tRNA modification activities

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

The genome sequence of the soft-rot fungusPenicillium purpurogenumreveals a high gene dosage for lignocellulolytic enzymes

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