The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

Schattner, Peter; Brooks, Angela N.; Lowe, Todd M.

doi:10.1093/nar/gki366

Cited by 2,040 publications

(1,577 citation statements)

References 15 publications

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“…bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl) and GLIMMER (https://www.ncbi.nlm.nih.gov/genomes/MICROBES/ glimmer_3.cgi). tRNAs were annotated using tRNAscan-SE (Schattner et al 2005). All ORFs were searched and identified by ORFFinder.…”

Section: Phlebopus Portentosus; Mitogenome; Phylogenetic Relationshipmentioning

confidence: 99%

The complete mitochondrial genome of the edible Basidiomycete mushroom Phlebopus Portentosus

Jiang

Yang

Cao

et al. 2017

Mitochondrial DNA Part B

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Section: Phlebopus Portentosus; Mitogenome; Phylogenetic Relationshipmentioning

confidence: 99%

The complete mitochondrial genome of the edible Basidiomycete mushroom Phlebopus Portentosus

Jiang

Yang

Cao

et al. 2017

Mitochondrial DNA Part B

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“…When loci on both strands were predicted, only the hit with the highest score was kept. Transfer RNAs were also predicted using tRNAscan‐SE v. 1.23 (Schattner et al ., 2005) with default parameters.…”

Section: Methodsmentioning

confidence: 99%

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

Brożyńska

Copetti

Furtado

et al. 2017

Plant Biotechnology Journal

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SummaryThe related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.

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“…Reads were mapped to the final assembly sequence, PCR duplicates were flagged using the MarkDuplicates tool of the Picard command-line tools software suite (http://picard.sourceforge.net/index.shtml), and a consensus was called using SAMtools v. 0.1.19 ). The reference genome assembly was initially annotated using DOGMA (Wyman et al, 2004), with the annotations refined using tRNAscan-SE (Schattner et al, 2005) and additional BLAST searches. The inverted repeats were analyzed using the program Inverted Repeats Finder (Warburton et al, 2004) with T7 set to 500,000 and a maximum loop size of 1,000,000.…”

Section: Assembly Of the Hawaiian Mint Reference Chloroplast Genomementioning

confidence: 99%

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

Welch

Collins

Drautz–Moses

et al. 2016

Molecular Phylogenetics and Evolution

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(2016) 'The quest to resolve recent radiations : plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae).', Molecular phylogenetics and evolution., 99 . pp. 16-33. Further information on publisher's website: Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractThe Hawaiian mints (Lamiaceae), one of the largest endemic plant lineages in the archipelago, provide an excellent system to study rapid diversification of a lineage with a remote, likely paleohybrid origin. Since their divergence from New World mints 4-5 million years ago the members of this lineage have diversified greatly and represent a remarkable array of vegetative and reproductive phenotypes. Today many members of this group are endangered or already extinct, and molecular phylogenetic work relies largely on herbarium samples collected during the last century. So far a gene-by-gene approach has been utilized, but the recent radiation of the Hawaiian mints has resulted in minimal sequence divergence and hence poor phylogenetic resolution. In our quest to trace the reticulate evolutionary history of the lineage, a resolved maternal phylogeny is necessary. We applied a high-throughput approach to sequence 12 complete or nearly complete plastid genomes from multiple Hawaiian mint species and relatives, including extinct and rare taxa. We also targeted 108 hypervariable regions from throughout the chloroplast genomes in nearly all of the remaining Hawaiian species, and relatives, using a nextgeneration amplicon sequencing approach. This procedure generated ~20Kb of sequence data for each taxon and considerably increased the total number of variable sites over previous analyses. Our results demonstrate the potential of high-throughput sequencing of historic material for evolutionary studies in rapidly evolving lineages. Our study, however, also highlights the challenges of resolving relationships within recent radiations even at the genomic level.

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The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

Cited by 2,040 publications

References 15 publications

The complete mitochondrial genome of the edible Basidiomycete mushroom Phlebopus Portentosus

The complete mitochondrial genome of the edible Basidiomycete mushroom Phlebopus Portentosus

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

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