nhmmer: DNA homology search with profile HMMs

Wheeler, Travis J.; Eddy, Sean R.

doi:10.1093/bioinformatics/btt403

Cited by 739 publications

(661 citation statements)

References 22 publications

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“…To identify conserved motifs at amplification junction sites, a similar analysis was conducted for CcBV proviral loci from C. congregata (11), followed by alignment to M. demolitor sequences using mafft and Jalview as described above. Inverted-repeat motif sequences identified from MdBV and CcBV proviral segments were made into a hidden Markov model (HMM) and then searched against the M. demolitor genome with nhmmer to identify additional motif sequences (30). Amplified regions outside proviral segment loci were also analyzed for sequence motifs of potential importance.…”

Section: Insects M Demolitor Was Reared By Established Methods Usinmentioning

confidence: 99%

Microplitis demolitor Bracovirus Proviral Loci and Clustered Replication Genes Exhibit Distinct DNA Amplification Patterns during Replication

Burke

Simmonds

Thomas

et al. 2015

J Virol

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Polydnaviruses are large, double-stranded DNA viruses that are beneficial symbionts of parasitoid wasps. Polydnaviruses in the genus Bracovirus (BVs) persist in wasps as proviruses, and their genomes consist of two functional components referred to as proviral segments and nudivirus-like genes. Prior studies established that the DNA domains where proviral segments reside are amplified during replication and that segments within amplified loci are circularized before packaging into nucleocapsids. One DNA domain where nudivirus-like genes are located is also amplified but never packaged into virions. We recently sequenced the genome of the braconid Microplitis demolitor, which carries M. demolitor bracovirus (MdBV). Here, we took advantage of this resource to characterize the DNAs that are amplified during MdBV replication using a combination of Illumina and Pacific Biosciences sequencing approaches. The results showed that specific nucleotide sites identify the boundaries of amplification for proviral loci. Surprisingly, however, amplification of loci 3, 4, 6, and 8 produced head-to-tail concatemeric intermediates; loci 1, 2, and 5 produced head-to-head/tail-to-tail concatemers; and locus 7 yielded no identified concatemers. Sequence differences at amplification junctions correlated with the types of amplification intermediates the loci produced, while concatemer processing gave rise to the circularized DNAs that are packaged into nucleocapsids. The MdBV nudivirus-like gene cluster was also amplified, albeit more weakly than most proviral loci and with nondiscrete boundaries. Overall, the MdBV genome exhibited three patterns of DNA amplification during replication. Our data also suggest that PacBio sequencing could be useful in studying the replication intermediates produced by other DNA viruses. IMPORTANCEPolydnaviruses are of fundamental interest because they provide a novel example of viruses evolving into beneficial symbionts. All polydnaviruses are associated with insects called parasitoid wasps, which are of additional applied interest because many are biological control agents of pest insects. Polydnaviruses in the genus Bracovirus (BVs) evolved ϳ100 million years ago from an ancestor related to the baculovirus-nudivirus lineage but have also established many novelties due to their symbiotic lifestyle. These include the fact that BVs are transmitted only vertically as proviruses and produce replication-defective virions that package only a portion of the viral genome. Here, we studied Microplitis demolitor bracovirus (MdBV) and report that its genome exhibits three distinct patterns of DNA amplification during replication. We also identify several previously unknown features of BV genomes that correlate with these different amplification patterns. P olydnaviruses (PDVs) are unusual double-stranded DNA (ds-DNA) viruses that have evolved into beneficial symbionts of insects called parasitoid wasps (order Hymenoptera) (1). Each PDV in a given wasp species persists as a provirus in every cell of every ...

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Section: Insects M Demolitor Was Reared By Established Methods Usinmentioning

confidence: 99%

Microplitis demolitor Bracovirus Proviral Loci and Clustered Replication Genes Exhibit Distinct DNA Amplification Patterns during Replication

Burke

Simmonds

Thomas

et al. 2015

J Virol

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“…Newly validated homologs were added to the HMM iteratively, and HMMer searches were repeated until no additional putative homologs were identified. For genomes without protein sequences, nHMMer (Wheeler and Eddy, 2013) was used to search nucleotide databases following the procedure described above.…”

Section: Comparative Genomicsmentioning

confidence: 99%

An ancestral role in peroxisome assembly is retained by the divisional peroxin Pex11 in the yeast Yarrowia lipolytica

Chang

Klute

Tower

et al. 2015

Journal of Cell Science

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The peroxin Pex11 has a recognized role in peroxisome division. Pex11p remodels and elongates peroxisomal membranes prior to the recruitment of dynamin-related GTPases that act in membrane scission to divide peroxisomes. We performed a comprehensive comparative genomics survey to understand the significance of the evolution of the Pex11 protein family in yeast and other eukaryotes. Pex11p is highly conserved and ancestral, and has undergone numerous lineage-specific duplications, whereas other Pex11 protein family members are fungal-specific innovations. Functional characterization of the in-silico-predicted Pex11 protein family members of the yeast Yarrowia lipolytica, i.e. Pex11p, Pex11Cp and Pex11/25p, demonstrated that Pex11Cp and Pex11/25p have a role in the regulation of peroxisome size and number characteristic of Pex11 protein family members. Unexpectedly, deletion of PEX11 in Y. lipolytica produces cells that lack morphologically identifiable peroxisomes, mislocalize peroxisomal matrix proteins and preferentially degrade peroxisomal membrane proteins, i.e. they exhibit the classical pex mutant phenotype, which has not been observed previously in cells deleted for the PEX11 gene. Our results are consistent with an unprecedented role for Pex11p in de novo peroxisome assembly.

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“…BUSCO (Benchmarking Universal Single-Copy Orthologs) is a measure for quantitative assessment of genome assembly and annotation completeness based on evolutionarily informed expectations of gene content. The obtained set of transcripts was first analyzed for the presence of mitochondrial transcripts by wise2 searches (Birney et al, 2004) using hmm profiles of mitochondrialy encoded proteins (Finn et al, 2010) and by nhmmer (Wheeler & Eddy, 2013) searches using hmm profiles of mitochondrialy encoded ribosomal RNA genes (GriffithsJones, 2003). The sequences of mitochondrial contigs were then used to design specific primers (Supplementary Table S1) for mtDNA amplification and Sanger sequencing.…”

Section: Methodsmentioning

confidence: 99%

Next-generation sequencing of Dreissena polymorpha transcriptome sheds light on its mitochondrial DNA

et al. 2017

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Zebra mussels Dreissena polymorpha (Veneroida, Dreissenidae) are known for their invasive behavior. Despite numerous studies dealing with this species, no results of large sequencing projects have been published to date, hampering marker development. In this study, we present a relatively large novel transcriptomic dataset obtained by Illumina MiSeq technology from mantle and male gonad of D. polymorpha sampled in Poland. The transcriptomic data were typical for the tissue analyzed. Moreover, they showed the expression of a single mitochondrial genome, indicating that this species do not have doubly uniparental inheritance of mitochondria. The sequences of mitochondrial transcripts were used to design primers and obtain nearly complete sequence of the zebra mussel mitochondrial genome by PCR and Sanger sequencing. This mitogenome has unique gene order, with the genes split into two blocks encoded in opposite directions. The closest mitogenome available in GenBank belongs to the marine clam Mya arenaria (Myoida, Myidae). The average divergence of the sequences of these mitogenomes is quite high, in the range of 20%. Both mitogenomic and transcriptomic resources should prove very useful for elucidating population genetics and conservation issues involving this important species.

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nhmmer: DNA homology search with profile HMMs

Cited by 739 publications

References 22 publications

Microplitis demolitor Bracovirus Proviral Loci and Clustered Replication Genes Exhibit Distinct DNA Amplification Patterns during Replication

Microplitis demolitor Bracovirus Proviral Loci and Clustered Replication Genes Exhibit Distinct DNA Amplification Patterns during Replication

An ancestral role in peroxisome assembly is retained by the divisional peroxin Pex11 in the yeast Yarrowia lipolytica

Next-generation sequencing of Dreissena polymorpha transcriptome sheds light on its mitochondrial DNA

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