PuMA: A papillomavirus genome annotation tool

Pace, Joshua; Youens‐Clark, Ken; Freeman, C. J.; Hurwitz, Bonnie; Doorslaer, Koenraad Van

doi:10.1093/ve/veaa068

Cited by 12 publications

(11 citation statements)

References 27 publications

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“…We determined the genomes of two novel circular dsDNA viruses using a metagenomics approach. The open reading frames (ORFs) of these putative new viruses were identified using PuMA ( 150 ). This analysis identified the typical papillomavirus open reading frames (E6, E7, E1, E2, L1, and L2) and the spliced E1^E4 and E8^E2 mRNAs.…”

Section: Resultsmentioning

confidence: 99%

Coevolutionary Analysis Implicates Toll-Like Receptor 9 in Papillomavirus Restriction

King

Larsen

Gryseels

et al. 2022

mBio

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Section: Resultsmentioning

confidence: 99%

Coevolutionary Analysis Implicates Toll-Like Receptor 9 in Papillomavirus Restriction

King

Larsen

Gryseels

et al. 2022

mBio

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“…We also identified two spliced products, E8^E2 and E1^E4 in two of the genomes. The splice donor and acceptor sequences were identified by homology in the PuMA tool [ 22 ]. The upstream regulatory regions (URRs) range in size from 504 to 613 bp.…”

Section: Resultsmentioning

confidence: 99%

“…The 7307-bp contig was annotated using the PuMA pipeline [ 22 ]. This sequence corresponded to a full papillomavirus genome encoding L1, L2, E1, E2, E6 and E7, in addition to two spliced products (E1^E4 and E8^E2).…”

Section: Methodsmentioning

confidence: 99%

Discovery of novel papillomaviruses in the critically endangered Malayan and Chinese pangolins

2023

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Pangolins are scaly and toothless mammals which are distributed across Africa and Asia. Currently, the Malayan, Chinese and Philippine pangolins are designated as critically endangered species. Although few pangolin viruses have been described, their viromes have received more attention following the discovery that they harbour sarbecoviruses related to SARS-CoV-2. Using large-scale genome mining, we discovered novel lineages of papillomaviruses infecting the Malayan and Chinese pangolins. We were able to assemble three complete circular papillomavirus genomes with an intact coding capacity and five additional L1 genes encoding the major capsid protein. Phylogenetic analysis revealed that seven out of eight L1 sequences formed a monophyletic group which is the sister lineage to the Tupaia belangeri papillomavirus 1, isolated from Yunnan province in China. Additionally, a single L1 sequence assembled from a Chinese pangolin was placed in a clade closer to Alphapapillomavirus and Omegapapillomavirus . Examination of the SRA data from 95 re-sequenced genomes revealed that 49.3% of Malayan pangolins and 50% of Chinese pangolins were positive for papillomavirus reads. Our results indicate that pangolins in South-East Asia are the hosts of diverse and highly prevalent papillomaviruses, and highlight the value of in silico mining of host sequencing data for the discovery of novel viruses.

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“…They may, however, result in incorrect functional annotations [ 52 ]. Annotating genomes correctly is critical for our knowledge and use of functional gene diversity [ 53 , 54 ]. In order to confirm the accuracy of the gene annotations, structural analysis or assessment of expression level is usually necessary [ 55 ].…”

Section: Discussionmentioning

confidence: 99%

Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation

et al. 2022

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The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.

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PuMA: A papillomavirus genome annotation tool

Cited by 12 publications

References 27 publications

Coevolutionary Analysis Implicates Toll-Like Receptor 9 in Papillomavirus Restriction

Coevolutionary Analysis Implicates Toll-Like Receptor 9 in Papillomavirus Restriction

Discovery of novel papillomaviruses in the critically endangered Malayan and Chinese pangolins

Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation

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