Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs
Genome and transcriptome assembly data often contain DNA and RNA contaminations from external organisms, introduced during nucleotide extraction or sequencing. In this study, contamination of seed plant (Spermatophyta) transcriptomes/genomes with p25alpha domain encoding RNA/DNA was systematically i...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/13/8/1664 |
| _version_ | 1797584104034664448 |
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| author | Ferenc Orosz |
| author_facet | Ferenc Orosz |
| author_sort | Ferenc Orosz |
| collection | DOAJ |
| description | Genome and transcriptome assembly data often contain DNA and RNA contaminations from external organisms, introduced during nucleotide extraction or sequencing. In this study, contamination of seed plant (Spermatophyta) transcriptomes/genomes with p25alpha domain encoding RNA/DNA was systematically investigated. This domain only occurs in organisms possessing a eukaryotic flagellum (cilium), which seed plants usually do not have. Nucleotide sequences available at the National Center for Biotechnology Information website, including transcriptome shotgun assemblies (TSAs), whole-genome shotgun contigs (WGSs), and expressed sequence tags (ESTs), were searched for sequences containing a p25alpha domain in Spermatophyta. Despite the lack of proteins containing the p25alpha domain, such fragments or complete mRNAs in some EST and TSA databases were found. A phylogenetic analysis showed that these were contaminations whose possible sources were microorganisms (flagellated fungi, protists) and arthropods/worms; however, there were cases where it cannot be excluded that the sequences found were genuine hits and not of external origin. |
| first_indexed | 2024-03-10T23:47:32Z |
| format | Article |
| id | doaj.art-680e85126598422aad60d8811807c0a4 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T23:47:32Z |
| publishDate | 2023-07-01 |
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| series | Life |
| spelling | doaj.art-680e85126598422aad60d8811807c0a42023-11-19T01:53:46ZengMDPI AGLife2075-17292023-07-01138166410.3390/life13081664Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or OrthologsFerenc Orosz0Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, HungaryGenome and transcriptome assembly data often contain DNA and RNA contaminations from external organisms, introduced during nucleotide extraction or sequencing. In this study, contamination of seed plant (Spermatophyta) transcriptomes/genomes with p25alpha domain encoding RNA/DNA was systematically investigated. This domain only occurs in organisms possessing a eukaryotic flagellum (cilium), which seed plants usually do not have. Nucleotide sequences available at the National Center for Biotechnology Information website, including transcriptome shotgun assemblies (TSAs), whole-genome shotgun contigs (WGSs), and expressed sequence tags (ESTs), were searched for sequences containing a p25alpha domain in Spermatophyta. Despite the lack of proteins containing the p25alpha domain, such fragments or complete mRNAs in some EST and TSA databases were found. A phylogenetic analysis showed that these were contaminations whose possible sources were microorganisms (flagellated fungi, protists) and arthropods/worms; however, there were cases where it cannot be excluded that the sequences found were genuine hits and not of external origin.https://www.mdpi.com/2075-1729/13/8/1664apicomplexaapicortingenomic contaminationSpermatophytaTPPPearly-branching fungi |
| spellingShingle | Ferenc Orosz Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs Life apicomplexa apicortin genomic contamination Spermatophyta TPPP early-branching fungi |
| title | Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs |
| title_full | Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs |
| title_fullStr | Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs |
| title_full_unstemmed | Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs |
| title_short | Presence of p25alpha-Domain in Seed Plants (Spermatophyta): Microbial/Animal Contaminations and/or Orthologs |
| title_sort | presence of p25alpha domain in seed plants spermatophyta microbial animal contaminations and or orthologs |
| topic | apicomplexa apicortin genomic contamination Spermatophyta TPPP early-branching fungi |
| url | https://www.mdpi.com/2075-1729/13/8/1664 |
| work_keys_str_mv | AT ferencorosz presenceofp25alphadomaininseedplantsspermatophytamicrobialanimalcontaminationsandororthologs |