User:NoahHendershott2019/Chimera (molecular biology)

This is the sandbox page where you will draft your initial Wikipedia contribution. If you're starting a new article, you can develop it here until it's ready to go live. If you're working on improvements to an existing article, copy only one section at a time of the article to this sandbox to work on, and be sure to use an edit summary linking to the article you copied from. Do not copy over the entire article. You can find additional instructions here. Remember to save your work regularly using the "Publish page" button. (It just means 'save'; it will still be in the sandbox.) You can add bold formatting to your additions to differentiate them from existing content. Bibliography sandbox

Article Draft

Lead

In genetics and molecular biology, a chimera is a single DNA sequence originating from multiple transcripts or parent sequences. It can occur in various contexts. Chimeras are generally considered a contaminant, as a chimera can be interpreted as a novel sequence while it is in fact an artifact. However, the formation of artificial chimeras can also be a useful tool in the molecular biology. For example, in protein engineering, "chimeragenesis (forming chimeras between proteins that are encoded by homologous cDNAs)" is one of the "two major techniques used to manipulate cDNA sequences".

Article body

Transcript chimera[edit]

A chimera can occur as a single cDNA sequence originating from two transcripts. It is usually considered to be a contaminant in transcript and expressed sequence tag (which results in the moniker of EST chimera) databases. It is estimated that approximately 1% of all transcripts in the National Center for Biotechnology Information's Unigene database contain a "chimeric sequence".

PCR chimera[edit]

A chimera can also be an artifact of PCR amplification. It occurs when the extension of an amplicon is aborted, and the aborted product functions as a primer in the next PCR cycle. The aborted product anneals to the wrong template and continues to extend, thereby synthesizing a single sequence sourced from two different templates.

PCR chimeras are an important issue to take into account during metabarcoding, where DNA sequences from environmental samples are used to determine biodiversity. A chimera is a novel sequence that will most probably not match to any known organism. Hence, it might be interpreted as a new species thereby inflating over diversity.

Chimeric read[edit]

A chimeric read is a digital DNA sequence (i.e. a string of letters in a file that can be read as a DNA sequence) that originates from an actual chimera (i.e. a physical DNA sequence in a sample) or produced due to misreading the sample. The latter is known to occur with sequencing of electrophoresis gels.

Some methods have been devised to detect chimeras, like:

• CHECK_CHIMERA of the Ribosomal Database Project
• ChimeraSlayer in QIIME
• uchime in usearch
• removeBimeraDenovo() in dada2
• Bellerophon
• CATCh
• DECIPHER

References

1. Mysara, Mohamed; Saeys, Yvan; Leys, Natalie; Raes, Jeroen; Monsieurs, Pieter (2015-03-01). Wommack, K. E. (ed.). "CATCh, an Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies". Applied and Environmental Microbiology. 81 (5): 1573–1584. doi:10.1128/AEM.02896-14. ISSN 0099-2240. PMC 4325141. PMID 25527546.
2. ^ Wright, Erik S.; Yilmaz, L. Safak; Noguera, Daniel R. (2012-02-01). "DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences". Applied and Environmental Microbiology. 78 (3): 717–725. doi:10.1128/AEM.06516-11. ISSN 0099-2240. PMC 3264099. PMID 22101057.
3. http://drive5.com/usearch/manual/chimeras.html
4. https://www.biorxiv.org/content/10.1101/074252v1.full
5. https://www.ncbi.nlm.nih.gov/genbank/rrnachimera/#:~:text=Chimeras%20are%20artifact%20sequences%20formed,i.e.%2C%20uncultured%20environmental%20samples).&text=The%20end%20result%20is%20a,sequence%20that%20exists%20in%20nature.