Chorus2: design of genome‐scale oligonucleotide‐based probes for fluorescence in situ hybridization

Autor:	Jiming Jiang, Guanqing Liu, Tao Zhang, Hainan Zhao, Guilherme T. Braz
Rok vydání:	2021
Předmět:	oligonucleotide 0106 biological sciences 0301 basic medicine medicine.medical_specialty Oligonucleotides Plant Science Computational biology Biology 01 natural sciences Genome cytogenetics Molecular cytogenetics 03 medical and health sciences FISH medicine Animals In Situ Hybridization Fluorescence Research Articles Selection (genetic algorithm) Repetitive Sequences Nucleic Acid medicine.diagnostic_test Oligonucleotide Cytogenetics genome research 030104 developmental biology Fish Oligonucleotide Probes Agronomy and Crop Science Software Function (biology) Research Article 010606 plant biology & botany Biotechnology Fluorescence in situ hybridization
Zdroj:	Plant Biotechnology Journal
ISSN:	1467-7652 1467-7644
DOI:	10.1111/pbi.13610
Popis:	Summary Oligonucleotide (oligo)‐fluorescence in situ hybridization (FISH) has rapidly becoming the new generation of FISH technique in plant molecular cytogenetics research. Genome‐scale identification of single‐copy oligos is the foundation of successful oligo‐FISH experiments. Here, we introduce Chorus2, a software that is developed specifically for oligo selection. We demonstrate that Chorus2 is highly effective to remove all repetitive elements in selection of single‐copy oligos, which is critical for the development of successful FISH probes. Chorus2 is more effective than Chorus, the original version of the pipeline, and OligoMiner for repeat removal. Chorus2 allows to select oligos that are conserved among related species, which extends the usage of oligo‐FISH probes among phylogenetically related plant species. We also implemented a new function in Chorus2 that allows development of FISH probes from plant species without an assembled genome. We anticipate that Chorus2 can be used in plants as well as in mammalian and other non‐plant species. Chorus2 will broadly facilitate the design of FISH probes for various types of application in molecular cytogenetics research.
Databáze:	OpenAIRE
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