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Home / Equine Research Bank / J Appl Genet / Another lesson from unmapped reads: in-depth analysis of RNA...
Journal of applied genetics2022; 63(3); 571-581; doi: 10.1007/s13353-022-00705-z

Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues.

Abstract: In recent years, a vast amount of sequencing data has been generated and large improvements have been made to reference genome sequences. Despite these advances, significant portions of reads still do not map to reference genomes and these reads have been considered as junk or artificial sequences. Recent studies have shown that these reads can be useful, e.g., for refining reference genomes or detecting contaminating microorganisms present in the analyzed biological samples. A special case of this is RNA sequencing (RNA-Seq) reads that come from tissue transcriptomes. Unmapped reads from RNA-Seq have received much less attention than those from whole-genome sequencing. In particular, in the horse, an analysis of unmapped RNA reads has not been performed yet. Thus, in this study, we analyzed the unmapped reads originating from the RNA-Seq performed through the Functional Annotation of Animal Genomes (FAANG) project in the horse, using eight different tissues from two mares. We demonstrated that unmapped reads from RNA-Seq could be easily assembled into transcripts relating to many important genes present in the sequences of other mammals. Large portions of these transcripts did not have coding potential and, thus, can be considered as non-coding RNA. Moreover, reads that were not mapped to the reference genome but aligned to the entries in NCBI database of horse proteins were enriched for biological processes that largely correspond to the functions of organ from which RNA was isolated and thus are presumably true transcripts of genes associated with cell metabolism in those tissues. In addition, a portion of reads aligned to the common pathogenic or neutral microbiota, of which the most common was Brucella spp. These data suggest that unmapped reads can be an important target for in-depth analysis that may substantially enrich results of initial RNA-Seq experiments for various tissues and organs.
© 2022. The Author(s), under exclusive licence to Institute of Plant Genetics Polish Academy of Sciences.
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Publication Date: 2022-06-07 PubMed ID: 35670911PubMed Central: 5657046DOI: 10.1007/s13353-022-00705-zGoogle Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research explores the value of unmapped RNA sequencing (RNA-Seq) reads from various horse tissues, suggesting these reads can sufficiently assemble into transcripts that reflect important genes found in other mammals, potentially enhancing the outcomes of initial RNA-Seq experiments.

Background of the Study

  • Despite the advancements in generating sequencing data and improving reference genome sequences, a significant amount of reads still do not map to these genomes, often being dismissed as junk or artificial sequences.
  • The researchers argue that these unmapped reads, especially those from RNA sequencing (RNA-Seq), can be useful for refining genome references and detecting contamination in biological samples.
  • This study focuses on unmapped RNA reads from horses, an area that previously hadn’t been addressed.

Methods and Findings

  • The research team took unmapped reads from eight different horse tissue samples using RNA-Seq methods under the Functional Annotation of Animal Genomes (FAANG) project.
  • Humongous portions of these unmapped reads could be assembled into transcripts correlating with many significant genes present in other mammals’ sequences.
  • Large portions of these constructed transcripts lack coding potential and can therefore be considered non-coding RNA.
  • Unmapped reads aligned themselves with entries in the NCBI database of horse proteins, suggesting a possible association with biological processes that directly link to the functionality of the organ from which the RNA was initially isolated.

Implications of the Findings

  • This denotes that these unmapped reads should potentially be authentic transcripts of genes connected with cell metabolism in those particular tissues.
  • In addition to this, some reads aligned themselves with common pathogenic or neutral microbiota, with Brucella spp. being the most prevalent.
  • The research implies that in-depth analyses of these unmapped reads could significantly enrich the results obtained from initial RNA-Seq experiments on various tissues and organs.

Cite This Article

APA
Gurgul A, Szmatoła T, Ocłoń E, Jasielczuk I, Semik-Gurgul E, Finno CJ, Petersen JL, Bellone R, Hales EN, Ząbek T, Arent Z, Kotula-Balak M, Bugno-Poniewierska M. (2022). Another lesson from unmapped reads: in-depth analysis of RNA-Seq reads from various horse tissues. J Appl Genet, 63(3), 571-581. https://doi.org/10.1007/s13353-022-00705-z

Publication

Journal of applied genetics
ISSN: 2190-3883
NlmUniqueID: 9514582
Country: England
Language: English
Volume: 63
Issue: 3
Pages: 571-581

Researcher Affiliations

Gurgul, Artur
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland. artur.gurgul@urk.edu.pl.
Szmatoła, Tomasz
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland.
Ocłoń, Ewa
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland.
Jasielczuk, Igor
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland.
Semik-Gurgul, Ewelina
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
Finno, Carrie J
  • Department of Population Health and Reproduction, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
Petersen, Jessica L
  • Department of Animal Science, University of Nebraska Lincoln, Lincoln, NB, USA.
Bellone, Rebecca
  • Department of Population Health and Reproduction, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
  • Veterinary Genetics Laboratory, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
Hales, Erin N
  • Department of Population Health and Reproduction, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
Ząbek, Tomasz
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
Arent, Zbigniew
  • Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248, Kraków, Poland.
Kotula-Balak, Małgorzata
  • University Centre of Veterinary Medicine, University of Agriculture in Krakow, Mickiewicza 24/28, 30-059, Krakow, Poland.
Bugno-Poniewierska, Monika
  • Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059, Kraków, Poland.

MeSH Terms

  • Animals
  • Base Sequence
  • Female
  • Genome / genetics
  • High-Throughput Nucleotide Sequencing
  • Horses / genetics
  • Mammals / genetics
  • RNA / genetics
  • RNA-Seq
  • Sequence Analysis, RNA
  • Transcriptome / genetics

Grant Funding

  • L40 TR001136 / NCATS NIH HHS

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Citations

This article has been cited 1 times.
  1. Cappelletti E, Piras FM, Sola L, Santagostino M, Petersen JL, Bellone RR, Finno CJ, Peng S, Kalbfleisch TS, Bailey E, Nergadze SG, Giulotto E. The localization of centromere protein A is conserved among tissues. Commun Biol 2023 Sep 21;6(1):963.
    doi: 10.1038/s42003-023-05335-7pubmed: 37735603google scholar: lookup
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