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Genes2022; 13(10); 1722; doi: 10.3390/genes13101722

Long-Read Transcriptome of Equine Bronchoalveolar Cells.

Abstract: We used Pacific Biosciences long-read isoform sequencing to generate full-length transcript sequences in equine bronchoalveolar lavage fluid (BALF) cells. Our dataset consisted of 313,563 HiFi reads comprising 805 Mb of polished sequence information. The resulting equine BALF transcriptome consisted of 14,234 full-length transcript isoforms originating from 7017 unique genes. These genes consisted of 6880 previously annotated genes and 137 novel genes. We identified 3428 novel transcripts in addition to 10,806 previously known transcripts. These included transcripts absent from existing genome annotations, transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. We provide transcript-level data for equine BALF cells as a resource to the scientific community.
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Publication Date: 2022-09-25 PubMed ID: 36292607PubMed Central: PMC9602388DOI: 10.3390/genes13101722Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't

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 study used a method known as long-read isoform sequencing to fully map and understand the genetic sequences present in equine lung cells. Over 300,000 genetic sequences were examined, identifying both previously known genes and transcripts, as well as discovering novel genes and transcripts.

Research Methodology and Process

  • The researchers employed Pacific Biosciences long-read isoform sequencing, a modern yet complex method that uses fluorochemistry and specialized sensors to obtain the complete sequences of transcripts, including all their variant forms or isoforms, from a given sample.
  • This sequencing technology was used to examine bronchoalveolar lavage fluid (BALF) cells in horses. BALF is a technique used to obtain cells and other materials from the lower respiratory tract to diagnose lung diseases.

Data Collection and Analysis

  • The researchers generated a dataset that included 313,563 HiFi reads. HiFi here refers to high-accuracy reads produced by the sequencing technology, which gives scientists a more accurate and reliable set of data to work with. These reads totaled to 805 megabytes of polished sequence information, indicating comprehensive data was gathered.
  • Through their analysis they were able to identify 14,234 full-length transcript isoforms originating from 7,017 unique genes within the equine BALF cells.

Key Findings

  • The identified genes consisted of both previously known and new genes. A total of 6,880 were already annotated, meaning they have been previously identified and cataloged in previous research, and 137 were novel genes, not identified or recorded in existing genetic databases.
  • Apart from the genes, they also found 3,428 novel transcripts in addition to 10,806 previously identified transcripts.
  • This includes transcripts that were not found in existing genome annotations, transcripts that were corresponding to potentially novel genes that aren’t yet annotated, and fusion transcripts, which incorporate components from multiple different genes.

Implications

  • The study provides the scientific community with transcript-level data for equine BALF cells, expanding the existing body of knowledge on horse genetics and potentially pushing forward research in equine lung health and diseases.
  • Unknown sequences and genes could pave the way for novel genetic disease marker discovery, breeding programs, and understanding the genetic basis of health and disease in horses.

Cite This Article

APA
Sage SE, Nicholson P, Leeb T, Gerber V, Jagannathan V. (2022). Long-Read Transcriptome of Equine Bronchoalveolar Cells. Genes (Basel), 13(10), 1722. https://doi.org/10.3390/genes13101722

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 13
Issue: 10
PII: 1722

Researcher Affiliations

Sage, Sophie Elena
  • Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.
Nicholson, Pamela
  • Next Generation Sequencing Platform, University of Bern, 3001 Bern, Switzerland.
Leeb, Tosso
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.
Gerber, Vinzenz
  • Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.
Jagannathan, Vidhya
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.

MeSH Terms

  • Horses / genetics
  • Animals
  • Transcriptome / genetics
  • Molecular Sequence Annotation
  • Sequence Analysis, RNA / methods
  • Genome
  • Protein Isoforms

Conflict of Interest Statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

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